diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
index c538f705e8c..bd2d2c5b17f 100644
--- a/.github/ISSUE_TEMPLATE.md
+++ b/.github/ISSUE_TEMPLATE.md
@@ -1,5 +1,6 @@
 <!--- Provide a general summary of the issue in the Title above -->
-
+<!--- Please select appropriate Priority, Status,and Type labels-->
+<!--- If you do not have permission to select labels please state which labels you would like -->
 ## Description
 <!--- What change or feature do you propose? -->
 
diff --git a/.github/ISSUE_TEMPLATE/Bug_report.md b/.github/ISSUE_TEMPLATE/Bug_report.md
new file mode 100644
index 00000000000..136d228f44f
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/Bug_report.md
@@ -0,0 +1,30 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Machine (please complete the following information):**
+ - Server [e.g. BU, NCSA, VM, etc.]
+ - OS: [e.g.Linux]
+ - Browser(if applicable) [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/Feature_request.md b/.github/ISSUE_TEMPLATE/Feature_request.md
new file mode 100644
index 00000000000..066b2d920a2
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/Feature_request.md
@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 360a257f7c8..8ec74b3fd1a 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,4 +1,6 @@
 <!--- Provide a general summary of your changes in the Title above -->
+<!--- Please select appropriate Priority, Status,and Type labels-->
+<!--- If you do not have permission to select labels please state which labels you would like -->
 
 ## Description
 <!--- Describe your changes in detail -->
diff --git a/.gitignore b/.gitignore
index f5b273444dc..bb039757250 100644
--- a/.gitignore
+++ b/.gitignore
@@ -83,3 +83,5 @@ shiny/BenchmarkReport/*
 .doc/
 # files generated by tests
 base/qaqc/tests/testthat/Rplots.pdf
+docker/base/build.*.log
+docker/models/build.*.log
diff --git a/.travis.yml b/.travis.yml
index bea85a41315..57a0df59da7 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,13 +5,15 @@
 # trusty. They are marked with TRUSTY for easy grepping.
 
 language: r
-
 r:
   - 3.4
 
 # TRUSTY: Change version when 16.04 image is available.
 dist: trusty
-sudo: false
+sudo: required
+
+env:
+  - PGHOST=localhost
 
 cache: 
   - directories:
@@ -22,30 +24,30 @@ cache:
   - packages
 
 addons:
-  postgresql: 9.6
   apt:
     sources:
       - sourceline: 'ppa:marutter/c2d4u'
       - sourceline: 'ppa:nschloe/hdf5-backports'
+      - sourceline: 'ppa:ubuntugis/ppa' # for GDAL 2 binaries
     packages:
-      - libnetcdf-dev
-      - liblapack-dev
-      - libcurl4-openssl-dev
-      - jags
-      - libudunits2-dev
-      - python-dev 
-      - postgresql-9.6-postgis-2.3
-      - postgresql-9.6-postgis-2.3-scripts
-      - netcdf-bin
       - bc
       - curl
-      - udunits-bin 
+      - gdal-bin
+      - jags
+      - libcurl4-openssl-dev
+      - libgdal-dev
       - libgmp-dev
+      - libhdf5-dev
+      - liblapack-dev
+      - libnetcdf-dev
       - libproj-dev
+      - libudunits2-dev
+      - netcdf-bin
       - pandoc
+      - python-dev
       - tcl
       - tcl-dev
-      - libhdf5-dev
+      - udunits-bin
       # R package binaries from c2d4u
       - r-bioc-biocinstaller
       - r-cran-ape
@@ -58,10 +60,10 @@ addons:
       - r-cran-lme4
       - r-cran-matrixstats
       - r-cran-mcmcpack
-      - r-cran-mcmcpack
       - r-cran-raster
       - r-cran-rcpp
       - r-cran-rcurl
+      - r-cran-redland
       - r-cran-rncl
       - r-cran-roxygen2
       - r-cran-shiny
@@ -69,24 +71,10 @@ addons:
       - r-cran-tidyverse
       - r-cran-xml
       - r-cran-xml2
-      # need to compile documentation
-      # BROKEN MISSING FONT
-      #- texinfo
-      #- texlive-latex-base
-      #- texlive-latex-recommended
-      #- texlive-latex-extra
-      #- texlive-fonts-recommended
-      #- texlive-fonts-extra
 
   
-## notifications should go to gitter
+## notifications should go to slack
 notifications:
-  webhooks:
-    urls:
-      - secure: "gL81TwDOcK/32Hxxl2BcY7pioyrtyV4y1f+D/vGEpQz8mYL+M+55tUkhHJF53779XSUdQdML/gsr8JZVtApJdLIBysFU67GVYXm1s7x/b8J61CkMfDgsmposEWK4NFYHfeIRj32ioeajrQ+RKi1I6chjzYT7gLyl70gtPelRJ4s="
-    on_success: always
-    on_failure: always
-    on_start: always
   slack:
     # Slack token created by Chris Black, 2018-02-17
     secure: "DHHSNmiCf71SLa/FFSqx9oOnJjJt2GHYk7NsFIBb9ZY10RvQtIPfaoNxkPjqu9HLyZWJSFtg/uNKKplEHc6W80NoXyqoTvwOxTPjMaViXaCNqsmzjjR/JaCWT/oWGXyAw0VX3S8cwuIexlKQGgZwJpIzoVOZqUrDrHI/O17kZoM="
@@ -96,7 +84,7 @@ notifications:
 
 ## list of services to be running
 services:
-  - postgresql
+  - docker
 
 install:
   - pushd $HOME
@@ -107,6 +95,14 @@ install:
   - popd
 
 before_script:
+  - sudo service postgresql stop
+  - docker run --detach --rm --name postgresql --publish 5432:5432 mdillon/postgis:9.6-alpine
+  - echo -n "Waiting for Postgres to start...";
+    until psql -U postgres -c 'select 1' >/dev/null 2>&1;
+      do echo -n ".";
+      sleep 1;
+    done;
+    echo " OK"
   - psql -q -o /dev/null -U postgres -c "CREATE ROLE BETY WITH LOGIN CREATEDB SUPERUSER CREATEROLE UNENCRYPTED PASSWORD 'bety'";
   - psql -q -o /dev/null -U postgres -c "CREATE DATABASE bety OWNER bety;"
   - curl -o bety.sql http://isda.ncsa.illinois.edu/~kooper/PEcAn/data/bety.sql
@@ -118,12 +114,20 @@ before_script:
 
 script:
   - set -e
-  # - scripts/build.sh --no-git --tests --name travis
   - echo 'Installing PEcAn packages'
-  - make
+  # TODO: Would be nice to add `-Otarget` after `-j` below,
+  # but not supported in Make 3.x.
+  # When Travis updates, check for Make 4 and add -O if available.
+  - make # TODO: add -j2 here after #1976 closed
   - echo 'Testing PEcAn packages'
-  - make test
-  - make document
+  - make -j2 test
+  - make -j2 document
+  # Skip modules with known broken checks
+  - mkdir -p .check/modules # only needed for `touch` below
+  - touch .check/modules/benchmark # delete when #1978 closed
+  - touch .check/modules/data.land # delete when #1977 closed
+  - touch .check/modules/rtm # delete when #1976 closed
+  - make -j2 check
   - echo 'Testing Integration'
   - ./tests/integration.sh travis
   - if [[ `git status -s` ]]; then 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index cbd85416714..be383273dae 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,7 +6,103 @@ section for the next release.
 For more information about this file see also [Keep a Changelog](http://keepachangelog.com/) .
 
 
-## [Unreleased]
+## [1.6.0] - 2018-09-01
+
+### Fixes
+- Fixed issue #2064 which sends one met path to write.sa.config.
+- Fixed issue #1939 which corrects output time vector for FATES output
+- Update to read.output to look for and read only PEcAn formatted .nc output based on the pecan standard filename format of YYYY.nc.  Solves issues with models such as FATES and dvm-dos-tem where the original model output is also in .nc file format and was not ignored by read.output, causing errors with output parsing and plotting with Shiny. Removed deprecated function convert.outputs
+- PEcAn.data.atmosphere: 
+    - download.Geostreams is pickier about formatting start/end datess, for fewer surprises in result timestamps
+    - Fixed swapped lat/lon in met2CF.Geostreams
+    - download.GFDL now records reference date in time units field, as required by the CF met standard
+    - Reduced download.GFDL network load by not preloading dimension data
+    - Fixed spurious `No geonamesUsername set` warning by updating geonames package to development version
+- ED:
+    - Change all history parameter files to have zero storage respiration
+- missing_port_bety    
+- dataone_download.R:
+
+    - Added functionality that spoofs our user address to prevent authentication errors with downloading files via wget. 
+- Could not specify the port for BETY in config.php. Can now use `db_bety_port` to specify port.
+
+    - Added functionality that spoofs our user address to prevent authentication errors with downloading files via wget.
+    
+- Data_Ingest_App:
+    - use `updateSelectizeInput` to populate `selectizeInput` with choices from BETYdb. This instantly loads the inputfields where other methods take minutes to load. 
+
+    
+### Added
+
+- PEcAn.undertainty gains one new function (input.ens.gen) and three functions moved from PEcAn.utils (see "Changed" below)
+- IC workflow now has functionality to generate ensembles.
+- You can now generate ensembles for parameters and met separatly and using different methods. 
+- Soil process is now capable of reading in soil data from gSSURGO databse.
+- In modules/rtm new function foursail()  to interface with the 4SAIL Fortran code. To enable the use of 4SAIL with any version of PROSPECT (i.e. 4, 5, 5b, D) and custom soil/background reflectance inputs
+- Shiny/Dependency explorer 
+- Explore the interdependencies between pecan packages/functions.
+- From history you can now select an old run and show the curl command to re-execute this run. This only works with runs submitted through web interface right now.
+- Experimental support for docker (#1028)
+
+- dataone_download.R:
+  - Added progress messages to indicate that the function is working during longer downloads via PEcAn logger. 
+  - Store path to downloaded data as newdir_D1 so that the download app can call this path. 
+  
+- shiny/Data-Ingest 
+  - Download data from DataONE to a temporary directory, display the contents of that directory, and then move files from the temporary directory to dbfiles
+  - Upload files from local machines (via drag and drop on some browsers), display files, and then move these files to a directory in dbfiles.
+  - Spinner displays when class "shiny-busy" is invoked during the dataONE download process. In this way, users can be sure that the app is live and is processing their request. 
+  - Users can now input the name of the destination directory that they wish to create within dbfiles. 
+  - Updated Travis.yml to include librdf0-dev so that it can download redland, datapack, and dataone. 
+  - Added Data-Ingest UI (inputs, dbfiles, and formats record UI and some basic server side functionality are online)
+  - Modularized input record, format record, and dbfiles record into shiny modules. This allows the app to be greatly simplified to two, single-page workflows. These functions can also be used "plug-and-play" style elsewhere in PEcAn shiny apps to load in data. 
+  - Replaced modularized input, format and dbfiles records with static "Ingest Workflow" page. On this page, the user can select either importing from dataONE or Uploading from local files. If creating a new format is necessary, the user can click "Create New Format" and a dropdown menu will walk them through this process. 
+  - Selected files now autofill name value in input record workflow
+  - Store inputs and formats in the global environment
+  - "Test BETY" button allows users create a record in BETY with `dbfile.input.insert`
+  - Added `input.format.vars` to query the BETYdb
+  - New File: `helper.R`
+  - New Function: `auto.name.directory` This function uses the format_name and the site_id for a given input to create a directory name in the style of other dbfiles names. 
+  - `Next Step` buttons progress workflow programmatically
+  - New formats-variables UI allows user to create a table of formats-variable records before completing the ingest process
+  - Two separate complete Ingest buttons are rendered at the end of the workflow to trigger actions specific to local upload or dataONE download workflows. These buttons are rendered programmatically depending on the state of the selectInputMethod radio button.
+  - Converted time inputs to properly merge startDate and startTime with EndDate and EndTime so they can be inserted into the start_date and end_date columns in BETYdb.
+  - Error handling introduced using `shinytoastr` package
+  - DESCRIPTION: `Depends`: PEcAn.visualization, shinytoastr, shinyWidgets, shinyjs
+  
+- pecan/base/db
+  - New File: `input.format.vars.R`. This function registers the format and the (optional) formats_variables record using `db_merge_into`. 
+
+- `data.atmosphere`
+	- `check_met_input_file` -- Check that target met file conforms to PEcAn meteorology data standard.
+	- `get_cf_variables_table` -- Retrieve CF variables table as a `data.frame` 
+
+
+- docker:
+  - Added updated docker container builds
+    - Use docker.sh to create docker images
+    - Use release.sh to push released images to push to docker registry (hub.docker.com by default)
+  - Create pecan/depends docker image that holds all PEcAn dependencies
+    - Needs to build seperatly, not part of the docker.sh build process to speed things up
+    - Build using `(cd docker ; docker build -t pecan/depends:latest -f Dockerfile.depends .)`
+  - docker-compose.yml file to bring up full PEcAn stack using docker
+    - First time to start requires to install BETY database (see documentation)
+  - SIPNET docker image which works with PEcAn docker stack
+  - Data container that will download and install demo data in /data folder
+
+  
+### Removed
+  - pecan.worldmap function no longer used, dropped from visualization package
+  - shiny/Data-Ingest/DESCRIPTION no longer `DEPENDS` on `shinyFiles` or `shinycssloaders`
+
+### Changed
+
+- Fixed Git instructions and remote execution instructions.
+- Five functions from PEcAn.utils functions have been moved to other packages. The versions in PEcAn.utils are deprecated, will not be updated with any new features, and will be removed in a future release.
+  - run.write.configs and runModule.run.write.configs have been moved to PEcAn.workflow 
+  - read.ensemble.output, get.ensemble.samples and write.ensemble.configs have been moved to PEcAn.uncertainty
+- Change the way packages are checked for and called in SHINY apps. DESCRIPTION files in SHINY apps are not the place to declare pacakge dpendencies.    
+
 
 ## [1.5.3] - 2018-05-15
 
@@ -30,10 +126,16 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - PEcAn now supports PFTs whose members are cultivars rather than species, and will automatically restrict the meta-analysis to matching records, e.g. runs with a PFT containing only Panicum virgatum 'Cave-In-Rock' will not use observations from Panicum virgatum 'Alamo', but a PFT containing the whole species will use observations from both. However, there is not yet any BETYdb interface to *create* cultivar-PFTs other than manual SQL.
 - New base package `PEcAn.workflow`, for functions used to perform the each major step of the analysis. These were previously scattered in other base packages.
 - Added PR review time estimate to PR template 
+- New set of `PEcAn.logger` functions similar to `stopifnot` to facilitate assertive programming: `severeifnot`, `errorifnot`, `warnifnot`, `infoifnot`, `debugifnot`
 - PEcAnRTM:
     - Exposed PROSPECT absorption coefficients and `gpm()` function ("generalized plate model"), facilitating experimentation with different absorption coefficients
     - Added `spectra` S3 class and methods for subsetting (e.g. `myspec[[400:700]]`), plotting (`plot()` and `matplot()`), and combining spectra by wavelength.
     - Added `resample` functions for quickly resampling spectra (and, more generally, vectors and functions) to different dimensions. 
+    - `EDR` API has been revised. Setup has been refactored from EDR via new `setup_edr` function, which relies on the ED utilities (see `PEcAn.ED2` below), and the `EDR` function now focuses only on execution. Also, added new `params2edr` function to make it easy to convert complex EDR parameters list to flat parameter vector required by `invert_bt` (or other optimization functions).
+- PEcAn.ED2:
+    - New set of utilities for working with ED meteorology and vegetation inputs, and the ED2IN file. Existing PEcAn code has been revised to use these utilities.
+- PEcAn.data.atmosphere:
+    - New utilities for efficiently downloading NARR time series using THREDDS/OpenDAP
 
 ### Removed
 - Removed deprecated copies of PEcAn.utils::SafeList, PEcAn.utils::listToXml (both moved to PEcAn.settings in v 1.5.2), and PEcAn.utils::fqdn (moved to PEcAn.remote in 1.5.2). This fixes the masses of deprecation warnings in otherwise normal run logs (#1719).
@@ -51,6 +153,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - Replaced `rhdf5` library with `hdf5r`, a more modern alternative that is available on CRAN.
 - PEcAn.DB function `runModule.get.trait.data` has been moved to the new PEcAn.workflow package to avoid a circular package dependency between PEcAn.DB and PEcAn.settings.
 - Major documentation refactoring. The documentation names are now directly tied to the order in which they are rendered, and all `Rmd` files in all subdirectories of the documentation source are rendered by default. The overall structure of the documentation has been revised for clarity and cohesiveness.
+- Edited met2model.ED2 to not enforce leap years. 
 - Integrate demo 1 into basic user guide
 
 ## [1.5.2] - 2017-12-07
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 3cc4571940e..5a33606f509 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -12,7 +12,7 @@ New functionality is typically directed toward modules to provide a slimmer PEcA
 Generally, new model should be added to the models folder and new modules should be added to the modules folder. 
 Exceptions include code that is reused in many models or modules and wrapper functions that call specific implementations in models; these can be placed in the core packages.
 
-If you are unsure of whether your contribution should be implemented as a model, module or part of PEcAn Core, you may visit [Gitter](https://gitter.im/PecanProject/pecan) or ask on the pecan-develop mailing list for advice.
+If you are unsure of whether your contribution should be implemented as a model, module or part of PEcAn Core, you may visit [Chat Room](https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE) or ask on the pecan-develop mailing list for advice.
 
 ## Creating Issues
 
diff --git a/Dockerfile b/Dockerfile
deleted file mode 100644
index d4829853229..00000000000
--- a/Dockerfile
+++ /dev/null
@@ -1,36 +0,0 @@
-FROM ubuntu:16.04
-MAINTAINER Aman Kumar (ak47su30@gmail.com)
-
-# updated ppa's
-RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" > /etc/apt/sources.list.d/R.list &&\
-    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
-
-# copy the installation script inside the container
-ADD docker/ /build
-
-# Set script mod +x for preprocessors
-RUN chmod 750 /build/*.sh
-
-# Run the OS System setup script
-RUN /build/system_services.sh
-
-# run update machine to update machine
-RUN /build/update_machine.sh
-
-# run install packages to install required packages
-RUN /build/install_packages.sh
-
-# run install R to install R packages
-RUN /build/install_R.sh
-
-# run install pecan to install pecan cores
-RUN /build/install_pecan.sh
-
-# run install sipnet to install SIPNET (default testing Model)
-RUN /build/install_sipnet.sh
-
-# Clean up APT when done.
-RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /build/*
-
-# startup
-CMD ["/sbin/my_init"]
diff --git a/Makefile b/Makefile
index 7bd678a999e..41c8d1e7cb8 100644
--- a/Makefile
+++ b/Makefile
@@ -70,17 +70,39 @@ $(subst .doc/base/logger,,$(ALL_PKGS_D)): | .install/base/logger
 
 $(call depends,base/utils): | .install/base/remote
 $(call depends,base/db): | .install/base/utils
+$(call depends,base/qaqc): | .install/base/utils
 $(call depends,base/settings): | .install/base/utils .install/base/db
 $(call depends,base/visualization): | .install/base/db
-$(call depends,modules/data.atmosphere): | .install/base/utils .install/base/remote
-$(call depends,modules/data.land): | .install/base/db .install/base/utils .install/base/remote
-$(call depends,modules/meta.analysis): | .install/base/utils .install/base/db .install/base/remote
-$(call depends,modules/priors): | .install/base/utils .install/base/remote
-$(call depends,modules/assim.batch): | .install/base/utils .install/base/db .install/modules/meta.analysis .install/base/remote
-$(call depends,modules/rtm): | .install/modules/assim.batch .install/base/remote
-$(call depends,modules/uncertainty): | .install/base/utils .install/modules/priors .install/base/remote
-$(call depends,models/template): | .install/base/utils .install/base/remote
+$(call depends,base/workflow): | .install/base/db .install/base/settings
+$(call depends,modules/allometry): | .install/base/db
+$(call depends,modules/assim.batch): | .install/base/utils .install/base/db .install/base/settings .install/base/remote .install/modules/meta.analysis
+$(call depends,modules/assim.sequential): | .install/base/remote
+$(call depends,modules/benchmark): | .install/base/remote .install/base/settings
+$(call depends,modules/data.atmosphere): | .install/base/utils .install/base/remote .install/base/db
+$(call depends,modules/data.hydrology): | .install/base/utils
+$(call depends,modules/data.land): | .install/base/db .install/base/utils .install/base/settings .install/base/remote
+$(call depends,modules/data.mining): | .install/base/utils
+$(call depends,modules/data.remote): | .install/base/remote
+$(call depends,modules/meta.analysis): | .install/base/utils .install/base/db .install/base/settings .install/modules/priors
+$(call depends,modules/priors): | .install/base/utils
+$(call depends,modules/rtm): | .install/modules/assim.batch .install/base/utils .install/models/ed
+$(call depends,modules/uncertainty): | .install/base/utils .install/modules/priors
 $(call depends,models/biocro): | .install/mockery .install/base/utils .install/base/settings .install/base/db .install/modules/data.atmosphere .install/modules/data.land .install/base/remote
+$(call depends,models/cable): | .install/base/utils
+$(call depends,models/clm45): | .install/base/utils
+$(call depends,models/dalec): | .install/base/remote
+$(call depends,models/dvmdostem): | .install/base/utils
+$(call depends,models/ed): | .install/base/utils .install/base/remote .install/base/settings
+$(call depends,models/fates): | .install/base/utils .install/base/remote
+$(call depends,models/gday): | .install/base/utils .install/base/remote
+$(call depends,models/jules): | .install/base/utils .install/base/remote
+$(call depends,models/linkages): | .install/base/utils .install/base/remote
+$(call depends,models/lpjguess): | .install/base/utils .install/base/remote
+$(call depends,models/maat): | .install/base/utils .install/base/remote .install/base/settings
+$(call depends,models/maespa): | .install/base/utils .install/base/remote .install/modules/data.atmosphere
+$(call depends,models/preles): | .install/base/utils .install/modules/data.atmosphere
+$(call depends,models/sipnet): | .install/base/utils .install/base/remote .install/modules/data.atmosphere
+$(call depends,models/template): | .install/base/utils
 
 clean:
 	rm -rf .install .check .test .doc
@@ -102,10 +124,10 @@ clean:
 	time Rscript -e "if(!require('mockery')) install.packages('mockery', repos = 'http://cran.rstudio.com', Ncpus = ${NCPUS})"
 	echo `date` > $@
 
-depends_R_pkg = time Rscript -e "devtools::install_deps('$(strip $(1))', threads = ${NCPUS});"
+depends_R_pkg = time Rscript -e "devtools::install_deps('$(strip $(1))', threads = ${NCPUS}, dependencies = TRUE);"
 install_R_pkg = time Rscript -e "devtools::install('$(strip $(1))', Ncpus = ${NCPUS});"
 check_R_pkg = Rscript scripts/check_with_errors.R $(strip $(1))
-test_R_pkg = Rscript -e "devtools::test('"$(strip $(1))"', reporter = 'stop')"
+test_R_pkg = Rscript -e "devtools::test('"$(strip $(1))"', stop_on_failure = TRUE, stop_on_warning = FALSE)" # TODO: Raise bar to stop_on_warning = TRUE when we can
 doc_R_pkg = Rscript -e "devtools::document('"$(strip $(1))"')"
 
 $(ALL_PKGS_I) $(ALL_PKGS_C) $(ALL_PKGS_T) $(ALL_PKGS_D): | .install/devtools .install/roxygen2 .install/testthat
diff --git a/README.md b/README.md
index a24129c32aa..cda6d76c292 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 [![Build Status](https://travis-ci.org/PecanProject/pecan.svg?branch=master)](https://travis-ci.org/PecanProject/pecan)
 [![Slack](https://img.shields.io/badge/slack-login-green.svg)](https://pecanproject.slack.com/) 
-[![Slack](https://img.shields.io/badge/slack-join_chat-green.svg)](https://publicslack.com/slacks/pecanproject/invites/new) 
+[![Slack](https://img.shields.io/badge/slack-join_chat-green.svg)](https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE)
 [![DOI](https://zenodo.org/badge/4469/PecanProject/pecan.svg)](https://zenodo.org/badge/latestdoi/4469/PecanProject/pecan)
 
 
diff --git a/base/all/DESCRIPTION b/base/all/DESCRIPTION
index b869b8fc8c9..ad80f6747ab 100644
--- a/base/all/DESCRIPTION
+++ b/base/all/DESCRIPTION
@@ -2,8 +2,8 @@ Package: PEcAn.all
 Type: Package
 Title: PEcAn functions used for ecological forecasts and
     reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
     Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <dlebauer@illinois.edu>
@@ -28,7 +28,8 @@ Depends:
     PEcAn.emulator,
     PEcAn.priors,
     PEcAn.benchmark,
-    PEcAn.remote
+    PEcAn.remote,
+    PEcAn.workflow
 Suggests:
     PEcAn.ed,
     PEcAn.sipnet,
@@ -42,4 +43,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/base/db/DESCRIPTION b/base/db/DESCRIPTION
index cb7237ab7d9..cf54cdf72c2 100644
--- a/base/db/DESCRIPTION
+++ b/base/db/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.DB
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Carl
     Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <dlebauer@illinois.edu>
@@ -40,4 +40,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/base/db/NAMESPACE b/base/db/NAMESPACE
index ab4d8325b59..e676304e3dd 100644
--- a/base/db/NAMESPACE
+++ b/base/db/NAMESPACE
@@ -34,6 +34,7 @@ export(get_run_ids)
 export(get_users)
 export(get_var_names)
 export(get_workflow_ids)
+export(insert.format.vars)
 export(insert_table)
 export(load_data_single_run)
 export(match_dbcols)
diff --git a/base/db/R/clone_pft.R b/base/db/R/clone_pft.R
new file mode 100644
index 00000000000..fc6a138a52b
--- /dev/null
+++ b/base/db/R/clone_pft.R
@@ -0,0 +1,105 @@
+##' Duplicate existing pft with associated priors, species, and cultivars
+##'
+##' Creates a new pft that is a duplicate of an existing pft,
+##' including relationships with priors, species, and cultivars (if any) of the existing pft.
+##' This function mimics the 'clone pft' button in the PFTs record view page in the 
+##' BETYdb web interface for PFTs that aggregate >=1 species, but adds the ability to 
+##' clone the cultivar associations.
+##'
+##' @param parent.pft.name name of PFT to duplicate
+##' @param new.pft.name name for new PFT. Must not be the same as parent.pft.name
+##' @param new.pft.definition text for the new PFT's definition field.
+##' @param settings PEcAn settings list, used only for BETYdb connection parameters
+##' @return ID of the newly created pft in database, creates new PFT as a side effect
+##' @author David LeBauer, Chris Black
+##' @examples \dontrun{
+##' clone_pft(parent.pft.name    = "tempdecid",
+##'           new.pft.name       = "mytempdecid",
+##'           new.pft.definition = "mytempdecid is a new pft",
+##'           settings = pecan_settings_list)
+##' }
+clone_pft <- function(parent.pft.name,
+                      new.pft.name,
+                      new.pft.definition,
+                      settings){
+
+  if (new.pft.name == parent.pft.name) {
+    PEcAn.logger::logger.severe("new.pft.name must not be the same as parent.pft.name")
+  }
+
+  if (length(new.pft.name) > 1 || length(parent.pft.name) > 1) {
+    PEcAn.logger::logger.severe("multiple PFT names given, and clone_pft only knows how to handle one at a time.")
+  }
+
+  con <- db.open(settings$database$bety)
+  on.exit(db.close(con))
+
+  parent.pft <- (dplyr::tbl(con, "pfts")
+    %>% dplyr::filter(name == parent.pft.name)
+    %>% dplyr::collect())
+
+  if (nrow(parent.pft) == 0) {
+    PEcAn.logger::logger.severe("No existing PFT named '", parent.pft.name, "' found in database")
+  }
+
+  new.pft <- (parent.pft
+    %>% dplyr::select(-id, -created_at, -updated_at)
+    %>% dplyr::mutate(
+      name = new.pft.name,
+      definition = new.pft.definition,
+      parent_id = parent.pft$id))
+
+  ## create new pft
+  DBI::dbWriteTable(
+    conn = con,
+    name = "pfts",
+    value = as.data.frame(new.pft),
+    append = TRUE,
+    row.names = FALSE)
+
+  new.pft$id <- (dplyr::tbl(con, "pfts")
+    %>% dplyr::filter(name == new.pft.name)
+    %>% dplyr::pull(id))
+
+
+  # PFT members are stored in different tables depending on pft_type.
+  # Both tables have two columns:
+  #   - `pft_id`, which we update;
+  #   - `cultivar_id` or `specie_id`, which we copy unchanged
+  if (new.pft$pft_type == "cultivar") {
+    member_tbl <- "cultivars_pfts"
+  } else {
+    member_tbl <- "pfts_species"
+  }
+  new_members <- (dplyr::tbl(con, member_tbl)
+    %>% dplyr::filter(pft_id == parent.pft$id)
+    %>% dplyr::mutate(pft_id = new.pft$id)
+    %>% dplyr::distinct()
+    %>% dplyr::collect())
+
+  if(nrow(new_members) > 0){
+    DBI::dbWriteTable(
+      conn = con,
+      name = member_tbl,
+      value = as.data.frame(new_members),
+      append = TRUE,
+      row.names = FALSE)
+  }
+
+  new_priors <- (dplyr::tbl(con, "pfts_priors")
+    %>% dplyr::filter(pft_id == parent.pft$id)
+    %>% dplyr::mutate(pft_id = new.pft$id)
+    %>% dplyr::distinct()
+    %>% dplyr::collect())
+
+  if(nrow(new_priors) > 0){
+    DBI::dbWriteTable(
+      conn = con,
+      name = "pfts_priors",
+      value = as.data.frame(new_priors),
+      append = TRUE,
+      row.names = FALSE)
+  }
+
+  return(new.pft$id)
+}
diff --git a/base/db/R/dbfiles.R b/base/db/R/dbfiles.R
index 418a79b409a..b21843fe409 100644
--- a/base/db/R/dbfiles.R
+++ b/base/db/R/dbfiles.R
@@ -48,6 +48,7 @@ dbfile.input.insert <- function(in.path, in.prefix, siteid, startdate, enddate,
     create = TRUE,
     dates = TRUE
   )
+  
 
   # setup parent part of query if specified
   if (is.na(parentid)) {
@@ -120,9 +121,17 @@ dbfile.input.insert <- function(in.path, in.prefix, siteid, startdate, enddate,
         "'" , parent, ";"
       ),
       con = con
-    )[['id']]
+    )$id
   }
-
+  
+  if (length(inputid) > 1) {
+    PEcAn.logger::logger.warn(paste0("Multiple input files found matching parameters format_id = ", formatid, 
+                                     ", startdate = ", startdate, ", enddate = ", enddate, ", parent = ", parent, ".  Selecting the", 
+                                     " last input file.  This is normal for when an entire ensemble is inserted iteratively, but ", 
+                                     " is likely an error otherwise."))
+    inputid = inputid[length(inputid)]
+  }
+  
   # find appropriate dbfile, if not in database, insert new dbfile
   dbfile <- dbfile.check(type = 'Input', container.id = inputid, con = con, hostname = hostname)
 
@@ -132,6 +141,7 @@ dbfile.input.insert <- function(in.path, in.prefix, siteid, startdate, enddate,
       PEcAn.logger::logger.warn("Multiple dbfiles found. Using last.")
       dbfile <- dbfile[nrow(dbfile),]
     }
+    
     if (dbfile$file_name != in.prefix || dbfile$file_path != in.path) {
       print(dbfile, digits = 10)
       PEcAn.logger::logger.error(paste0(
@@ -143,6 +153,7 @@ dbfile.input.insert <- function(in.path, in.prefix, siteid, startdate, enddate,
     } else {
       dbfileid <- dbfile[['id']]
     }
+    
   } else {
     #insert dbfile & return dbfile id
     dbfileid <- dbfile.insert(in.path = in.path, in.prefix = in.prefix, type = 'Input', id = inputid,
@@ -167,7 +178,7 @@ dbfile.input.insert <- function(in.path, in.prefix, siteid, startdate, enddate,
 ##' @param con database connection object
 ##' @param hostname the name of the host where the file is stored, this will default to the name of the current machine
 ##' @param exact.dates setting to include start and end date in input query
-##' @param pattern text to seach for in the file name (default NULL = no check). NOT YET IMPLEMENTED
+##' @param pattern text to seach for in the file name (default NULL = no check).
 ##' @return data.frame with the id, filename and pathname of the input that is requested
 ##' @export
 ##' @author Rob Kooper, Tony Gardella
@@ -177,15 +188,17 @@ dbfile.input.insert <- function(in.path, in.prefix, siteid, startdate, enddate,
 ##' }
 dbfile.input.check <- function(siteid, startdate=NULL, enddate=NULL, mimetype, formatname, parentid=NA,
                                con, hostname=PEcAn.remote::fqdn(), exact.dates=FALSE, pattern=NULL) {
+  
   hostname <- default_hostname(hostname)
-
+  
   mimetypeid <- get.id(table = 'mimetypes', colnames = 'type_string', values = mimetype, con = con)
   if (is.null(mimetypeid)) {
     return(invisible(data.frame()))
   }
-
+  
   # find appropriate format
   formatid <- get.id(table = 'formats', colnames = c("mimetype_id", "name"), values = c(mimetypeid, formatname), con = con)
+  
   if (is.null(formatid)) {
     invisible(data.frame())
   }
@@ -224,20 +237,18 @@ dbfile.input.check <- function(siteid, startdate=NULL, enddate=NULL, mimetype, f
     return(data.frame())
   } else {
 
+    if (!is.null(pattern)) {
+      ## Case where pattern is not NULL
+      inputs <- inputs[grepl(pattern, inputs$name),]
+    }
+    
     ## parent check when NA
     if (is.na(parentid)) {
-
-      if (!is.null(pattern)) {
-        ## Case where pattern is not NULL
-        inputs <- inputs[grepl(pattern, inputs$name),]
-      }
-
       inputs <- inputs[is.na(inputs$parent_id),]
     }
 
     if (length(inputs$id) > 1) {
       PEcAn.logger::logger.warn("Found multiple matching inputs. Checking for one with associate files on host machine")
-
       print(inputs)
       #      ni = length(inputs$id)
       #      dbfile = list()
@@ -623,4 +634,4 @@ dbfile.id <- function(type, file, con, hostname=PEcAn.remote::fqdn()) {
     PEcAn.logger::logger.warn("no id found for", file, "in database")
     invisible(NA)
   }
-}
+}
\ No newline at end of file
diff --git a/base/db/R/insert.format.vars.R b/base/db/R/insert.format.vars.R
new file mode 100644
index 00000000000..b4ed716d588
--- /dev/null
+++ b/base/db/R/insert.format.vars.R
@@ -0,0 +1,163 @@
+#' Insert Format and Format-Variable Records 
+#'
+#' @param con SQL connection to BETYdb
+#' @param format_name The name of the format. Type: character string.
+#' @param mimetype_id The id associated with the mimetype of the format. Type: integer. 
+#' @param header Boolean that indicates the presence of a header in the format. Defaults to "TRUE".
+#' @param skip Integer that indicates the number of lines to skip in the header. Defaults to 0. 
+#' @param formats_variables A 'tibble' consisting of entries that correspond to columns in the formats-variables table. See Details for further information. 
+#' @param notes Additional description of the format: character string.
+#' @param suppress Boolean that suppresses or allows a test for an existing variable id. This test is inconvenient in applications where the variable_ids are already known. 
+#' @details The formats_variables argument must be a 'tibble' and be structured in a specific format so that the SQL query functions properly. All arguments should be passed as vectors so that each entry will correspond with a specific row. All empty values should be specified as NA.  
+#' \describe{
+#' \item{variable_id}{(Required) Vector of integers.}
+#' \item{name}{(Optional) Vector of character strings. The variable name in the imported data need only be specified if it differs from the BETY variable name.} 
+#' \item{unit}{(Optional) Vector of type character string. Should be in a format parseable by the udunits library and need only be secified if the units of the data in the file differ from the BETY standard.}
+#' \item{storage_type}{(Optional) Vector of character strings. Storage type need only be specified if the variable is stored in a format other than would be expected (e.g. if numeric values are stored as quoted character strings). Additionally, storage_type stores POSIX codes that are used to store any time variables (e.g. a column with a 4-digit year would be \%Y). See also \code{[base::strptime]}}
+#' \item{column_number}{Vector of integers that list the column numbers associated with variables in a dataset. Required for text files that lack headers.}}
+#' @author Liam Burke (liam.burke24@gmail.com)
+#' @return format_id
+#' @export
+#' @examples
+#' \dontrun{
+#' bety <- PEcAn.DB::betyConnect()
+#' 
+#' formats_variables_tibble <- tibble::tibble(
+#'        variable_id = c(411, 135, 382), 
+#'        name = c("NPP", NA, "YEAR"),  
+#'        unit = c("g C m-2 yr-1", NA, NA),
+#'        storage_type = c(NA, NA, "%Y"),
+#'        column_number = c(2, NA, 4),
+#'  )
+#'   insert.format.vars(con = bety$con, format_name = "LTER-HFR-103", mimetype_id = 1090, notes = "NPP from Harvard Forest.", header = FALSE, skip = 0, formats_variables = formats_variables_tibble)
+#' }
+insert.format.vars <- function(con, format_name, mimetype_id, notes = NULL, header = TRUE, skip = 0, formats_variables = NULL, suppress = TRUE){
+  
+  # Test if name is a character string
+  if(!is.character(format_name)){
+    PEcAn.logger::logger.error(
+      "Name must be a character string"
+    )
+  }
+  
+  # Test if format name already exists
+  name_test <- dplyr::tbl(con, "formats") %>% dplyr::select(id, name) %>% dplyr::filter(name %in% format_name) %>% collect()
+  name_test_df <- as.data.frame(name_test)
+  if(!is.null(name_test_df[1,1])){
+    PEcAn.logger::logger.error(
+      "Name already exists"
+    )
+  }
+  
+   #Test if skip is an integer
+  if(!is.character(skip)){
+  PEcAn.logger::logger.error(
+    "Skip must be of type character"
+    )
+  }
+  
+  # Test if header is a Boolean
+  if(!is.logical(header)){
+    PEcAn.logger::logger.error(
+      "Header must be of type Boolean"
+    )
+  }
+  
+  # Test if notes are a character string
+  if(!is.character(notes)&!is.null(notes)){
+    PEcAn.logger::logger.error(
+      "Notes must be of type character"
+    )
+  }
+  
+  ######## Formats-Variables tests ###############
+  if(!is.null(formats_variables)){
+    for(i in 1:nrow(formats_variables)){
+      if(!is.numeric(formats_variables[[i,"variable_id"]])){
+        PEcAn.logger::logger.error(
+          "variable_id must be an integer"
+        )
+      }
+
+      if(suppress == FALSE){
+        ## Test if variable_id already exists ##
+        var_id_test <- dplyr::tbl(con, "variables") %>% dplyr::select(id) %>% dplyr::filter(id %in% formats_variables[[i, "variable_id"]]) %>% dplyr::collect(id)
+        if(!is.null(var_id_test[1,1])){
+          PEcAn.logger::logger.error(
+            "variable_id already exists"
+          )
+        }
+      }
+
+      if(!is.character(formats_variables[[i, "name"]])&!is.na(formats_variables[[i, "name"]])){
+        PEcAn.logger::logger.error(
+          "Variable name must be of type character or NA"
+        )
+      }
+      if(!is.character(formats_variables[[i, "unit"]])&!is.na(formats_variables[[i, "unit"]])){
+        PEcAn.logger::logger.error(
+          "Units must be of type character or NA"
+        )
+      }
+      if(!is.character(formats_variables[[i, "storage_type"]])&!is.na(formats_variables[[i, "storage_type"]])){
+        PEcAn.logger::logger.error(
+          "storage_type must be of type character or NA"
+        )
+      }
+      if(!is.numeric(formats_variables[[i, "column_number"]])&!is.na(formats_variables[[i, "column_number"]])){
+        PEcAn.logger::logger.error(
+          "column_number must be of type numeric or NA"
+        )
+      }
+    }
+    
+    ## convert NA to "" for inserting into db ##
+    formats_variables[is.na(formats_variables)] <- ""
+    
+    ###  udunit tests ###
+    for(i in 1:nrow(formats_variables)){
+      u1 <- formats_variables[1,"unit"]
+      u2 <- dplyr::tbl(con, "variables") %>% dplyr::select(id, units) %>% dplyr::filter(id %in% formats_variables[[1, "variable_id"]]) %>% dplyr::pull(units)
+      
+      if(!udunits2::ud.is.parseable(u1)){
+        PEcAn.logger::logger.error(
+          "Units not parseable. Please enter a unit that is parseable by the udunits library."
+        )
+      }
+      # Grab the bety units and 
+      if(!udunits2::ud.are.convertible(u1, u2)){
+        PEcAn.logger::logger.error(
+          "Units are not convertable."
+        )
+      }
+    }
+  }
+  
+    formats_df <- tibble::tibble(
+      header = as.character(header),
+      skip = skip,
+      mimetype_id = mimetype_id,
+      notes = notes,
+      name = format_name,
+      stringsAsFactors = FALSE
+    )
+
+    ## Insert format record
+    inserted_formats <- db_merge_into(formats_df, "formats", con = con, by = c("name", "mimetype_id")) ## Make sure to include a 'by' argument
+    format_id <- dplyr::pull(inserted_formats, id)
+    
+  if(!is.null(formats_variables)){
+    ## Insert format_id into 
+    n <- nrow(formats_variables)
+    format_id_df <- matrix(data = format_id, nrow = n, ncol = 1)
+    colnames(format_id_df) <- "format_id"
+    
+    ## Make query data.frame
+    formats_variables_input <- cbind(format_id_df, formats_variables) 
+    
+    ## Insert Format-Variable record
+    inserted_formats_variables <- db_merge_into(formats_variables_input, "formats_variables", con = con,  by = c("variable_id"))
+  }
+    return(format_id)
+    
+}
diff --git a/base/db/R/insert_table.R b/base/db/R/insert_table.R
index f9e45c488bf..99c9498a892 100644
--- a/base/db/R/insert_table.R
+++ b/base/db/R/insert_table.R
@@ -16,7 +16,7 @@
 #' @examples
 #' irisdb <- DBI::dbConnect(RSQLite::SQLite(), ":memory:")
 #' dplyr::copy_to(irisdb, iris[1,], name = "iris", overwrite = TRUE)
-#' insert_table(iris[-1,], "iris", irisdb$con)
+#' insert_table(iris[-1,], "iris", irisdb)
 #' dplyr::tbl(irisdb, "iris")
 insert_table <- function(values, table, con, coerce_col_class = TRUE, drop = TRUE) {
   values_fixed <- match_dbcols(values, table, con, coerce_col_class, drop = TRUE)
diff --git a/base/db/R/priordupe.R b/base/db/R/priordupe.R
deleted file mode 100644
index c01dd69ec14..00000000000
--- a/base/db/R/priordupe.R
+++ /dev/null
@@ -1,62 +0,0 @@
-##' Duplicate existing prior for new pft
-##'
-##' Creates a new pft that is a duplicate of an existing pft,
-##' including relationships with priors and species of the existing pft
-##' @title Duplicate PFT
-##' @param parent.pft.name name of PFT to duplicate
-##' @param new.pft.name name for new PFT. Must not be the same as parent.pft.name
-##' @param new.pft.definition text for the new PFT's definition field. If NULL the definition will be empty, not copied from the parent PFT.
-##' @return nothing, creates new pft in database as a side-effect
-##' @author David LeBauer
-##' @examples \dontrun{
-##' priordupe(parent.pft.name    = "tempdecid",
-##'           new.pft.name       = "mytempdecid",
-##'           new.pft.definition = "mytempdecid is a new pft")
-##' }
-priordupe <- function(parent.pft.name = NULL,
-                      new.pft.name   = NULL,
-                      new.pft.definition =  NULL,
-                      settings = NULL){
-
-  con <- db.open(settings$database$bety)
-  on.exit(db.close(con))
-
-  parent.pft.id <- db.query(query = paste("select id from pfts where name = ", parent.pft.name, ";"),
-                            con = con)
-
-  ## create new pft
-  db.query(
-    query = paste(
-      "insert into pfts set definition = ", newpftdefn,
-      " name = ", new.pft.name, ";"
-    ),
-    con = con
-  )
-  new.pft.id <- db.query(query = paste("select id from pfts where name =",
-                                       new.pft.name,";"), con = con)
-
-  old.species.id <- db.query(query = paste("select specie_id from pfts_species where pft_id =",
-                                     parent.pft.id, ";"), con = con)
-  new.pfts_species <- c(pft_id = new.pft.id, specie_id = unique(old.species.id))
-
-  db.query(
-    query = paste(
-      "insert into pfts_species set pft_id = ", new.pfts_species$pft_id,
-      "specie_id = ", new.pfts_species$specie_id, ";"
-    ),
-    con = con
-  )
-
-  old.priors <-  db.query(query = paste("select prior_id from pfts_priors where pft_id =",
-                                        parent.pft.id, ";"), con = con)
-  new.pfts_priors <- c(pft_id = new.pft.id,
-                       prior_id = unique(old.priors))
-  db.query(
-    query = paste(
-      "insert into pfts_priors set pft_id = ", new.pfts_priors$pft_id,
-      "specie_id = ", new.pfts_priors$priors_id,
-      ";"
-    ),
-    con = con
-  )
-}
diff --git a/base/db/R/query.format.vars.R b/base/db/R/query.format.vars.R
index fb93556a9d7..9ebf8ef355a 100644
--- a/base/db/R/query.format.vars.R
+++ b/base/db/R/query.format.vars.R
@@ -9,7 +9,7 @@
 ##'
 query.format.vars <- function(bety, input.id=NA, format.id=NA, var.ids=NA) {
 
-  if(is.na(input.id) & is.na(format.id)){
+  if ((is.null(input.id)||is.na(input.id)) & (is.null(format.id)||is.na(format.id))){
     PEcAn.logger::logger.error("Must specify input id or format id")
   }
 
diff --git a/base/db/inst/bety_mstmip_lookup.csv b/base/db/inst/bety_mstmip_lookup.csv
index cc739d20db8..e1b99b6b02a 100644
--- a/base/db/inst/bety_mstmip_lookup.csv
+++ b/base/db/inst/bety_mstmip_lookup.csv
@@ -30,7 +30,7 @@ LWdown,W/m2,LWdown
 LWdown,W/m2,surface_downwelling_longwave_flux_in_air
 Lwnet,W m-2,Lwnet
 NEE,kg C m-2 s-1,NEE
-NEE,kg C m-2 s-1,FC
+FC,kg C m-2 s-1,FC
 NPP,kg C m-2 s-1,NPP
 NPP,kg C m-2 s-1,NPP_2_C
 NPP,kg C m-2 s-1,NPP_1_C
diff --git a/base/db/man/arrhenius.scaling.traits.Rd b/base/db/man/arrhenius.scaling.traits.Rd
index 901b82d4cc2..2f9db05abd3 100644
--- a/base/db/man/arrhenius.scaling.traits.Rd
+++ b/base/db/man/arrhenius.scaling.traits.Rd
@@ -4,8 +4,8 @@
 \alias{arrhenius.scaling.traits}
 \title{Apply Arrhenius scaling to 25 degC for temperature-dependent traits}
 \usage{
-arrhenius.scaling.traits(data, covariates, temp.covariates, new.temp = 25,
-  missing.temp = 25)
+arrhenius.scaling.traits(data, covariates, temp.covariates,
+  new.temp = 25, missing.temp = 25)
 }
 \arguments{
 \item{data}{data frame of data to scale, as returned by query.data()}
diff --git a/base/db/man/clone_pft.Rd b/base/db/man/clone_pft.Rd
new file mode 100644
index 00000000000..824f15683f7
--- /dev/null
+++ b/base/db/man/clone_pft.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clone_pft.R
+\name{clone_pft}
+\alias{clone_pft}
+\title{Duplicate existing pft with associated priors, species, and cultivars}
+\usage{
+clone_pft(parent.pft.name, new.pft.name, new.pft.definition, settings)
+}
+\arguments{
+\item{parent.pft.name}{name of PFT to duplicate}
+
+\item{new.pft.name}{name for new PFT. Must not be the same as parent.pft.name}
+
+\item{new.pft.definition}{text for the new PFT's definition field.}
+
+\item{settings}{PEcAn settings list, used only for BETYdb connection parameters}
+}
+\value{
+ID of the newly created pft in database, creates new PFT as a side effect
+}
+\description{
+Creates a new pft that is a duplicate of an existing pft,
+including relationships with priors, species, and cultivars (if any) of the existing pft.
+This function mimics the 'clone pft' button in the PFTs record view page in the 
+BETYdb web interface for PFTs that aggregate >=1 species, but adds the ability to 
+clone the cultivar associations.
+}
+\examples{
+\dontrun{
+clone_pft(parent.pft.name    = "tempdecid",
+          new.pft.name       = "mytempdecid",
+          new.pft.definition = "mytempdecid is a new pft",
+          settings = pecan_settings_list)
+}
+}
+\author{
+David LeBauer, Chris Black
+}
diff --git a/base/db/man/dbfile.input.check.Rd b/base/db/man/dbfile.input.check.Rd
index ec1f45c120b..dabda042604 100644
--- a/base/db/man/dbfile.input.check.Rd
+++ b/base/db/man/dbfile.input.check.Rd
@@ -27,7 +27,7 @@ dbfile.input.check(siteid, startdate = NULL, enddate = NULL, mimetype,
 
 \item{exact.dates}{setting to include start and end date in input query}
 
-\item{pattern}{text to seach for in the file name (default NULL = no check). NOT YET IMPLEMENTED}
+\item{pattern}{text to seach for in the file name (default NULL = no check).}
 }
 \value{
 data.frame with the id, filename and pathname of the input that is requested
diff --git a/base/db/man/dbfile.input.insert.Rd b/base/db/man/dbfile.input.insert.Rd
index 77ab26acdcf..bcc6e4321a2 100644
--- a/base/db/man/dbfile.input.insert.Rd
+++ b/base/db/man/dbfile.input.insert.Rd
@@ -4,9 +4,9 @@
 \alias{dbfile.input.insert}
 \title{Insert file into tables}
 \usage{
-dbfile.input.insert(in.path, in.prefix, siteid, startdate, enddate, mimetype,
-  formatname, parentid = NA, con, hostname = PEcAn.remote::fqdn(),
-  allow.conflicting.dates = FALSE)
+dbfile.input.insert(in.path, in.prefix, siteid, startdate, enddate,
+  mimetype, formatname, parentid = NA, con,
+  hostname = PEcAn.remote::fqdn(), allow.conflicting.dates = FALSE)
 }
 \arguments{
 \item{in.path}{path to the directory containing the file to be inserted}
diff --git a/base/db/man/derive.traits.Rd b/base/db/man/derive.traits.Rd
index 96b10804116..578018a5a8d 100644
--- a/base/db/man/derive.traits.Rd
+++ b/base/db/man/derive.traits.Rd
@@ -4,8 +4,9 @@
 \alias{derive.traits}
 \title{Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait.}
 \usage{
-derive.traits(FUN, ..., input = list(...), match.columns = c("citation_id",
-  "site_id", "specie_id"), var.name = NA, sample.size = 10^6)
+derive.traits(FUN, ..., input = list(...),
+  match.columns = c("citation_id", "site_id", "specie_id"),
+  var.name = NA, sample.size = 10^6)
 }
 \arguments{
 \item{FUN}{arithmetic function}
diff --git a/base/db/man/insert.format.vars.Rd b/base/db/man/insert.format.vars.Rd
new file mode 100644
index 00000000000..c774b037231
--- /dev/null
+++ b/base/db/man/insert.format.vars.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/insert.format.vars.R
+\name{insert.format.vars}
+\alias{insert.format.vars}
+\title{Insert Format and Format-Variable Records}
+\usage{
+insert.format.vars(con, format_name, mimetype_id, notes = NULL,
+  header = TRUE, skip = 0, formats_variables = NULL,
+  suppress = TRUE)
+}
+\arguments{
+\item{con}{SQL connection to BETYdb}
+
+\item{format_name}{The name of the format. Type: character string.}
+
+\item{mimetype_id}{The id associated with the mimetype of the format. Type: integer.}
+
+\item{notes}{Additional description of the format: character string.}
+
+\item{header}{Boolean that indicates the presence of a header in the format. Defaults to "TRUE".}
+
+\item{skip}{Integer that indicates the number of lines to skip in the header. Defaults to 0.}
+
+\item{formats_variables}{A 'tibble' consisting of entries that correspond to columns in the formats-variables table. See Details for further information.}
+
+\item{suppress}{Boolean that suppresses or allows a test for an existing variable id. This test is inconvenient in applications where the variable_ids are already known.}
+}
+\value{
+format_id
+}
+\description{
+Insert Format and Format-Variable Records
+}
+\details{
+The formats_variables argument must be a 'tibble' and be structured in a specific format so that the SQL query functions properly. All arguments should be passed as vectors so that each entry will correspond with a specific row. All empty values should be specified as NA.  
+\describe{
+\item{variable_id}{(Required) Vector of integers.}
+\item{name}{(Optional) Vector of character strings. The variable name in the imported data need only be specified if it differs from the BETY variable name.} 
+\item{unit}{(Optional) Vector of type character string. Should be in a format parseable by the udunits library and need only be secified if the units of the data in the file differ from the BETY standard.}
+\item{storage_type}{(Optional) Vector of character strings. Storage type need only be specified if the variable is stored in a format other than would be expected (e.g. if numeric values are stored as quoted character strings). Additionally, storage_type stores POSIX codes that are used to store any time variables (e.g. a column with a 4-digit year would be \%Y). See also \code{[base::strptime]}}
+\item{column_number}{Vector of integers that list the column numbers associated with variables in a dataset. Required for text files that lack headers.}}
+}
+\examples{
+\dontrun{
+bety <- PEcAn.DB::betyConnect()
+
+formats_variables_tibble <- tibble::tibble(
+       variable_id = c(411, 135, 382), 
+       name = c("NPP", NA, "YEAR"),  
+       unit = c("g C m-2 yr-1", NA, NA),
+       storage_type = c(NA, NA, "\%Y"),
+       column_number = c(2, NA, 4),
+ )
+  insert.format.vars(con = bety$con, format_name = "LTER-HFR-103", mimetype_id = 1090, notes = "NPP from Harvard Forest.", header = FALSE, skip = 0, formats_variables = formats_variables_tibble)
+}
+}
+\author{
+Liam Burke (liam.burke24@gmail.com)
+}
diff --git a/base/db/man/insert_table.Rd b/base/db/man/insert_table.Rd
index c51740868ce..236d82b1479 100644
--- a/base/db/man/insert_table.Rd
+++ b/base/db/man/insert_table.Rd
@@ -30,6 +30,6 @@ database.
 \examples{
 irisdb <- DBI::dbConnect(RSQLite::SQLite(), ":memory:")
 dplyr::copy_to(irisdb, iris[1,], name = "iris", overwrite = TRUE)
-insert_table(iris[-1,], "iris", irisdb$con)
+insert_table(iris[-1,], "iris", irisdb)
 dplyr::tbl(irisdb, "iris")
 }
diff --git a/base/db/man/priordupe.Rd b/base/db/man/priordupe.Rd
deleted file mode 100644
index 26654e36819..00000000000
--- a/base/db/man/priordupe.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/priordupe.R
-\name{priordupe}
-\alias{priordupe}
-\title{Duplicate PFT}
-\usage{
-priordupe(parent.pft.name = NULL, new.pft.name = NULL,
-  new.pft.definition = NULL, settings = NULL)
-}
-\arguments{
-\item{parent.pft.name}{name of PFT to duplicate}
-
-\item{new.pft.name}{name for new PFT. Must not be the same as parent.pft.name}
-
-\item{new.pft.definition}{text for the new PFT's definition field. If NULL the definition will be empty, not copied from the parent PFT.}
-}
-\value{
-nothing, creates new pft in database as a side-effect
-}
-\description{
-Duplicate existing prior for new pft
-}
-\details{
-Creates a new pft that is a duplicate of an existing pft,
-including relationships with priors and species of the existing pft
-}
-\examples{
-\dontrun{
-priordupe(parent.pft.name    = "tempdecid",
-          new.pft.name       = "mytempdecid",
-          new.pft.definition = "mytempdecid is a new pft")
-}
-}
-\author{
-David LeBauer
-}
diff --git a/base/db/man/query.data.Rd b/base/db/man/query.data.Rd
index fc1705c7ded..e8bd1dfe0c8 100644
--- a/base/db/man/query.data.Rd
+++ b/base/db/man/query.data.Rd
@@ -6,7 +6,8 @@
 \usage{
 query.data(trait, spstr,
   extra.columns = "ST_X(ST_CENTROID(sites.geometry)) AS lon, ST_Y(ST_CENTROID(sites.geometry)) AS lat, ",
-  con = NULL, store.unconverted = FALSE, ids_are_cultivars = FALSE, ...)
+  con = NULL, store.unconverted = FALSE, ids_are_cultivars = FALSE,
+  ...)
 }
 \arguments{
 \item{trait}{trait to query from the database}
diff --git a/base/db/man/search_references.Rd b/base/db/man/search_references.Rd
index 8af809bf7a1..e27002b250c 100644
--- a/base/db/man/search_references.Rd
+++ b/base/db/man/search_references.Rd
@@ -20,5 +20,5 @@ search_references(queries, ...)
 `data.frame` containing crossref information converted to match bety citations table.
 }
 \description{
-Perform crossref search for a list of references
+Requires the `rcrossref` package.
 }
diff --git a/base/db/tests/testthat/test-get.trait.data.pft.R b/base/db/tests/testthat/test-get.trait.data.pft.R
index 096a2708156..4fdc80b2dbe 100644
--- a/base/db/tests/testthat/test-get.trait.data.pft.R
+++ b/base/db/tests/testthat/test-get.trait.data.pft.R
@@ -26,6 +26,7 @@ get_pft <- function(pftname) {
 
 
 test_that("reference species and cultivar PFTs write traits properly",{
+  skip("Disabled until Travis bety contains Pavi_alamo and Pavi_all (#1958)")
   pavi_sp <- get_pft("pavi")
   expect_equal(pavi_sp$name, "pavi")
   sp_csv = file.path(dbdir, "posterior", pavi_sp$posteriorid, "species.csv")
diff --git a/base/db/tests/testthat/test-query.pft.R b/base/db/tests/testthat/test-query.pft.R
index 07a83be4cbf..47f0b4557ef 100644
--- a/base/db/tests/testthat/test-query.pft.R
+++ b/base/db/tests/testthat/test-query.pft.R
@@ -36,6 +36,7 @@ test_that("nonexistant PFTs and modeltypes return empty dataframes", {
 
 
 test_that("query.pft_cultivars finds cultivars for a PFT", {
+  skip("Disabled until Travis bety contains Pavi_alamo and Pavi_all (#1958)")
   one_cv <- query.pft_cultivars(pft = "Pavi_alamo", modeltype = NULL, con)
   expect_is(one_cv, "data.frame")
   expect_equal(nrow(one_cv), 1)
diff --git a/base/logger/DESCRIPTION b/base/logger/DESCRIPTION
index 780873b0ea8..065a4642197 100644
--- a/base/logger/DESCRIPTION
+++ b/base/logger/DESCRIPTION
@@ -1,11 +1,12 @@
 Package: PEcAn.logger
 Title: Logger functions for PEcAn
-Version: 1.5.3
+Version: 1.6.0
 Author: Rob Kooper, Alexey Shiklomanov
 Maintainer: Alexey Shiklomanov <ashiklom@bu.edu>
 Description: Special logger functions for tracking execution status and the environment.
-Depends: R
+Suggests: testthat
 License: FreeBSD + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
+Roxygen: list(markdown = TRUE)
diff --git a/base/logger/NAMESPACE b/base/logger/NAMESPACE
index eec7c3cc8ef..9204650ddab 100644
--- a/base/logger/NAMESPACE
+++ b/base/logger/NAMESPACE
@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(debugifnot)
+export(errorifnot)
+export(infoifnot)
 export(logger.debug)
 export(logger.error)
 export(logger.getLevel)
@@ -11,3 +14,5 @@ export(logger.setUseConsole)
 export(logger.setWidth)
 export(logger.severe)
 export(logger.warn)
+export(severeifnot)
+export(warnifnot)
diff --git a/base/logger/R/logger.R b/base/logger/R/logger.R
index f42a1fdeeee..9feee614b11 100644
--- a/base/logger/R/logger.R
+++ b/base/logger/R/logger.R
@@ -96,13 +96,14 @@ logger.error <- function(msg, ...) {
 ##'
 ##' @param msg the message that should be printed.
 ##' @param ... any additional text that should be printed.
+##' @inheritParams logger.message
 ##' @export
 ##' @author Rob Kooper
 ##' @examples
 ##' \dontrun{
 ##' logger.severe('missing parameters')
 ##' }
-logger.severe <- function(msg, ...) {
+logger.severe <- function(msg, ..., wrap = TRUE) {
   logger.message("SEVERE", msg, ...)
   
   # run option
@@ -129,16 +130,20 @@ logger.severe <- function(msg, ...) {
 ##' @param level the level of the message (DEBUG, INFO, WARN, ERROR)
 ##' @param msg the message that should be printed.
 ##' @param ... any additional text that should be printed.
+##' @param wrap Whether or not to wrap long messages (default =
+##'   `TRUE`). If `FALSE`, preserve format of original string. Useful
+##'   for specifically formatted error messages.
 ##' @author Rob Kooper
 ##' @examples
 ##' \dontrun{
 ##' logger.message('DEBUG', 'variable', 5)
 ##' }
-logger.message <- function(level, msg, ...) {
+logger.message <- function(level, msg, ..., wrap = TRUE) {
   if (logger.getLevelNumber(level) >= .utils.logger$level) {
     dump.frames(dumpto = "dump.log")
     calls <- names(dump.log)
     calls <- calls[!grepl("^(#[0-9]+: )?(PEcAn\\.logger::)?logger", calls)]
+    calls <- calls[!grepl("(severe|error|warn|info|debug)ifnot", calls)]
     func <- sub("\\(.*", "", tail(calls, 1))
     if (length(func) == 0) {
       func <- "console"
@@ -146,7 +151,7 @@ logger.message <- function(level, msg, ...) {
     
     stamp.text <- sprintf("%s %-6s [%s] :", Sys.time(), level, func)
     long.msg <- paste(c(msg, ...), collapse = " ")
-    if (nchar(long.msg) > 20) {
+    if (nchar(long.msg) > 20 && wrap) {
       new.msg <- paste("\n", strwrap(long.msg, width = .utils.logger$width, 
                                      indent = 2, exdent = 2), collapse = " ")
     } else {
diff --git a/base/logger/R/logifnot.R b/base/logger/R/logifnot.R
new file mode 100644
index 00000000000..b368728ce5a
--- /dev/null
+++ b/base/logger/R/logifnot.R
@@ -0,0 +1,89 @@
+#' Logger message if conditions are not met
+#'
+#' Similar to [base::stopifnot], but allows you to use a custom message and 
+#' logger level. If all conditions are `TRUE`, silently exit.
+#'
+#' Conditions can be vectorized, or can return non-logical values.The 
+#' underlying function automatically applies `isTRUE(all(.))` to the 
+#' conditions.
+#'
+#' @param msg Logger message to write, as a single character string.
+#' @param ... Conditions to evaluate 
+#' @return Invisibly, `TRUE` if conditions are met, `FALSE` otherwise
+#' @examples
+#' a <- 1:5
+#' b <- list(6, 7, 8)
+#' debugifnot("By the way, something is not a list.", is.list(a), is.list(b))
+#' infoifnot("Something is not a list.", is.list(a), is.list(b))
+#' warnifnot("I would prefer it if you used lists.", is.list(a), is.list(b))
+#' errorifnot("You should definitely use lists.", is.list(a), is.list(b))
+#' try({
+#'   severeifnot("I absolutely cannot deal with the fact that something is not a list.", is.list(a), is.list(b))
+#' })
+#' @export
+severeifnot <- function(msg, ...) {
+  if (!check_conditions(...)) {
+    PEcAn.logger::logger.severe(msg)
+  } else {
+    invisible(TRUE)
+  }
+}
+
+#' @rdname severeifnot
+#' @export
+errorifnot <- function(msg, ...) {
+  if (!check_conditions(...)) {
+    PEcAn.logger::logger.error(msg)
+    invisible(FALSE)
+  } else {
+    invisible(TRUE)
+  }
+}
+
+#' @rdname severeifnot
+#' @export
+warnifnot <- function(msg, ...) {
+  if (!check_conditions(...)) {
+    PEcAn.logger::logger.warn(msg)
+    invisible(FALSE)
+  } else {
+    invisible(TRUE)
+  }
+}
+
+#' @rdname severeifnot
+#' @export
+infoifnot <- function(msg, ...) {
+  if (!check_conditions(...)) {
+    PEcAn.logger::logger.info(msg)
+    invisible(FALSE)
+  } else {
+    invisible(TRUE)
+  }
+}
+
+#' @rdname severeifnot
+#' @export
+debugifnot <- function(msg, ...) {
+  if (!check_conditions(...)) {
+    PEcAn.logger::logger.debug(msg)
+    invisible(FALSE)
+  } else {
+    invisible(TRUE)
+  }
+}
+
+#' Check a list of conditions
+check_conditions <- function(...) {
+  dots <- list(...)
+  conditions <- vapply(dots, is_definitely_true, logical(1))
+  all(conditions)
+}
+
+#' Robust logical check
+is_definitely_true <- function(x) {
+  if (is.null(x) || length(x) == 0 || !is.logical(x)) {
+    return(FALSE)
+  }
+  isTRUE(all(x))
+}
diff --git a/base/logger/man/check_conditions.Rd b/base/logger/man/check_conditions.Rd
new file mode 100644
index 00000000000..4ef381d29f6
--- /dev/null
+++ b/base/logger/man/check_conditions.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/logifnot.R
+\name{check_conditions}
+\alias{check_conditions}
+\title{Check a list of conditions}
+\usage{
+check_conditions(...)
+}
+\description{
+Check a list of conditions
+}
diff --git a/base/logger/man/is_definitely_true.Rd b/base/logger/man/is_definitely_true.Rd
new file mode 100644
index 00000000000..4e060c0879c
--- /dev/null
+++ b/base/logger/man/is_definitely_true.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/logifnot.R
+\name{is_definitely_true}
+\alias{is_definitely_true}
+\title{Robust logical check}
+\usage{
+is_definitely_true(x)
+}
+\description{
+Robust logical check
+}
diff --git a/base/logger/man/logger.message.Rd b/base/logger/man/logger.message.Rd
index 3a70d60a4e0..88f95648da2 100644
--- a/base/logger/man/logger.message.Rd
+++ b/base/logger/man/logger.message.Rd
@@ -4,7 +4,7 @@
 \alias{logger.message}
 \title{Prints a message at a certain log level.}
 \usage{
-logger.message(level, msg, ...)
+logger.message(level, msg, ..., wrap = TRUE)
 }
 \arguments{
 \item{level}{the level of the message (DEBUG, INFO, WARN, ERROR)}
@@ -12,6 +12,10 @@ logger.message(level, msg, ...)
 \item{msg}{the message that should be printed.}
 
 \item{...}{any additional text that should be printed.}
+
+\item{wrap}{Whether or not to wrap long messages (default =
+\code{TRUE}). If \code{FALSE}, preserve format of original string. Useful
+for specifically formatted error messages.}
 }
 \description{
 This function will print a message. This is the function that is responsible for
diff --git a/base/logger/man/logger.setQuitOnSevere.Rd b/base/logger/man/logger.setQuitOnSevere.Rd
index 63fdeeef907..344bd843a9e 100644
--- a/base/logger/man/logger.setQuitOnSevere.Rd
+++ b/base/logger/man/logger.setQuitOnSevere.Rd
@@ -11,7 +11,7 @@ logger.setQuitOnSevere(severeQuits)
 }
 \description{
 The default is for a non-interactive session to quit. Setting this to false is
-especially useful for running tests when placed in \code{inst/tests/test.<fn>.R}, 
+especially useful for running tests when placed in \code{inst/tests/test.<fn>.R},
 but is not passed from \code{tests/run.all.R}.
 }
 \examples{
diff --git a/base/logger/man/logger.severe.Rd b/base/logger/man/logger.severe.Rd
index 06f1cc1b43c..1ea4c76cca9 100644
--- a/base/logger/man/logger.severe.Rd
+++ b/base/logger/man/logger.severe.Rd
@@ -4,12 +4,16 @@
 \alias{logger.severe}
 \title{Prints an severe message and stops execution.}
 \usage{
-logger.severe(msg, ...)
+logger.severe(msg, ..., wrap = TRUE)
 }
 \arguments{
 \item{msg}{the message that should be printed.}
 
 \item{...}{any additional text that should be printed.}
+
+\item{wrap}{Whether or not to wrap long messages (default =
+\code{TRUE}). If \code{FALSE}, preserve format of original string. Useful
+for specifically formatted error messages.}
 }
 \description{
 This function will print a message and stop execution of the code. This
diff --git a/base/logger/man/severeifnot.Rd b/base/logger/man/severeifnot.Rd
new file mode 100644
index 00000000000..82f01737ea6
--- /dev/null
+++ b/base/logger/man/severeifnot.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/logifnot.R
+\name{severeifnot}
+\alias{severeifnot}
+\alias{errorifnot}
+\alias{warnifnot}
+\alias{infoifnot}
+\alias{debugifnot}
+\title{Logger message if conditions are not met}
+\usage{
+severeifnot(msg, ...)
+
+errorifnot(msg, ...)
+
+warnifnot(msg, ...)
+
+infoifnot(msg, ...)
+
+debugifnot(msg, ...)
+}
+\arguments{
+\item{msg}{Logger message to write, as a single character string.}
+
+\item{...}{Conditions to evaluate}
+}
+\value{
+Invisibly, \code{TRUE} if conditions are met, \code{FALSE} otherwise
+}
+\description{
+Similar to \link[base:stopifnot]{base::stopifnot}, but allows you to use a custom message and
+logger level. If all conditions are \code{TRUE}, silently exit.
+}
+\details{
+Conditions can be vectorized, or can return non-logical values.The
+underlying function automatically applies \code{isTRUE(all(.))} to the
+conditions.
+}
+\examples{
+a <- 1:5
+b <- list(6, 7, 8)
+debugifnot("By the way, something is not a list.", is.list(a), is.list(b))
+infoifnot("Something is not a list.", is.list(a), is.list(b))
+warnifnot("I would prefer it if you used lists.", is.list(a), is.list(b))
+errorifnot("You should definitely use lists.", is.list(a), is.list(b))
+try({
+  severeifnot("I absolutely cannot deal with the fact that something is not a list.", is.list(a), is.list(b))
+})
+}
diff --git a/base/qaqc/DESCRIPTION b/base/qaqc/DESCRIPTION
index d7f4f1c0c6c..c80c3c5bab9 100644
--- a/base/qaqc/DESCRIPTION
+++ b/base/qaqc/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.qaqc
 Type: Package
 Title: QAQC
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer
 Maintainer: David LeBauer <dlebauer@illinois.edu>
 Description: PEcAn integration and model skill testing
@@ -10,8 +10,11 @@ Depends:
     plotrix
 Imports:
     PEcAn.logger
+Suggests:
+	testthat
 License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/base/qaqc/tests/testthat.R b/base/qaqc/tests/testthat.R
index 0ec2de56be0..f046421f15b 100644
--- a/base/qaqc/tests/testthat.R
+++ b/base/qaqc/tests/testthat.R
@@ -7,7 +7,7 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 library(testthat)
-library(PEcAn.utils)
+library(PEcAn.qaqc)
 
 PEcAn.logger::logger.setQuitOnSevere(FALSE)
 #test_check("PEcAn.qaqc")
diff --git a/base/remote/DESCRIPTION b/base/remote/DESCRIPTION
index f5aadc2ca21..2e99f82b10f 100644
--- a/base/remote/DESCRIPTION
+++ b/base/remote/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PEcAn.remote
 Type: Package
 Title: PEcAn model execution utilities
-Version: 1.5.3
+Version: 1.6.0
 Author: Alexey Shiklomanov, Rob Kooper, Shawn Serbin, David LeBauer
 Maintainer: Alexey Shiklomanov <ashiklom@bu.edu>
 Description: This package contains utilities for communicating with and executing code on local and remote hosts.
@@ -9,10 +9,11 @@ Description: This package contains utilities for communicating with and executin
 Imports:
     PEcAn.logger
 Suggests:
+    testthat,
     tools,
     getPass
 License: FreeBSD + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
diff --git a/base/remote/R/remote.copy.update.R b/base/remote/R/remote.copy.update.R
index 19ff1d5ea1e..af713d5f673 100644
--- a/base/remote/R/remote.copy.update.R
+++ b/base/remote/R/remote.copy.update.R
@@ -1,6 +1,7 @@
 #' Copy to remote and update DB
 #' @param input_id Input ID, as a numeric or character
 #' @param remote_dir remote folder path
+#' @param local_file_path full path name to local file that needs to be copied, e.g. "/fs/data1/dbfiles/.../.../*.css"
 #' @param remote_file_name remote file name, no need to provide if it's the same as local
 #' @param host as in settings$host
 #' @param con BETY database connection
@@ -9,30 +10,23 @@
 #'
 #' @author Istem Fer
 #' @export
-remote.copy.update <- function(input_id, remote_dir, remote_file_name = NULL, host, con){
+remote.copy.update <- function(input_id, remote_dir, local_file_path, remote_file_name = NULL, host, con){
 
   PEcAn.remote::remote.execute.cmd(host, "mkdir", c("-p", remote_dir))
 
-  local_file_record <- PEcAn.DB::db.query(paste("SELECT * from dbfiles where container_id =", input_id), con)
-
   if(is.null(remote_file_name)){
-    local_file_name <- local_file_record$file_name
-    if(length(local_file_name) > 1){
-      PEcAn.logger::logger.warn(paste0("Multiple file names found in the DB and no remote file name provided. Using the first file name for remote file name: ",
-                         local_file_record$file_name[1]))
-      local_file_name <- local_file_record$file_name[1]
-    }
-    remote_file_name <- local_file_name
+    remote_file_name <- basename(local_file_path)
   }
 
-  local_file_path  <- file.path(local_file_record$file_path, local_file_record$file_name)
   remote_file_path <- file.path(remote_dir, remote_file_name)
 
   remote.copy.to(host, local_file_path, remote_file_path)
 
+  type <- db.query(paste("SELECT container_type from dbfiles where container_id =", putveg.id[[i]]), con)
+  
   # update DB record
   remote_id <- PEcAn.DB::dbfile.insert(in.path = remote_dir, in.prefix = remote_file_name,
-                type = local_file_record$container_type, id = local_file_record$container_id,
+                type = unique(type), id = input_id$input.id,
                 con = con, hostname = host$name)
 
 
diff --git a/base/remote/R/start.model.runs.R b/base/remote/R/start.model.runs.R
index 0b4b0d52746..98783e205ba 100644
--- a/base/remote/R/start.model.runs.R
+++ b/base/remote/R/start.model.runs.R
@@ -41,6 +41,7 @@ start.model.runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
 
   is_local <- is.localhost(settings$host)
   is_qsub <- !is.null(settings$host$qsub)
+  is_rabbitmq <- !is.null(settings$host$rabbitmq)
   is_modellauncher <- !is.null(settings$host$modellauncher)
 
   # loop through runs and either call start run, or launch job on remote machine
@@ -75,7 +76,14 @@ start.model.runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
     }
 
     # check to see if we use the model launcer
-    if (is_modellauncher) {
+    if (is_rabbitmq) {
+      run_id_string <- format(run, scientific = FALSE)
+      folder <- file.path(settings$rundir, run_id_string)
+      out <- start_rabbitmq(folder, settings$host$rabbitmq$uri, settings$host$rabbitmq$queue)
+      PEcAn.logger::logger.debug("JOB.SH submit status:", out)
+      jobids[run] <- folder
+
+    } else if (is_modellauncher) {
       # set up launcher script if we use modellauncher
       if (is.null(firstrun)) {
         firstrun <- run
@@ -85,36 +93,35 @@ start.model.runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
       writeLines(c(file.path(settings$host$rundir, run_id_string)), con = jobfile)
       pbi <- pbi + 1
 
-    } else {
-      if (is_qsub) {
-        out <- start_qsub(run = run, qsub_string = settings$host$qsub, rundir = settings$rundir,
-                          host = settings$host,  host_rundir = settings$host$rundir, host_outdir = settings$host$outdir,
-                          stdout_log = "stdout.log", stderr_log = "stderr.log", job_script = "job.sh")
-        PEcAn.logger::logger.debug("JOB.SH submit status:", out)
-        jobids[run] <- qsub_get_jobid(out = out, qsub.jobid = settings$host$qsub.jobid, stop.on.error = stop.on.error)
+    } else if (is_qsub) {
+      out <- start_qsub(run = run, qsub_string = settings$host$qsub, rundir = settings$rundir,
+                        host = settings$host,  host_rundir = settings$host$rundir, host_outdir = settings$host$outdir,
+                        stdout_log = "stdout.log", stderr_log = "stderr.log", job_script = "job.sh")
+      PEcAn.logger::logger.debug("JOB.SH submit status:", out)
+      jobids[run] <- qsub_get_jobid(out = out, qsub.jobid = settings$host$qsub.jobid, stop.on.error = stop.on.error)
 
-      } else {
-        # if qsub option is not invoked.  just start model runs in serial.
-        out <- start_serial(run = run, host = settings$host, rundir = settings$rundir, host_rundir = settings$host$rundir, job_script = "job.sh")
+    } else {
+      # if qsub option is not invoked.  just start model runs in serial.
+      out <- start_serial(run = run, host = settings$host, rundir = settings$rundir, host_rundir = settings$host$rundir, job_script = "job.sh")
 
-        # check output to see if an error occurred during the model run
-        check_model_run(out = out, stop.on.error = stop.on.error)
+      # check output to see if an error occurred during the model run
+      check_model_run(out = out, stop.on.error = stop.on.error)
 
-        if (!is_local) {
-          # copy data back to local
-          PEcAn.remote::remote.copy.from(settings$host, file.path(settings$host$outdir, run_id_string), settings$modeloutdir)
-        }
+      if (!is_local) {
+        # copy data back to local
+        PEcAn.remote::remote.copy.from(settings$host, file.path(settings$host$outdir, run_id_string), settings$modeloutdir)
+      }
 
-        # write finished time to database
-        stamp_finished(con = dbcon, run = run)
+      # write finished time to database
+      stamp_finished(con = dbcon, run = run)
 
-        pbi <- pbi + 1
-        setTxtProgressBar(pb, pbi)
-      }
+      pbi <- pbi + 1
+      setTxtProgressBar(pb, pbi)
     }
   } # end loop over runs
   close(pb)
 
+  # need to actually launch the model launcher
   if (is_modellauncher) {
     close(jobfile)
 
@@ -151,7 +158,7 @@ start.model.runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
     }
   }
 
-  # wait for all qsub jobs to finish
+  # wait for all jobs to finish
   if (length(jobids) > 0) {
     PEcAn.logger::logger.debug("Waiting for the following jobs:", unlist(jobids, use.names = FALSE))
   }
@@ -160,8 +167,14 @@ start.model.runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
     Sys.sleep(10)
     for (run in names(jobids)) {
       run_id_string <- format(run, scientific = FALSE)
+
       # check to see if job is done
-      job_finished <- qsub_run_finished(run = jobids[run], host = settings$host, qstat = settings$host$qstat)
+      job_finished <- FALSE
+      if (is_rabbitmq) {
+        job_finished <- file.exists(file.path(jobids[run], "rabbitmq.out"))
+      } else if (is_qsub) {
+        job_finished <- qsub_run_finished(run = jobids[run], host = settings$host, qstat = settings$host$qstat)
+      }
 
       if (job_finished) {
         jobids[run] <- NULL
@@ -169,8 +182,8 @@ start.model.runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
         # Copy data back to local
         if (!is_local) {
           PEcAn.remote::remote.copy.from(host = settings$host,
-                           src = file.path(settings$host$outdir, run_id_string),
-                           dst = settings$modeloutdir)
+                                         src = file.path(settings$host$outdir, run_id_string),
+                                         dst = settings$modeloutdir)
         }
 
         # TODO check output log
@@ -188,13 +201,12 @@ start.model.runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
           pbi <- pbi + 1
         }
         setTxtProgressBar(pb, pbi)
-      } # End check if job finished
+      } # End job finished
     }  # end loop over runs
   }  # end while loop checking runs
 
 } # start.model.runs
 
-
 ##' @export
 runModule.start.model.runs <- function(settings,stop.on.error=TRUE) {
   if (is.MultiSettings(settings) || is.Settings(settings)) {
diff --git a/base/remote/R/start_rabbitmq.R b/base/remote/R/start_rabbitmq.R
new file mode 100644
index 00000000000..f61a813f217
--- /dev/null
+++ b/base/remote/R/start_rabbitmq.R
@@ -0,0 +1,7 @@
+#' Start model execution using rabbitmq
+#'
+#' @return Output of execution command, as a character (see [remote.execute.cmd()]).
+start_rabbitmq <- function(folder, rabbitmq_uri, rabbitmq_queue) {
+  out <- system2('python3', c('/work/sender.py', rabbitmq_uri, rabbitmq_queue, folder), stdout = TRUE, stderr = TRUE)
+  return(out)
+}
diff --git a/base/remote/man/remote.copy.update.Rd b/base/remote/man/remote.copy.update.Rd
index a41ea32a833..aa36139502b 100644
--- a/base/remote/man/remote.copy.update.Rd
+++ b/base/remote/man/remote.copy.update.Rd
@@ -4,13 +4,16 @@
 \alias{remote.copy.update}
 \title{Copy to remote and update DB}
 \usage{
-remote.copy.update(input_id, remote_dir, remote_file_name = NULL, host, con)
+remote.copy.update(input_id, remote_dir, local_file_path,
+  remote_file_name = NULL, host, con)
 }
 \arguments{
 \item{input_id}{Input ID, as a numeric or character}
 
 \item{remote_dir}{remote folder path}
 
+\item{local_file_path}{full path name to local file that needs to be copied, e.g. "/fs/data1/dbfiles/.../.../*.css"}
+
 \item{remote_file_name}{remote file name, no need to provide if it's the same as local}
 
 \item{host}{as in settings$host}
diff --git a/base/remote/man/remote.execute.R.Rd b/base/remote/man/remote.execute.R.Rd
index ae8f76b7aab..9c00555ba5e 100644
--- a/base/remote/man/remote.execute.R.Rd
+++ b/base/remote/man/remote.execute.R.Rd
@@ -4,8 +4,8 @@
 \alias{remote.execute.R}
 \title{Execute command remotely}
 \usage{
-remote.execute.R(script, host = "localhost", user = NA, verbose = FALSE,
-  R = "R", scratchdir = tempdir())
+remote.execute.R(script, host = "localhost", user = NA,
+  verbose = FALSE, R = "R", scratchdir = tempdir())
 }
 \arguments{
 \item{script}{the script to be invoked, as a list of commands.}
diff --git a/base/remote/man/start.model.runs.Rd b/base/remote/man/start.model.runs.Rd
index 85d06d5fbd9..02985be0760 100644
--- a/base/remote/man/start.model.runs.Rd
+++ b/base/remote/man/start.model.runs.Rd
@@ -4,7 +4,8 @@
 \alias{start.model.runs}
 \title{Start selected ecosystem model runs within PEcAn workflow}
 \usage{
-\method{start}{model.runs}(settings, write = TRUE, stop.on.error = TRUE)
+\method{start}{model.runs}(settings, write = TRUE,
+  stop.on.error = TRUE)
 }
 \arguments{
 \item{settings}{pecan settings object}
diff --git a/base/remote/man/start_qsub.Rd b/base/remote/man/start_qsub.Rd
index e5bb651e883..4c135b3d151 100644
--- a/base/remote/man/start_qsub.Rd
+++ b/base/remote/man/start_qsub.Rd
@@ -4,8 +4,8 @@
 \alias{start_qsub}
 \title{Start qsub runs}
 \usage{
-start_qsub(run, qsub_string, rundir, host, host_rundir, host_outdir, stdout_log,
-  stderr_log, job_script, qsub_extra = NULL)
+start_qsub(run, qsub_string, rundir, host, host_rundir, host_outdir,
+  stdout_log, stderr_log, job_script, qsub_extra = NULL)
 }
 \arguments{
 \item{run}{(numeric) run ID, as an integer}
diff --git a/base/remote/man/start_rabbitmq.Rd b/base/remote/man/start_rabbitmq.Rd
new file mode 100644
index 00000000000..209d06e1c4e
--- /dev/null
+++ b/base/remote/man/start_rabbitmq.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/start_rabbitmq.R
+\name{start_rabbitmq}
+\alias{start_rabbitmq}
+\title{Start model execution using rabbitmq}
+\usage{
+start_rabbitmq(folder, rabbitmq_uri, rabbitmq_queue)
+}
+\value{
+Output of execution command, as a character (see \code{\link[=remote.execute.cmd]{remote.execute.cmd()}}).
+}
+\description{
+Start model execution using rabbitmq
+}
diff --git a/base/remote/tests/testthat/test.remote.R b/base/remote/tests/testthat/test.remote.R
index abb7ea35372..d7fee881e03 100644
--- a/base/remote/tests/testthat/test.remote.R
+++ b/base/remote/tests/testthat/test.remote.R
@@ -1,4 +1,4 @@
-# Quick test of remote functions
+context("Quick test of remote functions")
 library(PEcAn.remote)
 library(testthat)
 
diff --git a/base/settings/DESCRIPTION b/base/settings/DESCRIPTION
index 139a344708e..7574e716fd8 100644
--- a/base/settings/DESCRIPTION
+++ b/base/settings/DESCRIPTION
@@ -2,8 +2,8 @@ Package: PEcAn.settings
 Title: PEcAn Settings package
 Maintainer: David LeBauer <dlebauer@illinois.edu>
 Author: David LeBauer, Rob Kooper
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
@@ -22,4 +22,5 @@ Imports:
     XML (>= 3.98-1.3)
 Suggests:
     testthat (>= 1.0.2)
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/base/settings/NAMESPACE b/base/settings/NAMESPACE
index f2faf410374..8ebcfe66db3 100644
--- a/base/settings/NAMESPACE
+++ b/base/settings/NAMESPACE
@@ -24,6 +24,7 @@ export(as.Settings)
 export(check.bety.version)
 export(check.database)
 export(check.database.settings)
+export(check.ensemble.settings)
 export(check.inputs)
 export(check.model.settings)
 export(check.run.settings)
diff --git a/base/settings/R/check.all.settings.R b/base/settings/R/check.all.settings.R
index 38972a4ebde..26b50a3fcab 100644
--- a/base/settings/R/check.all.settings.R
+++ b/base/settings/R/check.all.settings.R
@@ -244,7 +244,10 @@ check.settings <- function(settings, force=FALSE) {
   on.exit(options(scipen=scipen))
   options(scipen=12)
   
+
   settings <- check.database.settings(settings)
+  #checking the ensemble tag in settings
+  settings <- check.ensemble.settings(settings)
   
   if(!is.null(settings$database$bety)) {
     dbcon <- PEcAn.DB::db.open(settings$database$bety)
@@ -491,64 +494,7 @@ check.run.settings <- function(settings, dbcon=NULL) {
     }
   }
   
-  # check ensemble
-  if (!is.null(settings$ensemble)) {
-    if (is.null(settings$ensemble$variable)) {
-      if (is.null(settings$sensitivity.analysis$variable)) {
-        PEcAn.logger::logger.severe("No variable specified to compute ensemble for.")
-      }
-      PEcAn.logger::logger.info("Setting ensemble variable to the same as sensitivity analysis variable [", settings$sensitivity.analysis$variable, "]")
-      settings$ensemble$variable <- settings$sensitivity.analysis$variable
-    }
-    
-    if (is.null(settings$ensemble$size)) {
-      PEcAn.logger::logger.info("Setting ensemble size to 1.")
-      settings$ensemble$size <- 1
-    }
-    
-    if(is.null(settings$ensemble$start.year)) {
-      if(!is.null(settings$run$start.date)) {
-        settings$ensemble$start.year <- lubridate::year(settings$run$start.date) 
-        PEcAn.logger::logger.info("No start date passed to ensemble - using the run date (", 
-                    settings$ensemble$start.year, ").")
-      } else if(!is.null(settings$sensitivity.analysis$start.year)) {
-        settings$ensemble$start.year <- settings$sensitivity.analysis$start.year 
-        PEcAn.logger::logger.info("No start date passed to ensemble - using the sensitivity.analysis date (",
-                    settings$ensemble$start.year, ").")
-      } else {
-        PEcAn.logger::logger.info("No start date passed to ensemble, and no default available.")
-      }
-    }
-    
-    if(is.null(settings$ensemble$end.year)) {
-      if(!is.null(settings$run$end.date)) {
-        settings$ensemble$end.year <- lubridate::year(settings$run$end.date) 
-        PEcAn.logger::logger.info("No end date passed to ensemble - using the run date (", 
-                    settings$ensemble$end.year, ").")
-      } else if(!is.null(settings$sensitivity.analysis$end.year)){ 
-        settings$ensemble$end.year <- settings$sensitivity.analysis$end.year 
-        PEcAn.logger::logger.info("No end date passed to ensemble - using the sensitivity.analysis date (",  
-                    settings$ensemble$end.year, ").")
-      } else {
-        PEcAn.logger::logger.info("No end date passed to ensemble, and no default available.")
-      }
-    }
-    
-    # check start and end dates
-    if (exists("startdate") && !is.null(settings$ensemble$start.year) &&
-        lubridate::year(startdate) > settings$ensemble$start.year) {
-      PEcAn.logger::logger.severe("Start year of ensemble should come after the start.date of the run")
-    }
-    if (exists("enddate") && !is.null(settings$ensemble$end.year) &&
-        lubridate::year(enddate) < settings$ensemble$end.year) {
-      PEcAn.logger::logger.severe("End year of ensemble should come before the end.date of the run")
-    }
-    if (!is.null(settings$ensemble$start.year) && !is.null(settings$ensemble$end.year) &&
-        settings$ensemble$start.year > settings$ensemble$end.year) {
-      PEcAn.logger::logger.severe("Start year of ensemble should come before the end year of the ensemble")
-    }
-  }
-  
+
   # check sensitivity analysis
   if (!is.null(settings$sensitivity.analysis)) {
     if (is.null(settings$sensitivity.analysis$variable)) {
@@ -867,3 +813,78 @@ check.database.settings <- function(settings) {
   }
   return(settings)
 }
+
+##' @title Check ensemble Settings
+##' @param settings settings file
+##' @export check.ensemble.settings
+check.ensemble.settings <- function(settings) {
+  # check ensemble
+  if (!is.null(settings$ensemble)) {
+    if (is.null(settings$ensemble$variable)) {
+      if (is.null(settings$sensitivity.analysis$variable)) {
+        PEcAn.logger::logger.severe("No variable specified to compute ensemble for.")
+      }
+      PEcAn.logger::logger.info("Setting ensemble variable to the same as sensitivity analysis variable [", settings$sensitivity.analysis$variable, "]")
+      settings$ensemble$variable <- settings$sensitivity.analysis$variable
+    }
+    
+    if (is.null(settings$ensemble$size)) {
+      PEcAn.logger::logger.info("Setting ensemble size to 1.")
+      settings$ensemble$size <- 1
+    }
+    
+    if(is.null(settings$ensemble$start.year)) {
+      if(!is.null(settings$run$start.date)) {
+        settings$ensemble$start.year <- lubridate::year(settings$run$start.date) 
+        PEcAn.logger::logger.info("No start date passed to ensemble - using the run date (", 
+                                  settings$ensemble$start.year, ").")
+      } else if(!is.null(settings$sensitivity.analysis$start.year)) {
+        settings$ensemble$start.year <- settings$sensitivity.analysis$start.year 
+        PEcAn.logger::logger.info("No start date passed to ensemble - using the sensitivity.analysis date (",
+                                  settings$ensemble$start.year, ").")
+      } else {
+        PEcAn.logger::logger.info("No start date passed to ensemble, and no default available.")
+      }
+    }
+    
+    if(is.null(settings$ensemble$end.year)) {
+      if(!is.null(settings$run$end.date)) {
+        settings$ensemble$end.year <- lubridate::year(settings$run$end.date) 
+        PEcAn.logger::logger.info("No end date passed to ensemble - using the run date (", 
+                                  settings$ensemble$end.year, ").")
+      } else if(!is.null(settings$sensitivity.analysis$end.year)){ 
+        settings$ensemble$end.year <- settings$sensitivity.analysis$end.year 
+        PEcAn.logger::logger.info("No end date passed to ensemble - using the sensitivity.analysis date (",  
+                                  settings$ensemble$end.year, ").")
+      } else {
+        PEcAn.logger::logger.info("No end date passed to ensemble, and no default available.")
+      }
+    }
+    
+    # check start and end dates
+    if (exists("startdate") && !is.null(settings$ensemble$start.year) &&
+        lubridate::year(startdate) > settings$ensemble$start.year) {
+      PEcAn.logger::logger.severe("Start year of ensemble should come after the start.date of the run")
+    }
+    if (exists("enddate") && !is.null(settings$ensemble$end.year) &&
+        lubridate::year(enddate) < settings$ensemble$end.year) {
+      PEcAn.logger::logger.severe("End year of ensemble should come before the end.date of the run")
+    }
+    if (!is.null(settings$ensemble$start.year) && !is.null(settings$ensemble$end.year) &&
+        settings$ensemble$start.year > settings$ensemble$end.year) {
+      PEcAn.logger::logger.severe("Start year of ensemble should come before the end year of the ensemble")
+    }
+  }
+  #Old version of pecan xml files which they don't have a sampling space or it's just sampling space and nothing inside it.
+  if (is.null(settings$ensemble$samplingspace) | !is.list(settings$ensemble$samplingspace)){
+    PEcAn.logger::logger.info("We are updating the ensemble tag inside the xml file.")
+    #I try to put ensemble method in older versions into the parameter space - If I fail (when no method is defined) I just set it as uniform
+    settings$ensemble$samplingspace$parameters$method <- settings$ensemble$method
+    if (is.null(settings$ensemble$samplingspace$parameters$method)) {
+      settings$ensemble$samplingspace$parameters$method <- "uniform"
+    }
+    #putting something simple in the met
+    settings$ensemble$samplingspace$met$method <- "sampling"
+  }
+  return(settings)
+}
diff --git a/base/settings/R/update.settings.R b/base/settings/R/update.settings.R
index 8f5ab053855..9cd9ad8fbf6 100644
--- a/base/settings/R/update.settings.R
+++ b/base/settings/R/update.settings.R
@@ -1,4 +1,4 @@
-##-------------------------------------------------------------------------------
+ ##-------------------------------------------------------------------------------
 ## Copyright (c) 2012 University of Illinois, NCSA.
 ## All rights reserved. This program and the accompanying materials
 ## are made available under the terms of the 
diff --git a/base/settings/man/check.bety.version.Rd b/base/settings/man/check.bety.version.Rd
index f0b267365c0..e6e9d30415c 100644
--- a/base/settings/man/check.bety.version.Rd
+++ b/base/settings/man/check.bety.version.Rd
@@ -9,3 +9,6 @@ check.bety.version(dbcon)
 \arguments{
 \item{settings}{settings file}
 }
+\description{
+Check BETY Version
+}
diff --git a/base/settings/man/check.database.Rd b/base/settings/man/check.database.Rd
index 3a612054f55..3ae07d2e9bf 100644
--- a/base/settings/man/check.database.Rd
+++ b/base/settings/man/check.database.Rd
@@ -9,3 +9,6 @@ check.database(database)
 \arguments{
 \item{settings}{settings file}
 }
+\description{
+Check Database
+}
diff --git a/base/settings/man/check.database.settings.Rd b/base/settings/man/check.database.settings.Rd
index 3d567cdfb12..845e2bc08a8 100644
--- a/base/settings/man/check.database.settings.Rd
+++ b/base/settings/man/check.database.settings.Rd
@@ -9,3 +9,6 @@ check.database.settings(settings)
 \arguments{
 \item{settings}{settings file}
 }
+\description{
+Check Database Settings
+}
diff --git a/base/settings/man/check.ensemble.settings.Rd b/base/settings/man/check.ensemble.settings.Rd
new file mode 100644
index 00000000000..50007eac8fc
--- /dev/null
+++ b/base/settings/man/check.ensemble.settings.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check.all.settings.R
+\name{check.ensemble.settings}
+\alias{check.ensemble.settings}
+\title{Check ensemble Settings}
+\usage{
+check.ensemble.settings(settings)
+}
+\arguments{
+\item{settings}{settings file}
+}
+\description{
+Check ensemble Settings
+}
diff --git a/base/settings/man/check.model.settings.Rd b/base/settings/man/check.model.settings.Rd
index f209fd5be0d..b3d0314c72b 100644
--- a/base/settings/man/check.model.settings.Rd
+++ b/base/settings/man/check.model.settings.Rd
@@ -9,3 +9,6 @@ check.model.settings(settings, dbcon = NULL)
 \arguments{
 \item{settings}{settings file}
 }
+\description{
+Check Model Settings
+}
diff --git a/base/settings/man/check.run.settings.Rd b/base/settings/man/check.run.settings.Rd
index 76136c4563d..8dd2d6fad04 100644
--- a/base/settings/man/check.run.settings.Rd
+++ b/base/settings/man/check.run.settings.Rd
@@ -9,3 +9,6 @@ check.run.settings(settings, dbcon = NULL)
 \arguments{
 \item{settings}{settings file}
 }
+\description{
+Check Run Settings
+}
diff --git a/base/settings/man/check.workflow.settings.Rd b/base/settings/man/check.workflow.settings.Rd
index 62630705a76..00416872adf 100644
--- a/base/settings/man/check.workflow.settings.Rd
+++ b/base/settings/man/check.workflow.settings.Rd
@@ -9,3 +9,6 @@ check.workflow.settings(settings, dbcon = NULL)
 \arguments{
 \item{settings}{settings file}
 }
+\description{
+Check Workflow Settings
+}
diff --git a/base/settings/man/createSitegroupMultiSettings.Rd b/base/settings/man/createSitegroupMultiSettings.Rd
index fa5f63edf67..89033399ece 100644
--- a/base/settings/man/createSitegroupMultiSettings.Rd
+++ b/base/settings/man/createSitegroupMultiSettings.Rd
@@ -4,8 +4,8 @@
 \alias{createSitegroupMultiSettings}
 \title{Create Sitegroup MultiSettings}
 \usage{
-createSitegroupMultiSettings(templateSettings, sitegroupId, nSite, con = NULL,
-  params = templateSettings$database$bety)
+createSitegroupMultiSettings(templateSettings, sitegroupId, nSite,
+  con = NULL, params = templateSettings$database$bety)
 }
 \arguments{
 \item{templateSettings}{A \code{\link{Settings}} object that will be the template for the resulting
diff --git a/base/utils/DESCRIPTION b/base/utils/DESCRIPTION
index f9a97dd5624..89114af8ece 100644
--- a/base/utils/DESCRIPTION
+++ b/base/utils/DESCRIPTION
@@ -2,8 +2,8 @@ Package: PEcAn.utils
 Type: Package
 Title: PEcAn functions used for ecological forecasts and
     reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
     Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <dlebauer@illinois.edu>
@@ -15,37 +15,41 @@ Description: The Predictive Ecosystem Carbon Analyzer
     models, and to improve the efficacy of scientific
     investigation.
 Imports:
+    abind (>= 1.4.5),
+    coda (>= 0.18),
     data.table,
+    dplyr,
     getPass,
     ggplot2,
+    lubridate (>= 1.6.0),
+    magrittr,
+    ncdf4 (>= 1.15),
     PEcAn.logger,
     PEcAn.remote,
+    PeriodicTable,
+    plyr (>= 1.8.4),
+    purrr,
     randtoolbox,
     raster,
     RCurl,
     rjags,
     sp,
     stringi,
+    udunits2 (>= 0.11),
     xtable,
-    XML,
-    abind (>= 1.4.5),
-    coda (>= 0.18),
-    lubridate (>= 1.6.0),
-    ncdf4 (>= 1.15),
-    plyr (>= 1.8.4),
-    PeriodicTable,
-    udunits2 (>= 0.11)
+    XML
 Suggests:
+    MASS,
     PEcAn.data.atmosphere,
     PEcAn.data.land,
     PEcAn.emulator,
     PEcAn.priors,
     PEcAn.settings,
     PEcAn.DB,
-    MASS,
     testthat (>= 2.0.0)
 License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyData: true
 Require: hdf5, plyr
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/base/utils/NAMESPACE b/base/utils/NAMESPACE
index b490b2f4865..2ccbf4251aa 100644
--- a/base/utils/NAMESPACE
+++ b/base/utils/NAMESPACE
@@ -6,7 +6,6 @@ export(bugs.rdist)
 export(clear.scratch)
 export(convert.expr)
 export(convert.input)
-export(convert.outputs)
 export(counter)
 export(create.base.plot)
 export(days_in_year)
@@ -20,7 +19,6 @@ export(full.path)
 export(get.ensemble.inputs)
 export(get.ensemble.samples)
 export(get.model.output)
-export(get.parameter.samples)
 export(get.parameter.stat)
 export(get.quantiles)
 export(get.results)
@@ -40,6 +38,7 @@ export(logger.setQuitOnSevere)
 export(logger.setWidth)
 export(logger.severe)
 export(logger.warn)
+export(match_file)
 export(mcmc.list2init)
 export(misc.are.convertible)
 export(misc.convert)
@@ -74,6 +73,7 @@ export(to_ncvar)
 export(trait.lookup)
 export(transformstats)
 export(tryl)
+export(units_are_equivalent)
 export(vecpaste)
 export(write.ensemble.configs)
 export(write.sa.configs)
diff --git a/base/utils/R/clear.scratch.R b/base/utils/R/clear.scratch.R
index e649d0f1011..afc37df0221 100644
--- a/base/utils/R/clear.scratch.R
+++ b/base/utils/R/clear.scratch.R
@@ -12,6 +12,7 @@
 ##' @title Clear EBI-CLUSTER worker node local scratch directories of old PEcAn output
 ##' @name clear.scratch
 ##' @author Shawn Serbin
+##' @param settings list of PEcAn settings. Only \code{settings$host$name} is used
 ##' @return nothing
 ##' @export
 ##' @examples
diff --git a/base/utils/R/convert.input.R b/base/utils/R/convert.input.R
index e20ff17ccfa..137933e5f07 100644
--- a/base/utils/R/convert.input.R
+++ b/base/utils/R/convert.input.R
@@ -1,15 +1,72 @@
-##' Convert input by applying fcn and insert new record into database
+##' Convert between formats, reusing existing files where possible
 ##'
+##' \code{convert.input} is a relatively generic function that applies the function \code{fcn} and inserts a record of it into the database. It is primarily designed for converting meteorological data between formats and can be used on observed data, forecasts, and ensembles of forecasts.
+##' To minimize downloading and storing duplicate data, it first checks to see if a given file is already in the
+##' database before applying \code{fcn}.
+##' 
+##' @section Executing the function:
+##' convert.input executes the function fcn in package pkg via PEcAn.remote::remote.execute.R.  All additional arguments passed to
+##' convert.input (...) are in turn passed along to fcn as arguments.  In addition, several named arguments to convert.input are passed
+##' along to fcn.  The command to execute fcn is built as a string.
+##' 
+##' @section Database files:
+##' There are two kinds of database records (in different tables) that represent a given data file in the file system.  An input file
+##' contains information about the contents of the data file.  A dbfile contains machine spacific information for a given input file, 
+##' such as the file path.  Because duplicates of data files for a given input can be on multiple different machines, there can be more 
+##' than one dbfile for a given input file.
+##' 
+##' @section Time-span appending:
+##' By default, convert.input tries to optimize the download of most data products by only downloading the years of data not present on 
+##' the current machine.  (For example, if files for 2004-2008 exist for a given data product exist on this machine and the user requests
+##' 2006-2010, the function will only download data for 2009 and 2010).  In year-long data files, each year exists as a separate file.
+##' The database input file contains records of the bounds of the range stored by those years.  The data optimization can be turned off
+##' by overriding the default values for exact.dates and allow.conflicting.dates.
+##' 
+##' @section Forecast data:
+##' If the flag forecast is TRUE, convert.input treats data as if it were forecast data.  Forecast data do not undergo time span
+##' appending.
+##' 
+##' @section Ensembles:
+##' convert.input has the capability to handle ensembles of met data.  If ensemble = an integer > 1, convert.input checks the database
+##' for records of all ensemble members, and calls fcn if at least one is missing.  convert.input assumes that fcn will return records
+##' for all ensembles. convert.input can also be called iteratevely for each ensemble member.  In this case ensemble_name contains the
+##' unique identifying name/number of the ensemble to be processed.
+##'
+##' @param input.id The database id of the input file of the parent of the file being processed here.  The parent will have the same data, but in a different format.
+##' @param outfolder The directory where files generated by functions called by convert.input will be placed
+##' @param formatname data product specific format name
+##' @param mimetype data product specific file format
+##' @param site.id The id of the site
+##' @param start_date Start date of the data being requested or processed
+##' @param end_date End date of the data being requested or processed
+##' @param pkg The package that the function being executed is in (as a string)
+##' @param fcn The function to be executed if records of the output file aren't found in the database. (as a string)
+##' @param con Database connection object
+##' @param host Named list identifying the machine where conversion should be performed.
+##'   Currently only \code{host$name} is used by \code{convert.input}, but whole list is passed to other functions
+##' @param browndog List of information related to browndog conversion.  NULL if browndog is not to be used for conversion
+##' @param write Logical: Write new file records to the database?
+##' @param format.vars Passed on as arguments to \code{fcn}
+##' @param overwrite Logical: If a file already exists, create a fresh copy? Passed along to fcn.
+##' @param exact.dates Ignore time-span appending and enforce exact start and end dates on the database input file? (logical)
+##' @param allow.conflicting.dates Should overlapping years ignore time-span appending and exist as separate input files? (logical)
+##' @param insert.new.file Logical: force creation of a new database record even if one already exists?
+##' @param pattern A regular expression, passed to \code{PEcAn.DB::dbfile.input.check}, used to match the name of the input file.
+##' @param forecast Logical: Is the data product a forecast?
+##' @param ensemble An integer representing the number of ensembles, or FALSE if it data product is not an ensemble.
+##' @param ensemble_name If convert.input is being called iteratively for each ensemble, ensemble_name contains the identifying name/number for that ensemble.
+##' @param ... Additional arguments, passed unchanged to \code{fcn}
+##'
+##' @return A list of two BETY IDs (input.id, dbfile.id) identifying a pre-existing file if one was available, or a newly created file if not.  Each id may be a vector of ids if the function is processing an entire ensemble at once.
 ##'
-##' @name convert.input
-##' @title convert.input
 ##' @export
-##' @author Betsy Cowdery, Michael Dietze, Ankur Desai, Tony Gardella
+##' @author Betsy Cowdery, Michael Dietze, Ankur Desai, Tony Gardella, Luke Dramko
 
 convert.input <- function(input.id, outfolder, formatname, mimetype, site.id, start_date, 
                           end_date, pkg, fcn, con = con, host, browndog, write = TRUE, 
                           format.vars, overwrite = FALSE, exact.dates = FALSE, 
-                          allow.conflicting.dates = TRUE, insert.new.file = FALSE, pattern = NULL,...) {
+                          allow.conflicting.dates = TRUE, insert.new.file = FALSE, pattern = NULL,
+                          forecast = FALSE, ensemble = FALSE, ensemble_name = NULL, ...) {
   input.args <- list(...)
   
   PEcAn.logger::logger.debug(paste("Convert.Inputs", fcn, input.id, host$name, outfolder, formatname, 
@@ -26,12 +83,150 @@ convert.input <- function(input.id, outfolder, formatname, mimetype, site.id, st
   outname <- utils::tail(unlist(strsplit(outfolder, "/")), n = 1)
   
   PEcAn.logger::logger.info(paste("start CHECK Convert.Inputs", fcn, input.id, host$name, outfolder, 
-                    formatname, mimetype, site.id, start_date, end_date))
+                    formatname, mimetype, site.id, start_date, end_date, forecast, ensemble))
   
   
   ##----------------------------------------------------------------------------------------------------------------##  
-  
-  if (exact.dates) {
+  # Forecast data sets require their own set of database checking operations, making the following else if and else irrelevant
+  # for such data.  Forecast data are different if their start date (and if they are part of an ensemble, their ensemble id) are 
+  # different.
+  if (forecast) {
+    #if the data is an ensemble, ensemble will be set equal to the number of ensemble members.
+    #However, if the data is not an ensemble, ensemble will be equal to FALSE.  In order to treat ensemble and 
+    #non-ensemble members together in one piece of code, we set ensemble=1 if it's FALSE.
+    if (!is.integer(ensemble)) {ensemble = as.integer(1) }
+    
+    # Convert dates to Date objects and strip all time zones
+    # (DB values are timezone-free)
+    start_date <- lubridate::force_tz(lubridate::as_datetime(start_date), "UTC")
+    end_date   <- lubridate::force_tz(lubridate::as_datetime(end_date), "UTC")
+    
+    # Each ensemble member is associated with its own input file.  Therefore, each of these need to be lists.
+    existing.dbfile <- list()
+    existing.input <- list()
+    
+    existing_records <- list(input.id = NULL, dbfile.id = NULL)  # Empty vectors are null
+    files.to.delete <- list()
+    
+    for (i in seq_len(ensemble)) {
+      # In dbfile.input.check, pattern searches the file path for the specified regular expression.  filename_pattern
+      # contains a portion of the file name which can uniquely identify a particular data product at a particular 
+      # site and time, regardless of similarities in formatname, mimetype, etc. Because sitenames can contain
+      # regular expression specific special characters and site-specific identification is already present through
+      # site.id, a regex placeholder is used instead.
+      
+      # This regular expression identifies a particular ensemble from input$name
+      # It can recognize the following components:
+      # name of the data product, followed by a dot, and optionally a site name followed by a dot, then
+      # the ensemble number/name, followed either by a dot or a termination of the string.
+      # This last dot/string terminator matcher is required so that the regex does not recognize 12, 13, etc. as 1.
+      # Example: NOAA_GEFS.Willow Creek(US-WCr).3.<additional text>
+      # Met product name: NOAA_GEFS, site name: Willow Creek(US-WCr), ensemble number: 3
+      # The regular expression does not have to match the entire file name.
+      
+      # pattern is the name of the data product
+      filename_pattern = paste0(pattern, "\\.([^.]*\\.)?") #double backslash for regex
+      
+      # Specify ensemble name/number and add termination sequence to ensure each number is recognized uniquely (e.g. 
+      # 12 is not recognized as 1).
+      if (!is.null(ensemble_name)) {
+        filename_pattern = paste0(filename_pattern, ensemble_name, "($|\\.)")
+      } else if (ensemble > 1) {
+        filename_pattern = paste0(filename_pattern, i, "($|\\.)")
+      }
+      
+      existing.dbfile[[i]] <- PEcAn.DB::dbfile.input.check(siteid = site.id,
+                                                             mimetype = mimetype, 
+                                                             formatname = formatname, 
+                                                             parentid = input.id, 
+                                                             startdate = start_date,
+                                                             enddate = end_date, 
+                                                             con = con, 
+                                                             hostname = host$name, 
+                                                             exact.dates = TRUE,
+                                                             pattern = filename_pattern)
+      
+      if(nrow(existing.dbfile[[i]]) > 0) {
+        existing.input[[i]] <- PEcAn.DB::db.query(paste0("SELECT * FROM inputs WHERE id=", existing.dbfile[[i]]$container_id),con)
+        
+        # Date/time processing for existing input
+        existing.input[[i]]$start_date <- lubridate::force_tz(lubridate::as_datetime(existing.input[[i]]$start_date), "UTC")
+        existing.input[[i]]$end_date   <- lubridate::force_tz(lubridate::as_datetime(existing.input[[i]]$end_date), "UTC")
+        
+        ## Obtain machine information
+        #Grab machine info of file that exists
+        existing.machine <- PEcAn.DB::db.query(paste0("SELECT * from machines where id  = '",
+                                                      existing.dbfile[[i]]$machine_id, "'"), con)
+        
+        #Grab machine info of host machine
+        machine.host <- ifelse(host$name == "localhost", PEcAn.remote::fqdn(), host$name)
+        machine <- PEcAn.DB::db.query(paste0("SELECT * from machines where hostname = '",
+                                             machine.host, "'"), con)
+        
+        
+        # If the files aren't on the machine, we have to download them, so "overwrite" is meaningless.
+        if (existing.machine$id == machine$id) {
+          if (overwrite) { #If the files are on the current machine, check to see if we should overwrite them.
+            #Collect files for deletion, and store them in a list.
+            #Actually setting up the deletion will be done after the loop.
+            #c() concantanes the elements in a list, not just vectors.
+            files.to.delete <- c(files.to.delete, as.list(PEcAn.remote::remote.execute.R( paste0("list.files('",
+                                                                                                 existing.dbfile[[i]]$file_path,
+                                                                                                 "', full.names=TRUE)"),
+                                                                                          host, user = NA, verbose = TRUE,R = Rbinary, scratchdir = outfolder)))
+          } else { # If we're not overriding, we can just use the files that are already here.
+            existing_records$input.id = c(existing_records$input.id, existing.input[[i]]$id)
+            existing_records$dbfile.id = c(existing_records$dbfile.id, existing.dbfile[[i]]$id)
+          }
+        } else { # Else to "existing.machine$id == machine$id"
+          insert.new.file <- TRUE
+        }
+        
+      } else { # Else to "nrow(existing.dbfile[[i]]) > 0)"
+        existing.input[[i]] <- data.frame() # We don't want there to be a "gap" in existing input which would cause the lists to not be parellel.
+                                            # Empty data frames are screened for when input/dbfile are processed below.
+      }
+    } # -- End for loop --
+    
+    # Set up files to be deleted.  The deletion will actually happen after the function finishes execution.  In case there
+    # are any errors, this practice will make sure that the old files are preserved.
+    if (length(files.to.delete) > 0) { # Each list item is a file to delete.
+      file.deletion.commands <- .get.file.deletion.commands(unlist(files.to.delete)) 
+      
+      PEcAn.remote::remote.execute.R( file.deletion.commands$move.to.tmp,
+                                      host, user = NA, 
+                                      verbose = TRUE,R = Rbinary, scratchdir = outfolder)
+      
+      successful <- FALSE
+      on.exit(if (exists("successful") && successful) {
+        PEcAn.logger::logger.info("Conversion successful, with overwrite=TRUE. Deleting old files.")
+        PEcAn.remote::remote.execute.R( file.deletion.commands$delete.tmp, 
+                                        host, user = NA, 
+                                        verbose = TRUE,  R = Rbinary, scratchdir = outfolder )
+      } else {
+        PEcAn.logger::logger.info("Conversion failed. Replacing old files.")
+        PEcAn.remote::remote.execute.R( file.deletion.commands$replace.from.tmp, 
+                                        host, user = NA, 
+                                        verbose = TRUE, R = Rbinary, scratchdir = outfolder )
+      }
+      )#Close on.exit
+    }
+    
+    # If all of the files for an existing ensemble exist, we'll just use those files.  Otherwise, we'll need to run the function to
+    # fill in the gaps.  (The function should be smart enough not to overwrite previous files unless overwrite == TRUE).  If overwrite is TRUE,
+    # then exisitng_records$input.id will have length 0, and this if statement won't be entered.
+    if (length(existing_records$input.id) == ensemble) {
+      if (ensemble == 1) { # Used to give a little more precise of an info message.
+        PEcAn.logger::logger.info("File with forecast data in the given range already exists on this machine.")
+      } else {
+        PEcAn.logger::logger.info("Files for all ensemble members for this forecast already exist on this machine.")
+      }
+      
+      return(existing_records)
+    }
+    ##----------------------------------------- End of forecast section --------------------------------##
+    
+  } else if (exact.dates) {
     
     # Find Existing input with exact dates.
     
@@ -157,7 +352,6 @@ convert.input <- function(input.id, outfolder, formatname, mimetype, site.id, st
       
       existing.input <- PEcAn.DB::db.query(paste0("SELECT * FROM inputs WHERE id=", existing.dbfile[["container_id"]]),con)
       
-      
       # Convert dates to Date objects and strip all time zones
       # (DB values are timezone-free)
       start_date <- lubridate::force_tz(lubridate::as_date(start_date), "UTC")
@@ -393,6 +587,10 @@ convert.input <- function(input.id, outfolder, formatname, mimetype, site.id, st
     fcn.args$start_date <- start_date
     fcn.args$end_date   <- end_date
     
+    if (forecast && !is.null(input.id) && !is.na(input.id)) { # for downstream code adapted to handle forecast file conventions
+      fcn.args$year.fragment = TRUE                           # such as met2model conversions; arguments will be extraneous otherwise.
+    }
+    
     arg.string <- listToArgString(fcn.args)
     
     if (!missing(format.vars)) {
@@ -403,75 +601,133 @@ convert.input <- function(input.id, outfolder, formatname, mimetype, site.id, st
     PEcAn.logger::logger.debug(paste0("convert.input executing the following function:\n", cmdFcn))
     
     result <- PEcAn.remote::remote.execute.R(script = cmdFcn, host, user = NA, verbose = TRUE, R = Rbinary, scratchdir = outfolder)
+    
+    # Wraps the result in a list.  This way, everything returned by fcn will be a list, and all of the 
+    # code below can process everything as if it were a list without worrying about data types.
+    if (is.data.frame(result)) {
+      result <- list(result)  
+    }
   }
   
   PEcAn.logger::logger.info("RESULTS: Convert.Input")
   PEcAn.logger::logger.info(result)
-  PEcAn.logger::logger.info(names(result))
   
-  if (length(result) <= 1){
+  if (length(result[[1]]) <= 1){ # result, a list, is guaranteed to have at least one element.  However, that element could be an empty data frame.
     PEcAn.logger::logger.debug(paste0("Processing data failed, please check validity of args:", arg.string))
     PEcAn.logger::logger.severe(paste0("Unable to process data using this function:",fcn))
   }
   
   #--------------------------------------------------------------------------------------------------#
+  # Check if result has empty or missing files
+  
+  result_sizes <- purrr::map_dfr(
+    result,
+    ~ dplyr::mutate(
+      .,
+      file_size = purrr::map_dbl(file, file.size),
+      missing = is.na(file_size),
+      empty = file_size == 0
+    )
+  )
+  
+  if (any(result_sizes$missing) || any(result_sizes$empty)){
+    log_format_df = function(df){
+      df  %>%
+        format() %>%
+        rbind(colnames(.), .) %>%
+        purrr::reduce( paste, sep=" ") %>%
+        paste(collapse="\n")
+    }
+    
+    PEcAn.logger::logger.severe(
+      "Requested Processing produced empty files or Nonexistant files :\n",
+      log_format_df(result_sizes[,c(1,8,9,10)]),
+      "\n Table of results printed above.",
+      wrap = FALSE)
+  }
+  
   # Insert into Database
   outlist <- unlist(strsplit(outname, "_"))
   
-  ## insert new record into database
+  # Wrap in a list for consistant processing later
+  if (exists("existing.input") && is.data.frame(existing.input)) {
+    existing.input <- list(existing.input)
+  }
+  
+  if (exists("existing.dbfile") && is.data.frame(existing.dbfile)) {
+    existing.dbfile <- list(existing.dbfile)
+  }
+  
+  #---------------------------------------------------------------#
+  # New arrangement of database adding code to deal with ensembles.
   if (write) {
-    
-    if (exists("existing.input") && nrow(existing.input) > 0 && 
-        (existing.input$start_date != start_date || existing.input$end_date != end_date)) {
-      # Updating record with new dates
-      PEcAn.DB::db.query(paste0("UPDATE inputs SET start_date='", start_date, "', end_date='",
-                      end_date, "'  WHERE id=", existing.input$id), 
-               con)
-      #Record has been updated and file downloaded so just return existing dbfile and input pair
-      return(list(input.id = existing.input$id, dbfile.id = existing.dbfile$id))
-    }
-    
-    if (overwrite) {
-      # A bit hacky, but need to make sure that all fields are updated to expected
-      # values (i.e., what they'd be if convert.input was creating a new record)
-      if (exists("existing.input") && nrow(existing.input) > 0) {
-        PEcAn.DB::db.query(paste0("UPDATE inputs SET name='", basename(dirname(result$file[1])),
-                        "' WHERE id=", existing.input$id), con)
+    # Setup newinput.  This list will contain two variables: a vector of input IDs and a vector of DB IDs for each entry in result.
+    # This list will be returned.
+    newinput = list(input.id = NULL, dbfile.id = NULL) #Blank vectors are null.
+    for(i in 1:length(result)) {  # Master for loop
+      id_not_added <- TRUE
+      
+      if (exists("existing.input") && nrow(existing.input[[i]]) > 0 && 
+          (existing.input[[i]]$start_date != start_date || existing.input[[i]]$end_date != end_date)) {
+        
+        # Updating record with new dates
+        PEcAn.DB::db.query(paste0("UPDATE inputs SET start_date='", start_date, "', end_date='",
+                                  end_date, "'  WHERE id=", existing.input[[i]]$id), 
+                           con)
+        id_not_added = FALSE
+        
+        # The overall structure of this loop has been set up so that exactly one input.id and one dbfile.id will be written to newinput every interation.
+        newinput$input.id = c(newinput$input.id, existing.input[[i]]$id)
+        newinput$dbfile.id = c(newinput$dbfile.id, existing.dbfile[[i]]$id)
+      }
+      
+      if (overwrite) {
+        # A bit hacky, but need to make sure that all fields are updated to expected
+        # values (i.e., what they'd be if convert.input was creating a new record)
+        if (exists("existing.input") && nrow(existing.input[[i]]) > 0) {
+            PEcAn.DB::db.query(paste0("UPDATE inputs SET name='", basename(dirname(result[[i]]$file[1])),
+                                      "' WHERE id=", existing.input[[i]]$id), con)
+          
+        }
+        
+        if (exists("existing.dbfile") && nrow(existing.dbfile[[i]]) > 0) {
+            PEcAn.DB::db.query(paste0("UPDATE dbfiles SET file_path='", dirname(result[[i]]$file[1]),
+                                      "', ", "file_name='", result[[i]]$dbfile.name[1], 
+                                      "' WHERE id=", existing.dbfile[[i]]$id), con)
+          
+        }
       }
-      if (exists("existing.dbfile") && nrow(existing.dbfile) > 0) {
-        PEcAn.DB::db.query(paste0("UPDATE dbfiles SET file_path='", dirname(result$file[1]),
-                        "', ", "file_name='", result$dbfile.name[1], 
-                        "' WHERE id=", existing.dbfile$id), con)
+      
+      parent.id <- ifelse(is.null(input[i]), NA, input[i]$id)
+      
+      if ("newsite" %in% names(input.args) && !is.null(input.args[["newsite"]])) {
+        site.id <- input.args$newsite
       }
-    }
-    
-    parent.id <- ifelse(is.null(input), NA, input$id)
-    
-    if ("newsite" %in% names(input.args) && !is.null(input.args[["newsite"]])) {
-      site.id <- input.args$newsite
-    }
-    
-    if (insert.new.file) {
-      dbfile.id <- PEcAn.DB::dbfile.insert(in.path = dirname(result$file[1]),
-                                 in.prefix = result$dbfile.name[1], 
-                                 'Input', existing.input$id, 
-                                 con, reuse=TRUE, hostname = machine$hostname)
-      newinput <- list()
-      newinput$input.id  <- existing.input$id
-      newinput$dbfile.id <- dbfile.id 
-    } else {
-      newinput <- PEcAn.DB::dbfile.input.insert(in.path = dirname(result$file[1]),
-                                      in.prefix = result$dbfile.name[1], 
-                                      siteid = site.id, 
-                                      startdate = start_date,
-                                      enddate = end_date, 
-                                      mimetype, 
-                                      formatname, 
-                                      parentid = parent.id,
-                                      con = con, 
-                                      hostname = machine$hostname,
-                                      allow.conflicting.dates = allow.conflicting.dates)  
-    }
+      
+      if (insert.new.file && id_not_added) {
+        dbfile.id <- PEcAn.DB::dbfile.insert(in.path = dirname(result[[i]]$file[1]),
+                                             in.prefix = result[[i]]$dbfile.name[1], 
+                                             'Input', existing.input[[i]]$id, 
+                                             con, reuse=TRUE, hostname = machine$hostname)
+        newinput$input.id  <- c(newinput$input.id, existing.input[[i]]$id)
+        newinput$dbfile.id <- c(newinput$dbfile.id, dbfile.id)
+      } else if (id_not_added) {
+        new_entry <- PEcAn.DB::dbfile.input.insert(in.path = dirname(result[[i]]$file[1]),
+                                                   in.prefix = result[[i]]$dbfile.name[1], 
+                                                   siteid = site.id, 
+                                                   startdate = start_date,
+                                                   enddate = end_date, 
+                                                   mimetype, 
+                                                   formatname, 
+                                                   parentid = parent.id,
+                                                   con = con, 
+                                                   hostname = machine$hostname,
+                                                   allow.conflicting.dates = allow.conflicting.dates)
+        newinput$input.id <- c(newinput$input.id, new_entry$input.id)
+        newinput$dbfile.id <- c(newinput$dbfile.id, new_entry$dbfile.id)
+      }
+      
+    } #End for loop
     
     successful <- TRUE
     return(newinput)
diff --git a/base/utils/R/days_in_year.R b/base/utils/R/days_in_year.R
index 42eca3c01ca..ef63c86fc45 100644
--- a/base/utils/R/days_in_year.R
+++ b/base/utils/R/days_in_year.R
@@ -3,6 +3,7 @@
 #' Calculate number of days in a year based on whether it is a leap year or not.
 #'
 #' @param year Numeric year (can be a vector)
+#' @param leap_year Default = TRUE. If set to FALSE will always return 365
 #'
 #' @author Alexey Shiklomanov
 #' @return integer vector, all either 365 or 366
@@ -11,9 +12,9 @@
 #' days_in_year(2010)  # Not a leap year -- returns 365
 #' days_in_year(2012)  # Leap year -- returns 366
 #' days_in_year(2000:2008)  # Function is vectorized over years
-days_in_year <- function(year) {
+days_in_year <- function(year, leap_year = TRUE) {
   if (any(year %% 1 != 0)) {
     PEcAn.logger::logger.severe("Year must be integer. Given ", year, '.')
   }
-  ifelse(lubridate::leap_year(year), yes = 366, no = 365)
+  ifelse( leap_year & lubridate::leap_year(year), yes = 366, no = 365)
 }
diff --git a/base/utils/R/do_conversions.R b/base/utils/R/do_conversions.R
index 9e3f5040002..9075e93f7b8 100644
--- a/base/utils/R/do_conversions.R
+++ b/base/utils/R/do_conversions.R
@@ -3,11 +3,11 @@
 ##' @name do_conversions
 ##' @title do_conversions
 ##' @description Input conversion workflow
-##'
 ##' @param settings PEcAn settings list
 ##' @param overwrite.met,overwrite.fia,overwrite.ic logical
 ##'
 ##' @author Ryan Kelly, Rob Kooper, Betsy Cowdery, Istem Fer
+
 do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALSE, overwrite.ic = FALSE) {
   if (PEcAn.settings::is.MultiSettings(settings)) {
     return(PEcAn.settings::papply(settings, do_conversions))
@@ -21,7 +21,6 @@ do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALS
   dbfiles.local <- settings$database$dbfiles
   dbfiles <- ifelse(!PEcAn.remote::is.localhost(settings$host) & !is.null(settings$host$folder), settings$host$folder, dbfiles.local)
   PEcAn.logger::logger.debug("do.conversion outdir",dbfiles)
-  
   for (i in seq_along(settings$run$inputs)) {
     input <- settings$run$inputs[[i]]
     if (is.null(input)) {
@@ -31,6 +30,7 @@ do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALS
     input.tag <- names(settings$run$input)[i]
     PEcAn.logger::logger.info("PROCESSING: ",input.tag)
     
+    
     ic.flag <- fia.flag <- FALSE
     
     if ((input.tag %in% c("css", "pss", "site")) && 
@@ -65,13 +65,13 @@ do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALS
       ## which is done locally in rundir and then rsync'ed to remote
       ## rather than having a model-format soils file that is processed remotely
     }
-    
     # met conversion
+    
     if (input.tag == "met") {
       name <- ifelse(is.null(settings$browndog), "MET Process", "BrownDog")
       if ( (PEcAn.utils::status.check(name) == 0)) { ## previously is.null(input$path) && 
         PEcAn.logger::logger.info("calling met.process: ",settings$run$inputs[[i]][['path']])
-        settings$run$inputs[[i]][['path']] <- 
+        settings$run$inputs[[i]] <- 
           PEcAn.data.atmosphere::met.process(
             site       = settings$run$site, 
             input_met  = settings$run$inputs$met,
diff --git a/base/utils/R/download.url.R b/base/utils/R/download.url.R
index a1595953003..5f0408f417b 100644
--- a/base/utils/R/download.url.R
+++ b/base/utils/R/download.url.R
@@ -11,7 +11,7 @@
 ##' @param url the url of the file to download
 ##' @param file the filename
 ##' @param timeout number of seconds to wait for file (default 600)
-##' @param list of options for curl, for example to download from a
+##' @param .opts list of options for curl, for example to download from a
 ##'        protected site use list(userpwd=userpass, httpauth = 1L)
 ##' @param retry404 retry on a 404, this is used by Brown Dog
 ##' @return returns name of file if successful or NA if not.
diff --git a/base/utils/R/ensemble.R b/base/utils/R/ensemble.R
index 0ef1f0094fe..d0526983599 100644
--- a/base/utils/R/ensemble.R
+++ b/base/utils/R/ensemble.R
@@ -11,6 +11,12 @@
 ##'
 ##' Reads output for an ensemble of length specified by \code{ensemble.size} and bounded by \code{start.year} 
 ##' and \code{end.year}
+##'
+##' DEPRECATED: This function has been moved to the \code{PEcAn.uncertainty} package.
+##' The version in \code{PEcAn.utils} is deprecated, will not be updated to add any new features,
+##' and will be removed in a future release of PEcAn.
+##' Please use \code{PEcAn.uncertainty::read.ensemble.output} instead.
+##'
 ##' @title Read ensemble output
 ##' @return a list of ensemble model output 
 ##' @param ensemble.size the number of ensemble members run
@@ -24,6 +30,15 @@
 #--------------------------------------------------------------------------------------------------#
 read.ensemble.output <- function(ensemble.size, pecandir, outdir, start.year, end.year, 
                                  variable, ens.run.ids = NULL) {
+
+  .Deprecated(
+    new = "PEcAn.uncertainty::read.ensemble.output",
+    msg = paste(
+      "read.ensemble.output has been moved to PEcAn.uncertainty and is deprecated from PEcAn.utils.",
+      "Please use PEcAn.uncertainty::read.ensemble.output instead.",
+      "PEcAn.utils::read.ensemble.output will not be updated and will be removed from a future version of PEcAn.",
+      sep = "\n"))
+
   if (is.null(ens.run.ids)) {
     samples.file <- file.path(pecandir, "samples.Rdata")
     if (file.exists(samples.file)) {
@@ -59,6 +74,11 @@ read.ensemble.output <- function(ensemble.size, pecandir, outdir, start.year, en
 
 ##' Get parameter values used in ensemble
 ##'
+##' DEPRECATED: This function has been moved to the \code{PEcAn.uncertainty} package.
+##' The version in \code{PEcAn.utils} is deprecated, will not be updated to add any new features,
+##' and will be removed in a future release of PEcAn.
+##' Please use \code{PEcAn.uncertainty::get.ensemble.samples} instead.
+
 ##' Returns a matrix of randomly or quasi-randomly sampled trait values 
 ##' to be assigned to traits over several model runs.
 ##' given the number of model runs and a list of sample distributions for traits
@@ -70,12 +90,22 @@ read.ensemble.output <- function(ensemble.size, pecandir, outdir, start.year, en
 ##' @param pft.samples random samples from parameter distribution, e.g. from a MCMC chain  
 ##' @param env.samples env samples
 ##' @param method the method used to generate the ensemble samples. Random generators: uniform, uniform with latin hypercube permutation. Quasi-random generators: halton, sobol, torus. Random generation draws random variates whereas quasi-random generation is deterministic but well equidistributed. Default is uniform. For small ensemble size with relatively large parameter number (e.g ensemble size < 5 and # of traits > 5) use methods other than halton. 
+##' @param param.names a list of parameter names that were fitted either by MA or PDA, important argument, if NULL parameters will be resampled independently
+##' 
 ##' @return matrix of (quasi-)random samples from trait distributions
 ##' @export
-##' @author David LeBauer
+##' @author David LeBauer, Istem Fer
 get.ensemble.samples <- function(ensemble.size, pft.samples, env.samples, 
-                                 method = "uniform", ...) {
+                                 method = "uniform", param.names = NULL, ...) {
   
+  .Deprecated(
+    new = "PEcAn.uncertainty::get.ensemble.samples",
+    msg = paste(
+      "get.ensemble.samples has been moved to PEcAn.uncertainty and is deprecated from PEcAn.utils.",
+      "Please use PEcAn.uncertainty::get.ensemble.samples instead.",
+      "PEcAn.utils::get.ensemble.samples will not be updated and will be removed from a future version of PEcAn.",
+      sep = "\n"))
+
   if (is.null(method)) {
     PEcAn.logger::logger.info("No sampling method supplied, defaulting to uniform random sampling")
     method <- "uniform"
@@ -95,9 +125,11 @@ get.ensemble.samples <- function(ensemble.size, pft.samples, env.samples,
       pft2col <- c(pft2col, rep(i, length(pft.samples[[i]])))
     }
     
+
     total.sample.num <- sum(sapply(pft.samples, length))
     random.samples <- NULL
     
+    
     if (method == "halton") {
       PEcAn.logger::logger.info("Using ", method, "method for sampling")
       random.samples <- randtoolbox::halton(n = ensemble.size, dim = total.sample.num, ...)
@@ -130,15 +162,32 @@ get.ensemble.samples <- function(ensemble.size, pft.samples, env.samples,
                                total.sample.num)
     }
     
+    
     ensemble.samples <- list()
     
+    
     col.i <- 0
     for (pft.i in seq(pft.samples)) {
       ensemble.samples[[pft.i]] <- matrix(nrow = ensemble.size, ncol = length(pft.samples[[pft.i]]))
+      
+      # meaning we want to keep MCMC samples together
+      if(length(pft.samples[[pft.i]])>0 & !is.null(param.names)){ 
+        # TODO: for now we are sampling row numbers uniformly
+        # stop if other methods were requested 
+        if(method != "uniform"){
+          PEcAn.logger::logger.severe("Only uniform sampling is available for joint sampling at the moment. Other approaches are not implemented yet.")
+        }
+        same.i <- sample.int(length(pft.samples[[pft.i]][[1]]), ensemble.size)
+      }
+      
       for (trait.i in seq(pft.samples[[pft.i]])) {
         col.i <- col.i + 1
-        ensemble.samples[[pft.i]][, trait.i] <- stats::quantile(pft.samples[[pft.i]][[trait.i]],
-                                                         random.samples[, col.i])
+        if(names(pft.samples[[pft.i]])[trait.i] %in% param.names[[pft.i]]){ # keeping samples
+          ensemble.samples[[pft.i]][, trait.i] <- pft.samples[[pft.i]][[trait.i]][same.i]
+        }else{
+          ensemble.samples[[pft.i]][, trait.i] <- stats::quantile(pft.samples[[pft.i]][[trait.i]],
+                                                                  random.samples[, col.i])
+        }
       }  # end trait
       ensemble.samples[[pft.i]] <- as.data.frame(ensemble.samples[[pft.i]])
       colnames(ensemble.samples[[pft.i]]) <- names(pft.samples[[pft.i]])
@@ -152,6 +201,11 @@ get.ensemble.samples <- function(ensemble.size, pft.samples, env.samples,
 
 ##' Write ensemble config files
 ##'
+##' DEPRECATED: This function has been moved to the \code{PEcAn.uncertainty} package.
+##' The version in \code{PEcAn.utils} is deprecated, will not be updated to add any new features,
+##' and will be removed in a future release of PEcAn.
+##' Please use \code{PEcAn.uncertainty::write.ensemble.configs} instead.
+##'
 ##' Writes config files for use in meta-analysis and returns a list of run ids.
 ##' Given a pft.xml object, a list of lists as supplied by get.sa.samples, 
 ##' a name to distinguish the output files, and the directory to place the files.
@@ -167,6 +221,14 @@ get.ensemble.samples <- function(ensemble.size, pft.samples, env.samples,
 write.ensemble.configs <- function(defaults, ensemble.samples, settings, model, 
                                    clean = FALSE, write.to.db = TRUE) {
   
+  .Deprecated(
+    new = "PEcAn.uncertainty::write.ensemble.configs",
+    msg = paste(
+      "write.ensemble.configs has been moved to PEcAn.uncertainty and is deprecated from PEcAn.utils.",
+      "Please use PEcAn.uncertainty::write.ensemble.configs instead.",
+      "PEcAn.utils::write.ensemble.configs will not be updated and will be removed from a future version of PEcAn.",
+      sep = "\n"))
+
   my.write.config <- paste("write.config.", model, sep = "")
   
   if (is.null(ensemble.samples)) {
diff --git a/base/utils/R/match_file.R b/base/utils/R/match_file.R
new file mode 100644
index 00000000000..863cb73328a
--- /dev/null
+++ b/base/utils/R/match_file.R
@@ -0,0 +1,38 @@
+#' Match a file
+#'
+#' Return a list of files given a full prefix and optional suffix. Optionally, 
+#' confirm that the right number of files are returned. If the wrong number of 
+#' files is returned, throw an error.
+#'
+#' If `path_prefix` points to a directory, then all files inside that directory 
+#' that match the suffix (if provided) are returned.
+#' @param path_prefix Full path and file prefix
+#' @param suffix File suffix, as character (default = `NULL`)
+#' @param expect Number of files expected to be returned (default = `NULL`)
+#' @return Character vector of matched file names, as full paths.
+#' @export
+match_file <- function(path_prefix, suffix = NULL, expect = NULL) {
+  if (file.exists(path_prefix) && file.info(path_prefix)$isdir) {
+    path <- path_prefix
+    prefix <- ""
+  } else {
+    path <- dirname(path_prefix)
+    prefix <- basename(path_prefix)
+  }
+  file_matches <- list.files(path, prefix, full.names = TRUE)
+  if (!is.null(suffix)) {
+    file_matches <- grep(paste0(suffix, "$"), file_matches, value = TRUE)
+  }
+  if (!is.null(expect) && length(file_matches) != expect) {
+    PEcAn.logger::logger.severe(
+      "Expected ", expect, " files but found ", length(file_matches), ". ",
+      "The following prefix was used: ", path_prefix
+    )
+  }
+  if (!length(file_matches) > 0 && (is.null(expect) || expect != 0)) {
+    PEcAn.logger::logger.warn(
+      "No files found. The following prefix was used: ", path_prefix
+    )
+  }
+  file_matches
+}
diff --git a/base/utils/R/read.output.R b/base/utils/R/read.output.R
index cbf4fd01ecd..019e0c7266e 100644
--- a/base/utils/R/read.output.R
+++ b/base/utils/R/read.output.R
@@ -36,11 +36,10 @@ read.output <- function(runid, outdir, start.year = NA, end.year = NA, variables
   ## 'TotalResp', 'AutoResp', 'HeteroResp', 'DOC_flux', 'Fire_flux') # kgC m-2 s-1
   ## wflux = c('Evap', 'TVeg', 'Qs', 'Qsb', 'Rainf') # kgH20 m-2 d-1
   
-  # create list of *.nc years
-  nc.years <- as.vector(unlist(strsplit(list.files(path = outdir, pattern = "\\.nc$", 
-                                                   full.names = FALSE), ".nc")),
-                        mode = "numeric") # N.B. coercing from character
-  ncfiles <- list.files(path = outdir, pattern = "\\.nc$", full.names = TRUE)
+  # create list of *.nc years - look only for files formatted as YYYY.nc, the default pecan output file name standard
+  ncfiles_sub <- list.files(path = outdir, pattern = "^-?[[:digit:]]{4}\\.nc$", full.names = FALSE)
+  ncfiles <- file.path(outdir, ncfiles_sub)
+  nc_years <- as.numeric(gsub("^(-?[[:digit:]]{4})\\.nc", "\\1", ncfiles_sub))
   
   if(!is.na(start.year) && !is.na(end.year)){
     if (lubridate::is.instant(start.year)) { # true if a Date, POSIXct, or POSIXlt
@@ -59,12 +58,12 @@ read.output <- function(runid, outdir, start.year = NA, end.year = NA, variables
     }
 
     # select only those *.nc years requested by user
-    keep <- which(nc.years >= start.year & nc.years <= end.year)
+    keep <- which(nc_years >= start.year & nc_years <= end.year)
     ncfiles <- ncfiles[keep]
-  } else if(length(nc.years) != 0){
+  } else if(length(nc_years) != 0){
       PEcAn.logger::logger.info("No start or end year provided; reading output for all years")
-      start.year <- min(nc.years)
-      end.year <- max(nc.years)
+      start.year <- min(nc_years)
+      end.year <- max(nc_years)
   }
 
   years <- start.year:end.year
@@ -75,8 +74,8 @@ read.output <- function(runid, outdir, start.year = NA, end.year = NA, variables
   if (length(ncfiles) == 0) {
     PEcAn.logger::logger.warn("read.output: no netCDF files of model output present for runid = ", 
                 runid, " in ", outdir, " for years ", start.year, ":", end.year, ". will return NA")
-    if (length(nc.years) > 0) {
-      PEcAn.logger::logger.info("netCDF files for other years present", nc.years)
+    if (length(nc_years) > 0) {
+      PEcAn.logger::logger.info("netCDF files for other years present", nc_years)
     }
     nofiles <- TRUE
   } else {
@@ -173,19 +172,4 @@ read.output <- function(runid, outdir, start.year = NA, end.year = NA, variables
     PEcAn.logger::logger.error("Error in dataframe variable. Dataframe boolean must be set to TRUE or FALSE")
   }
   
-} # read.output
-
-
-##'--------------------------------------------------------------------------------------------------#
-##' Converts the output of all model runs
-##'
-##' @title convert outputs from model specific code to 
-##' @name convert.outputs
-##' @param model name of simulation model currently accepts ('ED', 'SIPNET', 'BIOCRO')
-##' @param settings settings loaded from pecan.xml
-##' @param ... arguments passed to \code{\link{read.output}}, e.g. \code{variables}, \code{start.year}, \code{end.year}
-##' @export
-##' @author Rob Kooper
-convert.outputs <- function(model, settings, ...) {
-  PEcAn.logger::logger.severe("This function is not longer used and will be removed in the future.")
-} # convert.outputs
+} # read.output
\ No newline at end of file
diff --git a/base/utils/R/run.write.configs.R b/base/utils/R/run.write.configs.R
index 3e4cda644bf..78b05948c64 100644
--- a/base/utils/R/run.write.configs.R
+++ b/base/utils/R/run.write.configs.R
@@ -10,6 +10,8 @@
 ##' Main driver function to call the ecosystem model specific (e.g. ED, SiPNET) 
 ##' run and configuration file scripts 
 ##' 
+##' DEPRECATED: This function has been moved to the PEcAn.workflow package and will be removed from PEcAn.utils.
+##'
 ##' @name run.write.configs
 ##' @title Run model specific write configuration functions
 ##' @param model the ecosystem model to generate the configuration files for
@@ -22,12 +24,13 @@
 ##'    files within this workflow, to avoid confusion).
 ##'
 ##' @return an updated settings list, which includes ensemble IDs for SA and ensemble analysis
-##' @export
 ##'
 ##' @author David LeBauer, Shawn Serbin, Ryan Kelly, Mike Dietze
+##' @export
 run.write.configs <- function(settings, write = TRUE, ens.sample.method = "uniform", 
                               posterior.files = rep(NA, length(settings$pfts)), 
                               overwrite = TRUE) {
+  .Deprecated("PEcAn.workflow::run.write.configs")
   
   con <- PEcAn.DB::db.open(settings$database$bety)
   on.exit(PEcAn.DB::db.close(con))
@@ -40,7 +43,7 @@ run.write.configs <- function(settings, write = TRUE, ens.sample.method = "unifo
       if (!is.null(settings$pfts[[i]]$posteriorid)) {
         files <- PEcAn.DB::dbfile.check("Posterior",
                               settings$pfts[[i]]$posteriorid, 
-                              con, settings$host$name)
+                              con, settings$host$name, return.all = TRUE)
         pid <- grep("post.distns.*Rdata", files$file_name)  ## is there a posterior file?
         if (length(pid) == 0) {
           pid <- grep("prior.distns.Rdata", files$file_name)  ## is there a prior file?
@@ -57,6 +60,7 @@ run.write.configs <- function(settings, write = TRUE, ens.sample.method = "unifo
   model <- settings$model$type
   scipen <- getOption("scipen")
   options(scipen = 12)
+  #sample from parameters used for both sensitivity analysis and Ens
   get.parameter.samples(settings, posterior.files, ens.sample.method)
   load(file.path(settings$outdir, "samples.Rdata"))
   
@@ -151,8 +155,9 @@ run.write.configs <- function(settings, write = TRUE, ens.sample.method = "unifo
 } # run.write.configs
 
 
-##' @export
+#' @export
 runModule.run.write.configs <- function(settings, overwrite = TRUE) {
+  .Deprecated("PEcAn.workflow::runModule.run.write.configs")
   if (PEcAn.settings::is.MultiSettings(settings)) {
     if (overwrite && file.exists(file.path(settings$rundir, "runs.txt"))) {
       PEcAn.logger::logger.warn("Existing runs.txt file will be removed.")
@@ -161,8 +166,10 @@ runModule.run.write.configs <- function(settings, overwrite = TRUE) {
     return(PEcAn.settings::papply(settings, runModule.run.write.configs, overwrite = FALSE))
   } else if (PEcAn.settings::is.Settings(settings)) {
     write <- settings$database$bety$write
-    ens.sample.method <- settings$ensemble$method
-    return(run.write.configs(settings, write, ens.sample.method, overwrite = overwrite))
+    # double check making sure we have method for parameter sampling
+    if (is.null(settings$ensemble$samplingspace$parameters$method)) settings$ensemble$samplingspace$parameters$method <- "uniform"
+    ens.sample.method <-  settings$ensemble$samplingspace$parameters$method
+    return(PEcAn.workflow:run.write.configs(settings, write, ens.sample.method, overwrite = overwrite))
   } else {
     stop("runModule.run.write.configs only works with Settings or MultiSettings")
   }
diff --git a/base/utils/R/seconds_in_year.R b/base/utils/R/seconds_in_year.R
index 1703462a1d9..f8124d2b419 100644
--- a/base/utils/R/seconds_in_year.R
+++ b/base/utils/R/seconds_in_year.R
@@ -2,13 +2,15 @@
 #'
 #' @author Alexey Shiklomanov
 #' @param year Numeric year (can be a vector)
+#' @param leap_year Default = TRUE. If set to FALSE will always return 31536000
 #' @examples
 #' seconds_in_year(2000)  # Leap year -- 366 x 24 x 60 x 60 = 31622400
 #' seconds_in_year(2001)  # Regular year -- 365 x 24 x 60 x 60 = 31536000
 #' seconds_in_year(2000:2005)  # Vectorized over year
+#' @inheritParams days_in_year
 #' @export
-seconds_in_year <- function(year) {
-    diy <- days_in_year(year)
+seconds_in_year <- function(year, leap_year = TRUE, ...) {
+    diy <- days_in_year(year, leap_year)
     siy <- udunits2::ud.convert(diy, 'days', 'seconds')
     return(siy)
 }
diff --git a/base/utils/R/sensitivity.R b/base/utils/R/sensitivity.R
index 2e4119fe37d..c398e4cdc97 100644
--- a/base/utils/R/sensitivity.R
+++ b/base/utils/R/sensitivity.R
@@ -78,13 +78,14 @@ read.sa.output <- function(traits, quantiles, pecandir, outdir, pft.name = "",
 ##' Write sensitivity analysis config files
 ##'
 ##' Writes config files for use in sensitivity analysis.
-##' @title Write sensitivity analysis configs
-##' @param pft pft id used to query PEcAn database
-##' @param quantile.samples 
+##'
+##' @param defaults named list with default parameter values
+##' @param quantile.samples list of lists supplied by \link{get.sa.samples}
 ##' @param settings list of settings
-##' @param write.config a model-specific function to write config files, e.g. \link{write.config.ED}  
-##' @param convert.samples a model-specific function that transforms variables from units used in database to units used by model, e.g. \link{convert.samples.ED} 
-##' @param ensemble.samples list of lists supplied by \link{get.sa.samples}
+##' @param model name of model to be run
+##' @param clean logical: Delete any existing contents of the directory specified by \code{settings$rundir} before writing to it?
+##' @param write.to.db logical: Record this run to BETY? If TRUE, uses connection settings specified in \code{settings$database}
+##'
 ##' @return list, containing $runs = data frame of runids, and $ensemble.id = the ensemble ID for these runs. Also writes sensitivity analysis configuration files as a side effect
 ##' @export
 ##' @author David LeBauer, Carl Davidson
@@ -295,6 +296,17 @@ write.sa.configs <- function(defaults, quantile.samples, settings, model,
               file = file.path(settings$rundir, run.id, "README.txt"), 
               sep = "")
           
+          # I check to make sure the path under the met is a list. if it's specified what met needs to be used in 'met.id' under sensitivity analysis of pecan xml we used that otherwise, I use the first met.
+          if (is.list(settings$run$inputs$met$path)){
+            # This checks for met.id tag in the settings under sensitivity analysis - if it's not there it creates it. Then it's gonna use what it created.
+            if (is.null(settings$sensitivity.analysis$met.id))  settings$sensitivity.analysis$met.id <- 1
+             
+              settings$run$inputs$met$path <- settings$run$inputs$met$path[[settings$sensitivity.analysis$met.id]]
+            
+          }
+          
+          
+          
           # write configuration
           do.call(my.write.config, args = list(defaults = defaults,
                                                trait.values = trait.samples, 
diff --git a/base/utils/R/units_are_equivalent.R b/base/utils/R/units_are_equivalent.R
new file mode 100644
index 00000000000..8e38dac9c93
--- /dev/null
+++ b/base/utils/R/units_are_equivalent.R
@@ -0,0 +1,13 @@
+#' Check if two unit strings are equivalent
+#'
+#' This is to allow multiple forms of the same unit to work, such as
+#' `m/s` vs. `m s-1` or `K` and `Kelvin`.
+#' @param x A unit string, as character
+#' @param y Another unit string for comparison, as character
+#' @return `TRUE` if equivalent, `FALSE` otherwise
+#' @author Alexey Shiklomanov
+#' @export
+units_are_equivalent <- function(x, y) {
+  x2y <- udunits2::ud.convert(1, x, y)
+  1 == x2y
+}
diff --git a/base/utils/R/utils.R b/base/utils/R/utils.R
index c32b5f2f7d1..852a3593cd0 100644
--- a/base/utils/R/utils.R
+++ b/base/utils/R/utils.R
@@ -180,6 +180,7 @@ get.run.id <- function(run.type, index, trait = NULL, pft.name = NULL) {
 ##' @title Zero Bounded Density
 ##' @param x data, as a numeric vector
 ##' @param bw The smoothing bandwidth to be used. See 'bw.nrd'
+##' @param n number of points to use in kernel density estimate. See \code{\link[stats]{density}}
 ##' @return data frame with back-transformed log density estimate
 ##' @author \href{http://stats.stackexchange.com/q/6588/2750}{Rob Hyndman}
 ##' @references M. P. Wand, J. S. Marron and D. Ruppert, 1991. Transformations in Density Estimation. Journal of the American Statistical Association. 86(414):343-353 \url{http://www.jstor.org/stable/2290569}
@@ -199,7 +200,7 @@ zero.bounded.density <- function(x, bw = "SJ", n = 1001) {
 ##' @title Summarize Results
 ##' @param result dataframe with results of trait data query
 ##' @return result with replicate observations summarized
-##' @export
+##' @export summarize.result
 ##' @author David LeBauer
 summarize.result <- function(result) {
   ans1 <- plyr::ddply(result[result$n == 1, ],
diff --git a/base/utils/data/trait.dictionary.csv b/base/utils/data/trait.dictionary.csv
index 14056741c54..e2d728ac5cb 100644
--- a/base/utils/data/trait.dictionary.csv
+++ b/base/utils/data/trait.dictionary.csv
@@ -70,13 +70,13 @@
 "wood_trans_nir";"wood NIR transmittance";"0-1";"wood_trans_nir"
 "orient_factor";"Leaf orientation";"0-1";"orient_factor"
 "num";"ED2 PFT Number";"Constant";"num"
-"HTMAX";"Max Height";"meters";
-"DBHMAX";"Max DBH";"meters";
-"AGEMX";"Max Age";"years";
-"G";"G";"cm";
-"D3";"D3";"percent";
-"FROST";"Min January Temp";"Celsius";
-"TL";"TL";"index";
+"HTMAX";"Max Height";"meters";""
+"DBHMAX";"Max DBH";"meters";""
+"AGEMX";"Max Age";"years";""
+"G";"G";"cm";""
+"D3";"D3";"percent";""
+"FROST";"Min January Temp";"Celsius";""
+"TL";"TL";"index";""
 "CM1";"CM1";"";""
 "CM2";"CM2";"";""
 "CM3";"CM3";"";""
@@ -92,5 +92,11 @@
 "DMAX";"DMAX";"degree days";""
 "DMIN";"DMIN";"degree days";""
 "leaf_longevity";"leaf longevity";"year";""
+"volume_fraction_of_water_in_soil_at_field_capacity";"Field Capacity";"volumetric fraction";"volume_fraction_of_water_in_soil_at_field_capacity"
+"volume_fraction_of_condensed_water_in_soil_at_wilting_point";"Wilting Point";"volumetric fraction";"volume_fraction_of_condensed_water_in_soil_at_wilting_point"
+"chi_leaf";"Leaf Angle Distribution Chi";"ratio";"chi_leaf"
+"pstemp_min";"Photosynthesis Minimum Temperature";"Celsius";"pstemp_min"
+"theta";"Collatz Curvature Parameter";"";"theta"
+"gdd_tbase";"GDD Base Temperature";"Celsius";"gdd_tbase"
 "frprod_perc_10";"fine root allocation percentage vertically in soils (every 10 cm)";"0-100";"frprod_perc_10"
 "gcmax";"Maximum canopy conductance";"m s-1";"gcmax"
diff --git a/base/utils/man/clear.scratch.Rd b/base/utils/man/clear.scratch.Rd
index 14b82814d62..3a8cc6cccc6 100644
--- a/base/utils/man/clear.scratch.Rd
+++ b/base/utils/man/clear.scratch.Rd
@@ -6,6 +6,9 @@
 \usage{
 clear.scratch(settings)
 }
+\arguments{
+\item{settings}{list of PEcAn settings. Only \code{settings$host$name} is used}
+}
 \value{
 nothing
 }
diff --git a/base/utils/man/convert.input.Rd b/base/utils/man/convert.input.Rd
index 80c1aab2621..e653c06ee64 100644
--- a/base/utils/man/convert.input.Rd
+++ b/base/utils/man/convert.input.Rd
@@ -2,16 +2,109 @@
 % Please edit documentation in R/convert.input.R
 \name{convert.input}
 \alias{convert.input}
-\title{convert.input}
+\title{Convert between formats, reusing existing files where possible}
 \usage{
-convert.input(input.id, outfolder, formatname, mimetype, site.id, start_date,
-  end_date, pkg, fcn, con = con, host, browndog, write = TRUE, format.vars,
-  overwrite = FALSE, exact.dates = FALSE, allow.conflicting.dates = TRUE,
-  insert.new.file = FALSE, pattern = NULL, ...)
+convert.input(input.id, outfolder, formatname, mimetype, site.id,
+  start_date, end_date, pkg, fcn, con = con, host, browndog,
+  write = TRUE, format.vars, overwrite = FALSE, exact.dates = FALSE,
+  allow.conflicting.dates = TRUE, insert.new.file = FALSE,
+  pattern = NULL, forecast = FALSE, ensemble = FALSE,
+  ensemble_name = NULL, ...)
+}
+\arguments{
+\item{input.id}{The database id of the input file of the parent of the file being processed here.  The parent will have the same data, but in a different format.}
+
+\item{outfolder}{The directory where files generated by functions called by convert.input will be placed}
+
+\item{formatname}{data product specific format name}
+
+\item{mimetype}{data product specific file format}
+
+\item{site.id}{The id of the site}
+
+\item{start_date}{Start date of the data being requested or processed}
+
+\item{end_date}{End date of the data being requested or processed}
+
+\item{pkg}{The package that the function being executed is in (as a string)}
+
+\item{fcn}{The function to be executed if records of the output file aren't found in the database. (as a string)}
+
+\item{con}{Database connection object}
+
+\item{host}{Named list identifying the machine where conversion should be performed.
+Currently only \code{host$name} is used by \code{convert.input}, but whole list is passed to other functions}
+
+\item{browndog}{List of information related to browndog conversion.  NULL if browndog is not to be used for conversion}
+
+\item{write}{Logical: Write new file records to the database?}
+
+\item{format.vars}{Passed on as arguments to \code{fcn}}
+
+\item{overwrite}{Logical: If a file already exists, create a fresh copy? Passed along to fcn.}
+
+\item{exact.dates}{Ignore time-span appending and enforce exact start and end dates on the database input file? (logical)}
+
+\item{allow.conflicting.dates}{Should overlapping years ignore time-span appending and exist as separate input files? (logical)}
+
+\item{insert.new.file}{Logical: force creation of a new database record even if one already exists?}
+
+\item{pattern}{A regular expression, passed to \code{PEcAn.DB::dbfile.input.check}, used to match the name of the input file.}
+
+\item{forecast}{Logical: Is the data product a forecast?}
+
+\item{ensemble}{An integer representing the number of ensembles, or FALSE if it data product is not an ensemble.}
+
+\item{ensemble_name}{If convert.input is being called iteratively for each ensemble, ensemble_name contains the identifying name/number for that ensemble.}
+
+\item{...}{Additional arguments, passed unchanged to \code{fcn}}
+}
+\value{
+A list of two BETY IDs (input.id, dbfile.id) identifying a pre-existing file if one was available, or a newly created file if not.  Each id may be a vector of ids if the function is processing an entire ensemble at once.
 }
 \description{
-Convert input by applying fcn and insert new record into database
+\code{convert.input} is a relatively generic function that applies the function \code{fcn} and inserts a record of it into the database. It is primarily designed for converting meteorological data between formats and can be used on observed data, forecasts, and ensembles of forecasts.
+To minimize downloading and storing duplicate data, it first checks to see if a given file is already in the
+database before applying \code{fcn}.
+}
+\section{Executing the function}{
+
+convert.input executes the function fcn in package pkg via PEcAn.remote::remote.execute.R.  All additional arguments passed to
+convert.input (...) are in turn passed along to fcn as arguments.  In addition, several named arguments to convert.input are passed
+along to fcn.  The command to execute fcn is built as a string.
+}
+
+\section{Database files}{
+
+There are two kinds of database records (in different tables) that represent a given data file in the file system.  An input file
+contains information about the contents of the data file.  A dbfile contains machine spacific information for a given input file, 
+such as the file path.  Because duplicates of data files for a given input can be on multiple different machines, there can be more 
+than one dbfile for a given input file.
+}
+
+\section{Time-span appending}{
+
+By default, convert.input tries to optimize the download of most data products by only downloading the years of data not present on 
+the current machine.  (For example, if files for 2004-2008 exist for a given data product exist on this machine and the user requests
+2006-2010, the function will only download data for 2009 and 2010).  In year-long data files, each year exists as a separate file.
+The database input file contains records of the bounds of the range stored by those years.  The data optimization can be turned off
+by overriding the default values for exact.dates and allow.conflicting.dates.
+}
+
+\section{Forecast data}{
+
+If the flag forecast is TRUE, convert.input treats data as if it were forecast data.  Forecast data do not undergo time span
+appending.
+}
+
+\section{Ensembles}{
+
+convert.input has the capability to handle ensembles of met data.  If ensemble = an integer > 1, convert.input checks the database
+for records of all ensemble members, and calls fcn if at least one is missing.  convert.input assumes that fcn will return records
+for all ensembles. convert.input can also be called iteratevely for each ensemble member.  In this case ensemble_name contains the
+unique identifying name/number of the ensemble to be processed.
 }
+
 \author{
-Betsy Cowdery, Michael Dietze, Ankur Desai, Tony Gardella
+Betsy Cowdery, Michael Dietze, Ankur Desai, Tony Gardella, Luke Dramko
 }
diff --git a/base/utils/man/convert.outputs.Rd b/base/utils/man/convert.outputs.Rd
deleted file mode 100644
index c76bb151763..00000000000
--- a/base/utils/man/convert.outputs.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read.output.R
-\name{convert.outputs}
-\alias{convert.outputs}
-\title{convert outputs from model specific code to}
-\usage{
-convert.outputs(model, settings, ...)
-}
-\arguments{
-\item{model}{name of simulation model currently accepts ('ED', 'SIPNET', 'BIOCRO')}
-
-\item{settings}{settings loaded from pecan.xml}
-
-\item{...}{arguments passed to \code{\link{read.output}}, e.g. \code{variables}, \code{start.year}, \code{end.year}}
-}
-\description{
---------------------------------------------------------------------------------------------------#
-Converts the output of all model runs
-}
-\author{
-Rob Kooper
-}
diff --git a/base/utils/man/days_in_year.Rd b/base/utils/man/days_in_year.Rd
index a0d291ecd9d..9ddcaae27f4 100644
--- a/base/utils/man/days_in_year.Rd
+++ b/base/utils/man/days_in_year.Rd
@@ -4,10 +4,12 @@
 \alias{days_in_year}
 \title{Number of days in a year}
 \usage{
-days_in_year(year)
+days_in_year(year, leap_year = TRUE)
 }
 \arguments{
 \item{year}{Numeric year (can be a vector)}
+
+\item{leap_year}{Default = TRUE. If set to FALSE will always return 365}
 }
 \value{
 integer vector, all either 365 or 366
diff --git a/base/utils/man/download.url.Rd b/base/utils/man/download.url.Rd
index af7ef90e356..1cec6c212d9 100644
--- a/base/utils/man/download.url.Rd
+++ b/base/utils/man/download.url.Rd
@@ -4,7 +4,8 @@
 \alias{download.url}
 \title{Download file from the url.}
 \usage{
-download.url(url, file, timeout = 600, .opts = list(), retry404 = TRUE)
+download.url(url, file, timeout = 600, .opts = list(),
+  retry404 = TRUE)
 }
 \arguments{
 \item{url}{the url of the file to download}
@@ -13,10 +14,10 @@ download.url(url, file, timeout = 600, .opts = list(), retry404 = TRUE)
 
 \item{timeout}{number of seconds to wait for file (default 600)}
 
-\item{retry404}{retry on a 404, this is used by Brown Dog}
-
-\item{list}{of options for curl, for example to download from a
+\item{.opts}{list of options for curl, for example to download from a
 protected site use list(userpwd=userpass, httpauth = 1L)}
+
+\item{retry404}{retry on a 404, this is used by Brown Dog}
 }
 \value{
 returns name of file if successful or NA if not.
diff --git a/base/utils/man/ensemble.filename.Rd b/base/utils/man/ensemble.filename.Rd
index a06b1a0d346..6e37db3fa62 100644
--- a/base/utils/man/ensemble.filename.Rd
+++ b/base/utils/man/ensemble.filename.Rd
@@ -4,8 +4,9 @@
 \alias{ensemble.filename}
 \title{Generate ensemble filenames}
 \usage{
-ensemble.filename(settings, prefix = "ensemble.samples", suffix = "Rdata",
-  all.var.yr = TRUE, ensemble.id = settings$ensemble$ensemble.id,
+ensemble.filename(settings, prefix = "ensemble.samples",
+  suffix = "Rdata", all.var.yr = TRUE,
+  ensemble.id = settings$ensemble$ensemble.id,
   variable = settings$ensemble$variable,
   start.year = settings$ensemble$start.year,
   end.year = settings$ensemble$end.year)
diff --git a/base/utils/man/get.ensemble.samples.Rd b/base/utils/man/get.ensemble.samples.Rd
index 1c5f25932ea..f389f5402c9 100644
--- a/base/utils/man/get.ensemble.samples.Rd
+++ b/base/utils/man/get.ensemble.samples.Rd
@@ -5,7 +5,7 @@
 \title{Get Ensemble Samples}
 \usage{
 get.ensemble.samples(ensemble.size, pft.samples, env.samples,
-  method = "uniform", ...)
+  method = "uniform", param.names = NULL, ...)
 }
 \arguments{
 \item{ensemble.size}{number of runs in model ensemble}
@@ -15,6 +15,8 @@ get.ensemble.samples(ensemble.size, pft.samples, env.samples,
 \item{env.samples}{env samples}
 
 \item{method}{the method used to generate the ensemble samples. Random generators: uniform, uniform with latin hypercube permutation. Quasi-random generators: halton, sobol, torus. Random generation draws random variates whereas quasi-random generation is deterministic but well equidistributed. Default is uniform. For small ensemble size with relatively large parameter number (e.g ensemble size < 5 and # of traits > 5) use methods other than halton.}
+
+\item{param.names}{a list of parameter names that were fitted either by MA or PDA, important argument, if NULL parameters will be resampled independently}
 }
 \value{
 matrix of (quasi-)random samples from trait distributions
@@ -23,11 +25,15 @@ matrix of (quasi-)random samples from trait distributions
 Get parameter values used in ensemble
 }
 \details{
+DEPRECATED: This function has been moved to the \code{PEcAn.uncertainty} package.
+The version in \code{PEcAn.utils} is deprecated, will not be updated to add any new features,
+and will be removed in a future release of PEcAn.
+Please use \code{PEcAn.uncertainty::get.ensemble.samples} instead.
 Returns a matrix of randomly or quasi-randomly sampled trait values 
 to be assigned to traits over several model runs.
 given the number of model runs and a list of sample distributions for traits
 The model run is indexed first by model run, then by trait
 }
 \author{
-David LeBauer
+David LeBauer, Istem Fer
 }
diff --git a/base/utils/man/match_file.Rd b/base/utils/man/match_file.Rd
new file mode 100644
index 00000000000..ab5339bdd2a
--- /dev/null
+++ b/base/utils/man/match_file.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/match_file.R
+\name{match_file}
+\alias{match_file}
+\title{Match a file}
+\usage{
+match_file(path_prefix, suffix = NULL, expect = NULL)
+}
+\arguments{
+\item{path_prefix}{Full path and file prefix}
+
+\item{suffix}{File suffix, as character (default = `NULL`)}
+
+\item{expect}{Number of files expected to be returned (default = `NULL`)}
+}
+\value{
+Character vector of matched file names, as full paths.
+}
+\description{
+Return a list of files given a full prefix and optional suffix. Optionally, 
+confirm that the right number of files are returned. If the wrong number of 
+files is returned, throw an error.
+}
+\details{
+If `path_prefix` points to a directory, then all files inside that directory 
+that match the suffix (if provided) are returned.
+}
diff --git a/base/utils/man/newxtable.Rd b/base/utils/man/newxtable.Rd
index cd84d688b0c..a2099408db6 100644
--- a/base/utils/man/newxtable.Rd
+++ b/base/utils/man/newxtable.Rd
@@ -4,8 +4,9 @@
 \alias{newxtable}
 \title{newxtable}
 \usage{
-newxtable(x, environment = "table", table.placement = "ht", label = NULL,
-  caption = NULL, caption.placement = NULL, align = NULL)
+newxtable(x, environment = "table", table.placement = "ht",
+  label = NULL, caption = NULL, caption.placement = NULL,
+  align = NULL)
 }
 \arguments{
 \item{x}{data.frame to be converted to latex table}
diff --git a/base/utils/man/read.ensemble.output.Rd b/base/utils/man/read.ensemble.output.Rd
index 53015f9c223..0ae2431ee08 100644
--- a/base/utils/man/read.ensemble.output.Rd
+++ b/base/utils/man/read.ensemble.output.Rd
@@ -29,6 +29,11 @@ Reads output from model ensemble
 \details{
 Reads output for an ensemble of length specified by \code{ensemble.size} and bounded by \code{start.year} 
 and \code{end.year}
+
+DEPRECATED: This function has been moved to the \code{PEcAn.uncertainty} package.
+The version in \code{PEcAn.utils} is deprecated, will not be updated to add any new features,
+and will be removed in a future release of PEcAn.
+Please use \code{PEcAn.uncertainty::read.ensemble.output} instead.
 }
 \author{
 Ryan Kelly, David LeBauer, Rob Kooper
diff --git a/base/utils/man/read.sa.output.Rd b/base/utils/man/read.sa.output.Rd
index e5271089cb8..c09a06a2898 100644
--- a/base/utils/man/read.sa.output.Rd
+++ b/base/utils/man/read.sa.output.Rd
@@ -4,8 +4,8 @@
 \alias{read.sa.output}
 \title{Read Sensitivity Analysis output}
 \usage{
-read.sa.output(traits, quantiles, pecandir, outdir, pft.name = "", start.year,
-  end.year, variable, sa.run.ids = NULL, per.pft = FALSE)
+read.sa.output(traits, quantiles, pecandir, outdir, pft.name = "",
+  start.year, end.year, variable, sa.run.ids = NULL, per.pft = FALSE)
 }
 \arguments{
 \item{traits}{model parameters included in the sensitivity analysis}
diff --git a/base/utils/man/run.write.configs.Rd b/base/utils/man/run.write.configs.Rd
index 1375fd9c518..a403bd2f94e 100644
--- a/base/utils/man/run.write.configs.Rd
+++ b/base/utils/man/run.write.configs.Rd
@@ -4,8 +4,9 @@
 \alias{run.write.configs}
 \title{Run model specific write configuration functions}
 \usage{
-run.write.configs(settings, write = TRUE, ens.sample.method = "uniform",
-  posterior.files = rep(NA, length(settings$pfts)), overwrite = TRUE)
+run.write.configs(settings, write = TRUE,
+  ens.sample.method = "uniform", posterior.files = rep(NA,
+  length(settings$pfts)), overwrite = TRUE)
 }
 \arguments{
 \item{write}{should the runs be written to the database}
@@ -27,6 +28,9 @@ an updated settings list, which includes ensemble IDs for SA and ensemble analys
 Main driver function to call the ecosystem model specific (e.g. ED, SiPNET) 
 run and configuration file scripts
 }
+\details{
+DEPRECATED: This function has been moved to the PEcAn.workflow package and will be removed from PEcAn.utils.
+}
 \author{
 David LeBauer, Shawn Serbin, Ryan Kelly, Mike Dietze
 }
diff --git a/base/utils/man/seconds_in_year.Rd b/base/utils/man/seconds_in_year.Rd
index 66498a0cd67..663467547f0 100644
--- a/base/utils/man/seconds_in_year.Rd
+++ b/base/utils/man/seconds_in_year.Rd
@@ -4,10 +4,12 @@
 \alias{seconds_in_year}
 \title{Number of seconds in a given year}
 \usage{
-seconds_in_year(year)
+seconds_in_year(year, leap_year = TRUE, ...)
 }
 \arguments{
 \item{year}{Numeric year (can be a vector)}
+
+\item{leap_year}{Default = TRUE. If set to FALSE will always return 31536000}
 }
 \description{
 Number of seconds in a given year
diff --git a/base/utils/man/units_are_equivalent.Rd b/base/utils/man/units_are_equivalent.Rd
new file mode 100644
index 00000000000..6edfa1cfd54
--- /dev/null
+++ b/base/utils/man/units_are_equivalent.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/units_are_equivalent.R
+\name{units_are_equivalent}
+\alias{units_are_equivalent}
+\title{Check if two unit strings are equivalent}
+\usage{
+units_are_equivalent(x, y)
+}
+\arguments{
+\item{x}{A unit string, as character}
+
+\item{y}{Another unit string for comparison, as character}
+}
+\value{
+`TRUE` if equivalent, `FALSE` otherwise
+}
+\description{
+This is to allow multiple forms of the same unit to work, such as
+`m/s` vs. `m s-1` or `K` and `Kelvin`.
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/base/utils/man/write.ensemble.configs.Rd b/base/utils/man/write.ensemble.configs.Rd
index f9d74b9f541..4432c884d06 100644
--- a/base/utils/man/write.ensemble.configs.Rd
+++ b/base/utils/man/write.ensemble.configs.Rd
@@ -25,6 +25,11 @@ list, containing $runs = data frame of runids, and $ensemble.id = the ensemble I
 Write ensemble config files
 }
 \details{
+DEPRECATED: This function has been moved to the \code{PEcAn.uncertainty} package.
+The version in \code{PEcAn.utils} is deprecated, will not be updated to add any new features,
+and will be removed in a future release of PEcAn.
+Please use \code{PEcAn.uncertainty::write.ensemble.configs} instead.
+
 Writes config files for use in meta-analysis and returns a list of run ids.
 Given a pft.xml object, a list of lists as supplied by get.sa.samples, 
 a name to distinguish the output files, and the directory to place the files.
diff --git a/base/utils/man/write.sa.configs.Rd b/base/utils/man/write.sa.configs.Rd
index 7c97bdf3c8f..5bd0bfdf101 100644
--- a/base/utils/man/write.sa.configs.Rd
+++ b/base/utils/man/write.sa.configs.Rd
@@ -2,31 +2,28 @@
 % Please edit documentation in R/sensitivity.R
 \name{write.sa.configs}
 \alias{write.sa.configs}
-\title{Write sensitivity analysis configs}
+\title{Write sensitivity analysis config files}
 \usage{
-write.sa.configs(defaults, quantile.samples, settings, model, clean = FALSE,
-  write.to.db = TRUE)
+write.sa.configs(defaults, quantile.samples, settings, model,
+  clean = FALSE, write.to.db = TRUE)
 }
 \arguments{
-\item{quantile.samples}{}
+\item{defaults}{named list with default parameter values}
 
-\item{settings}{list of settings}
+\item{quantile.samples}{list of lists supplied by \link{get.sa.samples}}
 
-\item{pft}{pft id used to query PEcAn database}
+\item{settings}{list of settings}
 
-\item{write.config}{a model-specific function to write config files, e.g. \link{write.config.ED}}
+\item{model}{name of model to be run}
 
-\item{convert.samples}{a model-specific function that transforms variables from units used in database to units used by model, e.g. \link{convert.samples.ED}}
+\item{clean}{logical: Delete any existing contents of the directory specified by \code{settings$rundir} before writing to it?}
 
-\item{ensemble.samples}{list of lists supplied by \link{get.sa.samples}}
+\item{write.to.db}{logical: Record this run to BETY? If TRUE, uses connection settings specified in \code{settings$database}}
 }
 \value{
 list, containing $runs = data frame of runids, and $ensemble.id = the ensemble ID for these runs. Also writes sensitivity analysis configuration files as a side effect
 }
 \description{
-Write sensitivity analysis config files
-}
-\details{
 Writes config files for use in sensitivity analysis.
 }
 \author{
diff --git a/base/utils/man/zero.bounded.density.Rd b/base/utils/man/zero.bounded.density.Rd
index 5037f7b59e3..0f32e90edc5 100644
--- a/base/utils/man/zero.bounded.density.Rd
+++ b/base/utils/man/zero.bounded.density.Rd
@@ -10,6 +10,8 @@ zero.bounded.density(x, bw = "SJ", n = 1001)
 \item{x}{data, as a numeric vector}
 
 \item{bw}{The smoothing bandwidth to be used. See 'bw.nrd'}
+
+\item{n}{number of points to use in kernel density estimate. See \code{\link[stats]{density}}}
 }
 \value{
 data frame with back-transformed log density estimate
diff --git a/base/visualization/DESCRIPTION b/base/visualization/DESCRIPTION
index f118245749a..498aaba6208 100644
--- a/base/visualization/DESCRIPTION
+++ b/base/visualization/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.visualization
 Type: Package
 Title: PEcAn visualization functions.
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze, Carl
     Davidson, Rob Kooper, Alexey Shiklomanov
 Maintainer: David LeBauer <dlebauer@illinois.edu>
@@ -25,11 +25,15 @@ Depends:
     earth,
     XML,
     shiny,
+    shinyjs,
     PEcAn.DB,
     RPostgreSQL,
     dplyr,
     dbplyr,
-    plotly
+    plotly,
+    shinydashboard,
+    shinyFiles,
+    shinycssloaders
 Imports:
     PEcAn.logger,
     lubridate (>= 1.6.0),
@@ -45,4 +49,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/base/visualization/NAMESPACE b/base/visualization/NAMESPACE
index 8e5f5178736..0c403b16ea3 100644
--- a/base/visualization/NAMESPACE
+++ b/base/visualization/NAMESPACE
@@ -4,7 +4,6 @@ export(add_icon)
 export(ciEnvelope)
 export(create_status_page)
 export(map.output)
-export(pecan.worldmap)
 export(plot.netcdf)
 export(points2county)
 export(vwReg)
diff --git a/base/visualization/R/worldmap.R b/base/visualization/R/worldmap.R
deleted file mode 100644
index 2a42cf0c9c5..00000000000
--- a/base/visualization/R/worldmap.R
+++ /dev/null
@@ -1,100 +0,0 @@
-##' Plot map of world with model output
-##'
-##' This is just a first draft
-##' @title PEcAn worldmap
-##' @param df.in data.frame with columns lat, lon, and (variable) 
-##' @param outfile png file  
-##' @return NULL plot as side effect
-##' @author David LeBauer
-##' @export
-##' @examples
-##' miscanthusyield <- read.csv(system.file('extdata/miscanthusyield.csv',
-##'                                      package = 'PEcAn.visualization'))
-##' pecan.worldmap(df.in = miscanthusyield,
-##'                outfile = file.path(tempdir(), 'worldmap.png'))
-pecan.worldmap <- function(df.in, outfile = NULL, xlim = c(-130, -30), ylim = c(-40, 60), 
-                           range = NULL, legend.title = NULL, fig.title = NULL) {
-  
-  ### map of yields
-  world  <- map_data("world")
-  states <- map_data("state")
-  rawdf  <- df.in
-  var    <- colnames(rawdf)[!colnames(rawdf) %in% c("X", "lat", "lon")]
-  colnames(rawdf)[!colnames(rawdf) %in% c("X", "lat", "lon")] <- "var"
-  
-  ## from http://stackoverflow.com/a/15351169/513006
-  spdf <- SpatialPointsDataFrame(data.frame(x = rawdf$lon, y = rawdf$lat), data = data.frame(z = rawdf$var))
-  
-  e <- extent(spdf)
-  # Determine ratio between x and y dimensions
-  ratio <- (e@xmax - e@xmin) / (e@ymax - e@ymin)
-  
-  # Create template raster to sample to
-  r <- raster(nrows = 56, ncols = floor(56 * ratio), ext = extent(spdf))
-  rf <- rasterize(spdf, r, field = "z", fun = mean)
-  #   if(!var ==  "aet" ){
-  #     rf <- CRS("+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 
-  #            +units=m +nadgrids=@null +wktext  +no_defs")    
-  #   }
-  
-  rdf <- data.frame(rasterToPoints(rf))
-  
-  if (!var == "aet") {
-    p <- ggplot() + # geom_polygon(data = world, aes(x=long, y=lat, group = group), colour='grey',
-      # fill='white') +
-      geom_raster(data = rdf, aes(x, y, fill = layer)) + xlim(xlim) + ylim(ylim) + # geom_point(aes(x = c(-180, -180, 180, 180), y = c(-90, 90, -90, 90), size = 0.1)) +
-      # xlab('Longitude') + ylab('Latitude') + ggtitle(var) +
-      theme_nothing() + 
-      scale_fill_gradientn(colours = colorRampPalette(c("darkblue", "wheat", "darkred"))(20), 
-                           name = legend.title,
-                           limits = range,
-                           trans = "sqrt") +
-      ggtitle(fig.title)
-  } else {
-    p <- ggplot() + # geom_polygon(data = world, aes(x=long, y=lat, group = group), colour='grey',
-      # fill='white') +
-      geom_point(data = df.in, aes(lat, lon, color = aet)) +
-      xlim(-130, -30) + 
-      ylim(-40, 60) + # geom_point(aes(x = c(-180, -180, 180, 180), y = c(-90, 90, -90, 90), size = 0.1)) +
-      # xlab('Longitude') + ylab('Latitude') + ggtitle(var) +
-      theme_nothing() + 
-      scale_fill_gradientn(colours = colorRampPalette(c("darkblue", "wheat", "darkred"))(20))
-  }
-  
-  if (!is.null(outfile)) {
-    ggsave(filename = outfile, 
-           plot = p, 
-           width = 44 * diff(xlim) / 360, 
-           height = 34 * diff(ylim) / 180, 
-           units = "in", 
-           dpi = 100, 
-           bg = "transparent")
-    
-    library(grid)
-    
-    png(paste0(outfile, "-legend.png"), units = "px", bg = "transparent")    
-    g_legend <- function(a.gplot) {
-      tmp <- ggplot_gtable(ggplot_build(a.gplot))
-      leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
-      legend <- tmp$grobs[[leg]]
-      return(legend)
-    } # g_legend
-    
-    l <- ggplot(data = rdf, aes(x, y, fill = layer)) + 
-      geom_point(aes(0, 0)) + 
-      theme(legend.position = "right") + 
-      scale_fill_gradientn(name = "Yield (Mg/ha)", colours = colorRampPalette(c("darkblue", "wheat", "darkred"))(20))
-    l2 <- g_legend(l)
-    grid.draw(l2)
-    dev.off()
-  } else {
-    return(p + theme_bw())
-  }
-}  # pecan.worldmap
-
-
-## see ?toupper
-.simpleCap <- function(x) {
-  s <- strsplit(x, " ")[[1]]
-  return(paste(toupper(substring(s, 1, 1)), substring(s, 2), sep = "", collapse = " "))
-}  # .simpleCap
diff --git a/base/visualization/man/add_icon.Rd b/base/visualization/man/add_icon.Rd
index e1c749df89a..b16a660c942 100644
--- a/base/visualization/man/add_icon.Rd
+++ b/base/visualization/man/add_icon.Rd
@@ -13,6 +13,9 @@ add_icon(id = NULL, x = 0, y = 0)
 
 \item{y}{y-coordinate of logo}
 }
+\description{
+add_icon
+}
 \author{
 Mike Dietze
 }
diff --git a/base/visualization/man/pecan.worldmap.Rd b/base/visualization/man/pecan.worldmap.Rd
deleted file mode 100644
index 121b59069ff..00000000000
--- a/base/visualization/man/pecan.worldmap.Rd
+++ /dev/null
@@ -1,32 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/worldmap.R
-\name{pecan.worldmap}
-\alias{pecan.worldmap}
-\title{PEcAn worldmap}
-\usage{
-pecan.worldmap(df.in, outfile = NULL, xlim = c(-130, -30), ylim = c(-40,
-  60), range = NULL, legend.title = NULL, fig.title = NULL)
-}
-\arguments{
-\item{df.in}{data.frame with columns lat, lon, and (variable)}
-
-\item{outfile}{png file}
-}
-\value{
-NULL plot as side effect
-}
-\description{
-Plot map of world with model output
-}
-\details{
-This is just a first draft
-}
-\examples{
-miscanthusyield <- read.csv(system.file('extdata/miscanthusyield.csv',
-                                     package = 'PEcAn.visualization'))
-pecan.worldmap(df.in = miscanthusyield,
-               outfile = file.path(tempdir(), 'worldmap.png'))
-}
-\author{
-David LeBauer
-}
diff --git a/base/visualization/man/vwReg.Rd b/base/visualization/man/vwReg.Rd
index 86ce58e9738..e10f75882c9 100644
--- a/base/visualization/man/vwReg.Rd
+++ b/base/visualization/man/vwReg.Rd
@@ -7,10 +7,10 @@
 vwReg(formula, data, title = "", B = 1000, shade = TRUE,
   shade.alpha = 0.1, spag = FALSE, spag.color = "darkblue",
   mweight = TRUE, show.lm = FALSE, show.median = TRUE,
-  median.col = "white", shape = 21, show.CI = FALSE, method = loess,
-  bw = FALSE, slices = 200, palette = colorRampPalette(c("#FFEDA0",
-  "#DD0000"), bias = 2)(20), ylim = NULL, quantize = "continuous",
-  add = FALSE, ...)
+  median.col = "white", shape = 21, show.CI = FALSE,
+  method = loess, bw = FALSE, slices = 200,
+  palette = colorRampPalette(c("#FFEDA0", "#DD0000"), bias = 2)(20),
+  ylim = NULL, quantize = "continuous", add = FALSE, ...)
 }
 \arguments{
 \item{B}{= number bootstrapped smoothers}
diff --git a/base/visualization/tests/testthat/test.pecan.worldmap.R b/base/visualization/tests/testthat/test.pecan.worldmap.R
deleted file mode 100644
index 556629814c0..00000000000
--- a/base/visualization/tests/testthat/test.pecan.worldmap.R
+++ /dev/null
@@ -1,8 +0,0 @@
-test_that("pecan.worldmap runs with example input", {
-  
-  data(yielddf, package = "PEcAn.visualization")
-  outfile <- file.path(tempdir(), "worldmap.png")
-  pecan.worldmap(yielddf, outfile = outfile)
-  expect_true(file.exists(outfile))
-  
-})
\ No newline at end of file
diff --git a/base/visualization/tests/testthat/test.viz.R b/base/visualization/tests/testthat/test.viz.R
new file mode 100644
index 00000000000..3dffbdd7ca8
--- /dev/null
+++ b/base/visualization/tests/testthat/test.viz.R
@@ -0,0 +1,11 @@
+## -------------------------------------------------------------------------------
+##  Copyright (c) 2012 University of Illinois, NCSA.
+##  All rights reserved. This program and the accompanying materials
+##  are made available under the terms of the 
+##  University of Illinois/NCSA Open Source License
+##  which accompanies this distribution, and is available at
+##  http://opensource.ncsa.illinois.edu/license.html
+##-------------------------------------------------------------------------------
+
+context("Testing Visualization")
+
diff --git a/base/visualization/vignettes/usmap.Rmd b/base/visualization/vignettes/usmap.Rmd
index e568fc90e51..de1ea3d5dbb 100644
--- a/base/visualization/vignettes/usmap.Rmd
+++ b/base/visualization/vignettes/usmap.Rmd
@@ -8,7 +8,7 @@ require(ggplot2)
 require(PEcAn.visualization)
 data(yielddf, package = "PEcAn.visualization")
 
-pecan.worldmap(yielddf, outfile=file.path(tempdir(), 'foo.png'))
+#pecan.worldmap(yielddf, outfile=file.path(tempdir(), 'foo.png'))
 
 spdf <- SpatialPointsDataFrame( data.frame( x = testdf$y , y = testdf$x ) , data = data.frame( z = testdf$z ) )
 
@@ -29,14 +29,14 @@ for(file in yieldfiles){
 
     outfile <- gsub("csv", "png", file)
     
-    pecan.worldmap(df.in, outfile=outfile)
+    #pecan.worldmap(df.in, outfile=outfile)
 }
 
 
 for(file in etfiles){
   df.in <- read.csv(file, skip = 1)
   outfile <- gsub("csv", "png", file)
-  pecan.worldmap(df.in, outfile=outfile)
+  #pecan.worldmap(df.in, outfile=outfile)
 }
 
 ```
diff --git a/base/workflow/DESCRIPTION b/base/workflow/DESCRIPTION
index d2df179987a..0f988a0588a 100644
--- a/base/workflow/DESCRIPTION
+++ b/base/workflow/DESCRIPTION
@@ -2,8 +2,8 @@ Package: PEcAn.workflow
 Type: Package
 Title: PEcAn functions used for ecological forecasts and
     reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
     Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <dlebauer@illinois.edu>
@@ -19,9 +19,11 @@ License: FreeBSD + file LICENSE
 Imports:
 	PEcAn.DB,
 	PEcAn.logger,
-	PEcAn.settings
+	PEcAn.settings,
+	PEcAn.utils
 Suggests:
 	testthat,
     mockery
 Copyright: Authors
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/base/workflow/NAMESPACE b/base/workflow/NAMESPACE
index 691dd0dd45d..d3b95928d28 100644
--- a/base/workflow/NAMESPACE
+++ b/base/workflow/NAMESPACE
@@ -1,3 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
+export(run.write.configs)
 export(runModule.get.trait.data)
+export(runModule.run.write.configs)
diff --git a/base/workflow/R/run.write.configs.R b/base/workflow/R/run.write.configs.R
new file mode 100644
index 00000000000..1599e4b9fbc
--- /dev/null
+++ b/base/workflow/R/run.write.configs.R
@@ -0,0 +1,148 @@
+#' Write model-specific run scripts and configuration files
+#'
+#' Generates run scripts and configuration files for all analyses specified
+#' in the provided settings. Most of the heavy lifting is done by the
+#' \code{write.config.*} function for your specific ecosystem model
+#' (e.g. write.config.ED2, write.config.SIPNET).
+#'
+#' @param settings a PEcAn settings list
+#' @param write should the runs be written to the database?
+#' @param ens.sample.method how to sample the ensemble members('halton' sequence or 'uniform' random)
+#' @param posterior.files Filenames for posteriors for drawing samples for ensemble and sensitivity
+#'    analysis (e.g. post.distns.Rdata, or prior.distns.Rdata)
+#' @param overwrite logical: Replace output files that already exist?
+#'
+#' @details The default value for \code{posterior.files} is NA, in which case the
+#'    most recent posterior or prior (in that order) for the workflow is used.
+#'    When specified, \code{posterior.files} should be a vector of filenames with one entry for each PFT.
+#'    Specify filenames with no path; PFT outdirs will be appended. This forces use of only
+#'    files within this workflow, to avoid confusion.
+#'
+#' @return an updated settings list, which includes ensemble IDs for SA and ensemble analysis
+#' @export
+#'
+#' @author David LeBauer, Shawn Serbin, Ryan Kelly, Mike Dietze
+run.write.configs <- function(settings, write = TRUE, ens.sample.method = "uniform", 
+                              posterior.files = rep(NA, length(settings$pfts)), 
+                              overwrite = TRUE) {
+  
+  con <- PEcAn.DB::db.open(settings$database$bety)
+  on.exit(PEcAn.DB::db.close(con))
+  
+  ## Which posterior to use?
+  for (i in seq_along(settings$pfts)) {
+    ## if posterior.files is specified us that
+    if (is.na(posterior.files[i])) {
+      ## otherwise, check to see if posteriorid exists
+      if (!is.null(settings$pfts[[i]]$posteriorid)) {
+        files <- PEcAn.DB::dbfile.check("Posterior",
+                              settings$pfts[[i]]$posteriorid, 
+                              con, settings$host$name, return.all = TRUE)
+        pid <- grep("post.distns.*Rdata", files$file_name)  ## is there a posterior file?
+        if (length(pid) == 0) {
+          pid <- grep("prior.distns.Rdata", files$file_name)  ## is there a prior file?
+        }
+        if (length(pid) > 0) {
+          posterior.files[i] <- file.path(files$file_path[pid], files$file_name[pid])
+        }  ## otherwise leave posteriors as NA
+      }
+      ## otherwise leave NA and get.parameter.samples will look for local
+    }
+  }
+  
+  ## Sample parameters
+  model <- settings$model$type
+  scipen <- getOption("scipen")
+  options(scipen = 12)
+  PEcAn.uncertainty::get.parameter.samples(settings, posterior.files, ens.sample.method)
+  load(file.path(settings$outdir, "samples.Rdata"))
+  
+  ## remove previous runs.txt
+  if (overwrite && file.exists(file.path(settings$rundir, "runs.txt"))) {
+    PEcAn.logger::logger.warn("Existing runs.txt file will be removed.")
+    unlink(file.path(settings$rundir, "runs.txt"))
+  }
+  
+  PEcAn.utils::load.modelpkg(model)
+  
+  ## Check for model-specific write configs
+  
+  my.write.config <- paste0("write.config.",model)
+  if (!exists(my.write.config)) {
+    PEcAn.logger::logger.error(my.write.config, 
+                 "does not exist, please make sure that the model package contains a function called", 
+                 my.write.config)
+  }
+  
+  ## Prepare for model output.  Clean up any old config files (if exists)
+  my.remove.config <- paste0("remove.config.", model)
+  if (exists(my.remove.config)) {
+    do.call(my.remove.config, args = list(settings$rundir, settings))
+  }
+  
+  # TODO RK : need to write to runs_inputs table
+  
+  # Save names
+  pft.names <- names(trait.samples)
+  trait.names <- lapply(trait.samples, names)
+  
+  ### NEED TO IMPLEMENT: Load Environmental Priors and Posteriors
+  
+  ### Sensitivity Analysis
+  if ("sensitivity.analysis" %in% names(settings)) {
+    
+    ### Write out SA config files
+    if (!exists("cnt")) {
+      cnt <- 0
+      assign("cnt", cnt, .GlobalEnv)
+    }
+    PEcAn.logger::logger.info("\n ----- Writing model run config files ----")
+    sa.runs <- PEcAn.utils::write.sa.configs(defaults = settings$pfts,
+                                quantile.samples = sa.samples, 
+                                settings = settings, 
+                                model = model,
+                                write.to.db = write)
+    
+    # Store output in settings and output variables
+    runs.samples$sa <- sa.run.ids <- sa.runs$runs
+    settings$sensitivity.analysis$ensemble.id <- sa.ensemble.id <- sa.runs$ensemble.id
+    
+    # Save sensitivity analysis info
+    fname <- PEcAn.utils::sensitivity.filename(settings, "sensitivity.samples", "Rdata",
+                                  all.var.yr = TRUE, pft = NULL)
+    save(sa.run.ids, sa.ensemble.id, sa.samples, pft.names, trait.names, file = fname)
+    
+  }  ### End of SA
+  
+  ### Write ENSEMBLE
+  if ("ensemble" %in% names(settings)) {
+    ens.runs <- PEcAn.uncertainty::write.ensemble.configs(defaults = settings$pfts,
+                                       ensemble.samples = ensemble.samples, 
+                                       settings = settings,
+                                       model = model, 
+                                       write.to.db = write)
+    
+    # Store output in settings and output variables
+    runs.samples$ensemble <- ens.run.ids <- ens.runs$runs
+    settings$ensemble$ensemble.id <- ens.ensemble.id <- ens.runs$ensemble.id
+    ens.samples <- ensemble.samples  # rename just for consistency
+    
+    # Save ensemble analysis info
+    fname <- PEcAn.utils::ensemble.filename(settings, "ensemble.samples", "Rdata", all.var.yr = TRUE)
+    save(ens.run.ids, ens.ensemble.id, ens.samples, pft.names, trait.names, file = fname)
+  } else {
+    PEcAn.logger::logger.info("not writing config files for ensemble, settings are NULL")
+  }  ### End of Ensemble
+  
+  PEcAn.logger::logger.info("###### Finished writing model run config files #####")
+  PEcAn.logger::logger.info("config files samples in ", file.path(settings$outdir, "run"))
+  
+  ### Save output from SA/Ensemble runs
+  # A lot of this is duplicate with the ensemble/sa specific output above, but kept for backwards compatibility.   
+  save(ensemble.samples, trait.samples, sa.samples, runs.samples, pft.names, trait.names, 
+       file = file.path(settings$outdir, "samples.Rdata"))
+  PEcAn.logger::logger.info("parameter values for runs in ", file.path(settings$outdir, "samples.RData"))
+  options(scipen = scipen)
+  
+  return(invisible(settings))
+}
diff --git a/base/workflow/R/runModule.run.write.configs.R b/base/workflow/R/runModule.run.write.configs.R
new file mode 100644
index 00000000000..1e06def102c
--- /dev/null
+++ b/base/workflow/R/runModule.run.write.configs.R
@@ -0,0 +1,24 @@
+#' Generate model-specific run configuration files for one or more PEcAn runs
+#'
+#' @param settings a PEcAn Settings or MultiSettings object
+#' @param overwrite logical: Replace config files if they already exist?
+#' @return A modified settings object, invisibly
+#' @export
+runModule.run.write.configs <- function(settings, overwrite = TRUE) {
+
+  if (PEcAn.settings::is.MultiSettings(settings)) {
+    if (overwrite && file.exists(file.path(settings$rundir, "runs.txt"))) {
+      PEcAn.logger::logger.warn("Existing runs.txt file will be removed.")
+      unlink(file.path(settings$rundir, "runs.txt"))
+    }
+    return(PEcAn.settings::papply(settings, runModule.run.write.configs, overwrite = FALSE))
+  } else if (PEcAn.settings::is.Settings(settings)) {
+    write <- settings$database$bety$write
+    # double check making sure we have method for parameter sampling
+    if (is.null(settings$ensemble$samplingspace$parameters$method)) settings$ensemble$samplingspace$parameters$method <- "uniform"
+    ens.sample.method <-  settings$ensemble$samplingspace$parameters$method
+    return(PEcAn.workflow::run.write.configs(settings, write, ens.sample.method, overwrite = overwrite))
+  } else {
+    stop("runModule.run.write.configs only works with Settings or MultiSettings")
+  }
+}
diff --git a/base/workflow/man/run.write.configs.Rd b/base/workflow/man/run.write.configs.Rd
new file mode 100644
index 00000000000..c6e21b1261d
--- /dev/null
+++ b/base/workflow/man/run.write.configs.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run.write.configs.R
+\name{run.write.configs}
+\alias{run.write.configs}
+\title{Write model-specific run scripts and configuration files}
+\usage{
+run.write.configs(settings, write = TRUE,
+  ens.sample.method = "uniform", posterior.files = rep(NA,
+  length(settings$pfts)), overwrite = TRUE)
+}
+\arguments{
+\item{settings}{a PEcAn settings list}
+
+\item{write}{should the runs be written to the database?}
+
+\item{ens.sample.method}{how to sample the ensemble members('halton' sequence or 'uniform' random)}
+
+\item{posterior.files}{Filenames for posteriors for drawing samples for ensemble and sensitivity
+analysis (e.g. post.distns.Rdata, or prior.distns.Rdata)}
+
+\item{overwrite}{logical: Replace output files that already exist?}
+}
+\value{
+an updated settings list, which includes ensemble IDs for SA and ensemble analysis
+}
+\description{
+Generates run scripts and configuration files for all analyses specified
+in the provided settings. Most of the heavy lifting is done by the
+\code{write.config.*} function for your specific ecosystem model
+(e.g. write.config.ED2, write.config.SIPNET).
+}
+\details{
+The default value for \code{posterior.files} is NA, in which case the
+   most recent posterior or prior (in that order) for the workflow is used.
+   When specified, \code{posterior.files} should be a vector of filenames with one entry for each PFT.
+   Specify filenames with no path; PFT outdirs will be appended. This forces use of only
+   files within this workflow, to avoid confusion.
+}
+\author{
+David LeBauer, Shawn Serbin, Ryan Kelly, Mike Dietze
+}
diff --git a/base/workflow/man/runModule.run.write.configs.Rd b/base/workflow/man/runModule.run.write.configs.Rd
new file mode 100644
index 00000000000..fcb253947b3
--- /dev/null
+++ b/base/workflow/man/runModule.run.write.configs.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/runModule.run.write.configs.R
+\name{runModule.run.write.configs}
+\alias{runModule.run.write.configs}
+\title{Generate model-specific run configuration files for one or more PEcAn runs}
+\usage{
+runModule.run.write.configs(settings, overwrite = TRUE)
+}
+\arguments{
+\item{settings}{a PEcAn Settings or MultiSettings object}
+
+\item{overwrite}{logical: Replace config files if they already exist?}
+}
+\value{
+A modified settings object, invisibly
+}
+\description{
+Generate model-specific run configuration files for one or more PEcAn runs
+}
diff --git a/book_source/03_intermediate_users_guide/01_pecan_xml.Rmd b/book_source/03_intermediate_users_guide/01_pecan_xml.Rmd
index 989ff190e5a..091ca8ffd9b 100644
--- a/book_source/03_intermediate_users_guide/01_pecan_xml.Rmd
+++ b/book_source/03_intermediate_users_guide/01_pecan_xml.Rmd
@@ -165,20 +165,36 @@ Only if this section is defined an ensemble analysis is done.
 
 #### functions: 
 
-`write.configs()`, `run.ensemble.analysis()`
+`write.configs()`,`write.ensemble.configs`, `run.ensemble.analysis()`
 
 #### tags
 
 ```xml
 <ensemble>
-	<size>5</size>
+  <size>5</size>
   <variable>GPP</variable>
-  <variable>NPP</variable>
+  <start.year>1995</start.year>
+  <end.year>1999</end.year>
+  <samplingspace>
+  <parameters>
+    <method>lhc</method>
+  </parameters>
+  <met>
+    <method>sampling</method>
+  </met>
+  </samplingspace>
 </ensemble>
 ```
 
 * **size** : [required] the number of runs in the ensemble.
 * **variable**: [optional] name of one (or more) variables the analysis should be run for. If not specified, sensitivity.analysis variable is used, otherwise default is GPP.
+* **samplingspace**:[optional] Contains tags for defining how the ensembles will be generated.
+
+Each piece in the sampling space can potentially have a method tag and a parent tag. Method refers to the sampling method and parent refers to the cases where we need to link the samples of two components. When no tag is defined for one component, one sample will be generated and used for all the ensembles. This allows for partitioning/studying different sources of uncertainties. For example, if no met tag is defined then, one met path will be used for all the ensembles and as a result the outpus's uncertainty will come from the variability in the parameters. At the moment no sampling method is implemented for soil and vegetation.
+Available sampling methods for `parameters` can be found in the documentation of the `get.ensemble.samples` function in `PEcAn.utils` package.
+For the cases where we need simulations with a predefined set of parameters, met and initial condition we can use the restart argument. Restart needs to be a list with name tags of runid, inputs, new.params (parameters), new.state (initial condition), ensemble.id (ensemble ids), start.time and stop.time.
+
+The restart functionality is developed using model specific functions by called write_restart.modelname. You need to make sure first that this function is already exist for your desired model.
 
 Note: if the ensemble size is set to 1, PEcAn will select the **posterior median** parameter values rather than taking a single random draw from the posterior
 
diff --git a/book_source/03_intermediate_users_guide/03_hidden_analyses/02_sda.Rmd b/book_source/03_intermediate_users_guide/03_hidden_analyses/02_sda.Rmd
index 88b4ff65199..5818431d96c 100644
--- a/book_source/03_intermediate_users_guide/03_hidden_analyses/02_sda.Rmd
+++ b/book_source/03_intermediate_users_guide/03_hidden_analyses/02_sda.Rmd
@@ -1,7 +1,7 @@
 ## State data assimilation (SDA)
-
-`sda.enkf.R` is housed within: **/pecan/modules/assim.sequential/R**
-The tree ring tutorial is housed within: **/pecan/documentation/tutorials/StateAssimilation**
+## sda.enkf.R is housed within: **/pecan/modules/assim.sequential/R**
+## The tree ring tutorial is housed within: **/pecan/documentation/tutorials/StateAssimilation**
+## More descriptive SDA methods can be found at: **/pecan/book_source/adve_user_guide_web/SDA_Methods.Rmd**
 
 ### **sda.enkf.R Description**
 This is the main ensemble Kalman filter and generalized filter code. Originally, this was just ensemble Kalman filter code. Mike Dietze and Ann Raiho added a generalized ensemble filter to avoid filter divergence. The output of this function will be all the of run outputs, a PDF of diagnostics, and an Rdata object that includes three lists:
@@ -12,7 +12,7 @@ This is the main ensemble Kalman filter and generalized filter code. Originally,
 
 ### **sda.enkf.R Arguments**
 
-* settings - (required) [pecan.SDA.xml][State Data Assimilation Tags Example] settings object
+* settings - (required) [State Data Assimilation Tags Example] settings object
 
 * obs.mean - (required) a list of observation means named with dates in YYYY/MM/DD format
 
@@ -25,7 +25,7 @@ This is the main ensemble Kalman filter and generalized filter code. Originally,
 ### State Data Assimilation Workflow
 Before running sda.enkf, these tasks must be completed (in no particular order),
 
-* Read in a [pecan.SDA.xml][State Data Assimilation Tags Example] settings file with tags listed below. i.e. read.settings('pecan.SDA.xml')
+* Read in a [State Data Assimilation Tags Example] settings file with tags listed below. i.e. read.settings('pecan.SDA.xml')
 
 * Load data means (obs.mean) and covariances (obs.cov) as lists with PEcAn naming and unit conventions. Each observation must have a date in YYYY/MM/DD format  (optional time) associated with it. If there are missing data, the date must still be represented in the list with an NA as the list object.
 
diff --git a/book_source/03_intermediate_users_guide/03_hidden_analyses/03_sda_methods.Rmd b/book_source/03_intermediate_users_guide/03_hidden_analyses/03_sda_methods.Rmd
new file mode 100644
index 00000000000..7646cfa98a7
--- /dev/null
+++ b/book_source/03_intermediate_users_guide/03_hidden_analyses/03_sda_methods.Rmd
@@ -0,0 +1,172 @@
+## SDA_Methods
+
+*By Ann Raiho*
+
+Our goal is build a fully generalizable state data assimilation (SDA) workflow that will assimilate multiple types of data and data products into ecosystem models within PEcAn temporally and spatially. But, during development, specifically with PalEON goals in mind, we have been focusing on assimilating tree ring estimated NPP and AGB and pollen derived fractional composition into two ecosystem models, SIPNET and LINKAGES, at Harvard Forest. This methodology will soon be expanded to include the PalEON sites listed on the [state data assimilation wiki page](https://paleon.geography.wisc.edu/doku.php/working_groups;state_data_assimilation).
+
+## Data Products
+During workflow development, we have been working with tree ring estimated NPP and AGB and pollen derived fractional composition data products. Both of these data products have been estimated with a full accounting of uncertainty, which provides us with state variable observation mean vector and covariance matrix at each time step. These data products are discussed in more detail below. Even though we have been working with specific data products during development, our workflow is generalizable to alternative data products as long as we can calculate a state variable observation mean vector and covariance for a time point. 
+
+### Tree Rings
+We have been primarily been working with the tree ring data product created by Andria Dawson and Chris Paciorek and the PEcAn tree ring allometry module. They have developed a Bayesian model that estimates annual aboveground biomass increment (Mg/ha/yr) and aboveground biomass (Mg/ha) for each tree in a dataset. We obtain this data and aggregate to the level appropriate for the ecosystem model. In SIPNET, we are assimilating annual gross woody increment (Mg/ha/yr) and above ground woody biomass (Mg/ha). In LINKAGES, we are assimilating annual species biomass. More information on deriving these tree ring data products can be found in Dawson et al 201?.
+
+We have been working mostly with tree data collected at Harvard Forest. Tree rings and census data were collected at Lyford Plot between 1960 and 2010 in three separate plots. Other tree ring data will be added to this analysis in the future from past PEON courses (UNDERC), Kelly Heilman (Billy's Lake and Bigwoods), and Alex Dye (Huron Mt. Club).
+
+### Pollen
+STEPPS is a Bayesian model developed by Paciorek and McLachlan 2009 and Dawson et al 2016 to estimate spatially gridded fractional composition from fossil pollen. We have been working with STEPPS1 output, specifically with the grid cell that contains Harvard Forest. The temporal resolution of this data product is centennial. Our workflow currently operates at annual time steps, but does not require data at every time step. So, it is possible to assimilate fractional composition every one hundred years or to assimilate fractional composition data every year by accounting for variance inflation.
+
+In the future, pollen derived biomass (ReFAB) will also be available for data assimilation. Although, we have not discussed how STEPPS and ReFAB data assimilation will work. 
+
+#### Variance Inflation
+*Side Note: Probably want to call this something else now.
+
+Since the fractional composition data product has a centennial resolution, in order to use fractional composition information every year we need to change the weight the data has on the analysis. The basic idea is to downweight the likelihood relative to the prior to account for (a) the fact that we assimilate an observation multiple times and (b) the fact that the number of STEPPS observations is 'inflated' because of the autocorrelation. To do this, we take the likelihood and raise it to the power of (1/w) where 'w' is an inflation factor.
+
+w = D * (N / ESS)
+
+where D is the length of the time step. In our case D = 100. N is the number of time steps. In our case N = 11. and ESS is the effective sample size. The ESS is calculated with the following function where ntimes is the same as N above and sims is a matrix with the dimensions number of MCMC samples by number of state variables.
+
+```
+ESS_calc <- function(ntimes, sims){
+        # center based on mean at each time to remove baseline temporal correlation 
+        # (we want to estimate effective sample size effect from correlation of the errors)
+        row.means.sims <- sims - rowMeans(sims)  
+        
+        # compute all pairwise covariances at different times
+        covars <- NULL
+        for(lag in 1:(ntimes-1)){
+          covars <- c(covars, rowMeans(row.means.sims[(lag+1):ntimes, , drop = FALSE] * row.means.sims[1:(ntimes-lag), , drop = FALSE])) 
+        }
+        vars <- apply(row.means.sims, 1, var) # pointwise post variances at each time, might not be homoscedastic
+        
+        # nominal sample size scaled by ratio of variance of an average
+        # under independence to variance of average of correlated values
+        neff <- ntimes * sum(vars) / (sum(vars) + 2 * sum(covars))
+        return(neff)
+      }
+```
+
+The ESS for the STEPPS1 data product is 3.6, so w in our assimilation of fractional composition at Harvard Forest will be w = 305.6. 
+
+## Current Models
+SIPNET and LINKAGES are the two ecosystem models that have been used during state data assimilation development within PEcAn. SIPNET is a simple ecosystem model that was built for... LINKAGES is a forest gap model created to simulate the process of succession that occurs when a gap is opened in the forest canopy. LINKAGES has 72 species level plant functional types and the ability to simulate some below ground processes (C and N cycles).
+
+## Model Calibration
+Without model calibration both SIPNET and LINKAGES make incorrect predictions about Harvard Forest. To confront this problem, SIPNET and LINKAGES will both be calibrated using data collected at the Harvard Forest flux tower. Istem has completed calibration for SIPNET using a [parameter data assimilation emulator](https://github.com/PecanProject/pecan/blob/develop/modules/assim.batch/R/pda.emulator.R) contained within the PEcAn workflow. LINKAGES will also be calibrated using this method. This method is also generalizable to other sites assuming there is data independent of data assimilation data available to calibrate against.
+
+## Initial Conditions
+The initial conditions for SIPNET are sampled across state space based on data distributions at the time when the data assimilation will begin. We do not sample LINAKGES for initial conditions and instead perform model spin up for 100 years prior to beginning data assimilation. In the future, we would like to estimate initial conditions based on data. We achieve adequate spread in the initial conditions by allowing the parameters to vary across ensemble members. 
+
+## Drivers
+We are currently using Global Climate Model (GCM) drivers from the PaLEON model intercomparison. Christy Rollinson and John Tipton are creating MET downscaled GCM drivers for the Paleon data assimilation sites. We will use these drivers when they are available because they are a closer representation of reality.
+
+## Sequential State Data Assimilation
+We are using sequential state data assimilation methods to assimilate paleon data products into ecosystem models because less computation power is required for sequential state data assimilation than for particle filter methods.
+
+### General Description
+The general sequential data assimilation framework consists of three steps at each time step:
+1. Read the state variable output for time t from the model forecast ensembles and save the forecast mean (muf) and covariance (Pf).
+2. If there are data mean (y) and covariance (R) at this time step, perform data assimilation analysis (either EnKF or generalized ensemble filter) to calculate the new mean (mua) and covariance (Pa) of the state variables.
+3. Use mua and Pa to restart and run the ecosystem model ensembles with new state variables for time t+1.
+
+### EnKF
+There are two ways to implement sequential state data assimilation at this time. The first is the Ensemble Kalman Filter (EnKF). EnKF has an analytical solution, so the kalman gain, analysis mean vector, and analysis covariance matrix can be calculated directly:
+
+```
+       
+        K <- Pf %*% t(H) %*% solve((R + H %*% Pf %*% t(H))) ## Kalman Gain
+        
+        mu.a <- mu.f + K %*% (Y - H %*% mu.f) # Analysis mean vector
+        
+        Pa   <- (diag(ncol(X)) - K %*% H) %*% Pf # Analysis covariance matrix
+        
+```
+
+The EnKF is typically used for sequential state data assimilation, but we found that EnKF lead to filter divergence when combined with our uncertain data products. Filter divergence led us to create a generalized ensemble filter that estimates process variance.
+
+### Generalized Ensemble Filter
+The generalized ensemble filter follows generally the three steps of sequential state data assimilation. But, in the generalized ensemble filter we add a latent state vector that accounts for added process variance. Furthermore, instead of solving the analysis analytically like the EnKF, we have to estimate the mean analysis vector and covariance matrix with MCMC. 
+
+#### Mapping Ensemble Output to Tobit Space
+There are some instances when we have right or left censored variables from the model forecast. For example, a model estimating species level biomass may have several ensemble members that produce zero biomass for a given species. We are considering this case a left censored state variable that needs to be mapped to normal space using a tobit model. We do this by creating two matrices with dimensions number of ensembles by state variable. The first matrix is a matrix of indicator variables (y.ind), and the second is a matrix of censored variables (y.censored). When the indicator variable is 0 the state variable (j) for ensemble member (i) is sampled. This allows us to impute a normal distribution for each state variable that contains 'missing' forecasts or forecasts of zero. 
+
+```
+tobit2space.model <- nimbleCode({
+    for(i in 1:N){
+      y.censored[i,1:J] ~ dmnorm(muf[1:J], cov = pf[1:J,1:J])
+      for(j in 1:J){
+        y.ind[i,j] ~ dconstraint(y.censored[i,j] > 0)
+      }
+    }
+    
+    muf[1:J] ~ dmnorm(mean = mu_0[1:J], cov = pf[1:J,1:J])
+    
+    Sigma[1:J,1:J] <- lambda_0[1:J,1:J]/nu_0
+    pf[1:J,1:J] ~ dinvwish(S = Sigma[1:J,1:J], df = J)
+    
+  })
+```
+
+
+#### Generalized Ensemble Filter Model Description
+Below is the BUGS code for the full analysis model. The forecast mean an covariance are calculated from the tobit2space model above. We use a tobit likelihood in this model because there are instances when the data may be left or right censored. Process variance is included by adding a latent model state (X) with a process precision matrix (q). We update our prior on q at each time step using our estimate of q from the previous time step. 
+
+```
+  tobit.model <- nimbleCode({ 
+    
+    q[1:N,1:N]  ~ dwish(R = aq[1:N,1:N], df = bq) ## aq and bq are estimated over time
+    Q[1:N,1:N] <- inverse(q[1:N,1:N])
+    X.mod[1:N] ~ dmnorm(muf[1:N], prec = pf[1:N,1:N]) ## Model Forecast ##muf and pf are assigned from ensembles
+    
+    ## add process error
+    X[1:N]  ~ dmnorm(X.mod[1:N], prec = q[1:N,1:N])
+    
+    #agb linear
+    #y_star[1:YN,1:YN] <- X[1:YN,1:YN] #[choose]
+    
+    #f.comp non linear
+    #y_star[1:YN] <- X[1:YN] / sum(X[1:YN])
+    
+    ## Analysis
+    y.censored[1:YN] ~ dmnorm(X[1:YN], prec = r[1:YN,1:YN]) #is it an okay assumpution to just have X and Y in the same order?
+    
+    #don't flag y.censored as data, y.censored in inits
+    #remove y.censored samplers and only assign univariate samplers on NAs
+    
+    for(i in 1:YN){
+      y.ind[i] ~ dconstraint(y.censored[i] > 0)
+    }
+    
+  })
+```
+
+### Ensemble Adjustment
+Each ensemble member has a different set of species parameters. We adjust the updated state variables by using an ensemble adjustment. The ensemble adjustment weights the ensemble members based on their likelihood during the analysis step.  
+
+```
+      S_f  <- svd(Pf)
+      L_f  <- S_f$d
+      V_f  <- S_f$v
+      
+      ## normalize
+      Z <- X*0
+      for(i in seq_len(nrow(X))){
+          Z[i,] <- 1/sqrt(L_f) * t(V_f)%*%(X[i,]-mu.f)
+      }
+      Z[is.na(Z)]<-0
+      
+      ## analysis
+      S_a  <- svd(Pa)
+      L_a  <- S_a$d
+      V_a  <- S_a$v
+      
+      ## analysis ensemble
+      X_a <- X*0
+      for(i in seq_len(nrow(X))){
+        X_a[i,] <- V_a %*%diag(sqrt(L_a))%*%Z[i,] + mu.a
+      }
+```
+
+### Diagnostics
+There are three diagnostics we have currently implemented: time series, bias time series, and process variance. The time series diagnostics show the data, forecast, and analysis time series for each state variable. These are useful for visually assessing variance and magnitude of change of state variables through time. These time series are also updated throughout the analysis and are also created as a pdf at the end of the SDA workflow. There are two types of bias time series the first assess the bias in the update (the forecast minus the analysis) and the second assess the bias in the error (the forecast minus the data). These bias time series are useful for identifying which state variables have intrinsic bias within the model. For example, if red oak biomass in LINKAGES increases at every time step (the update and the error are always positive), this would suggest that LINKAGES has a positive growth or recruitment bias for red oak. Finally, when using the generalized ensemble filter to estimate process variance, there are two additional plots to assess estimation of process variance. The first is a correlation plot of the process covariance matrix. This tells us what correlations are incorrectly represented by the model. For example, if red oak biomass and white pine biomass are highly negatively correlated in the process covariance matrix, this means that the model either 1) has no relationship between red oak and white pine and they should affect each other negatively or 2) there is a positive relationship between red oak and white pine and there shouldn't be any relationship. We can determine which of these is true by comparing the process covariance matrix to the model covariance matrix. The second process variance diagnostic plot shows how the degrees of freedom associated with estimating the process covariance matrix have changed through time. This plot should show increasing degrees of freedom through time. 
+
diff --git a/book_source/03_intermediate_users_guide/03_hidden_analyses/03_multisettings.Rmd b/book_source/03_intermediate_users_guide/03_hidden_analyses/04_multisettings.Rmd
similarity index 100%
rename from book_source/03_intermediate_users_guide/03_hidden_analyses/03_multisettings.Rmd
rename to book_source/03_intermediate_users_guide/03_hidden_analyses/04_multisettings.Rmd
diff --git a/book_source/03_intermediate_users_guide/03_hidden_analyses/04_benchmarking.Rmd b/book_source/03_intermediate_users_guide/03_hidden_analyses/05_benchmarking.Rmd
similarity index 100%
rename from book_source/03_intermediate_users_guide/03_hidden_analyses/04_benchmarking.Rmd
rename to book_source/03_intermediate_users_guide/03_hidden_analyses/05_benchmarking.Rmd
diff --git a/book_source/03_intermediate_users_guide/04_remote_execution.Rmd b/book_source/03_intermediate_users_guide/04_remote_execution.Rmd
index 3b98a0cff98..4ecec7bb730 100644
--- a/book_source/03_intermediate_users_guide/04_remote_execution.Rmd
+++ b/book_source/03_intermediate_users_guide/04_remote_execution.Rmd
@@ -7,12 +7,17 @@ The infrastructure for remote execution lives in the `PEcAn.remote` package (`ba
 
 This section describes the following:
 
-- Basics of command line SSH
-- SSH authentication with keys and passwords
-- Basics of SSH tunnels, and how they are used in PEcAn
-- Basic remote exectuion R functions in `PEcAn.remote`
-- Remote model execution configuration in the `pecan.xml` and `config.php`
-- Additional information about preparing remote servers for execution
+1. Checking capabilities to connect to the remote machine correctly:
++ Basics of command line SSH
++ SSH authentication with keys and passwords
++ Basics of SSH tunnels, and how they are used in PEcAn
+
+2. Description of PEcAn related tools that control remote execution
++ Basic remote execution R functions in `PEcAn.remote`
+
+3. SETUP- Configuration Files and settings
++ Remote model execution configuration in the `pecan.xml` and `config.php`
++ Additional information about preparing remote servers for execution
 
 
 ## Basics of SSH
@@ -31,7 +36,7 @@ For instance, my connection to the BU shared computing cluster looks like:
 ssh ashiklom@geo.bu.edu
 ```
 
-...which will prompt me for my BU password, and, if successful, will drop me into a login shell on the remote machine.
+It will prompt me for my BU password, and, if successful, will drop me into a login shell on the remote machine.
 
 Alternatively to the login shell, `ssh` can be used to execute arbitrary code, whose output will be returned exactly as it would if you ran the command locally.
 For example, the following:
@@ -40,7 +45,7 @@ For example, the following:
 ssh ashiklom@geo.bu.edu pwd
 ```
 
-...will run the `pwd` command, and return the path to my home directory on the BU SCC.
+will run the `pwd` command, and return the path to my home directory on the BU SCC.
 The more advanced example below will run some simple R code on the BU SCC and return the output as if it was run locally.
 
 ```sh
@@ -224,8 +229,10 @@ Documentation for using the model launcher is currently unavailable.
 ### Configuration for PEcAn web interface
 
 The `config.php` has a few variables that will control where the web
-interface can run jobs, and how to run those jobs. These variables
-are `$hostlist`, `$qsublist`, `$qsuboptions`, and `$SSHtunnel`. In
+interface can run jobs, and how to run those jobs. It is located in the `/web` directory and if you have not touched it yet it will
+be named as `config.example.php`. Rename it to 'config.php` and edit by folowing the following directions.
+
+These variables are `$hostlist`, `$qsublist`, `$qsuboptions`, and `$SSHtunnel`. In
 the near future `$hostlist`, `$qsublist`, `$qsuboptions` will be
 combined into a single list.
 
@@ -248,7 +255,7 @@ that jobs on the local machine should use qsub to run the models.
 
 `$qsuboptions` : is an array that lists options for each machine.
 Currently it support the following options (see also
-[PEcAn-Configuration](PEcAn-Configuration.md#run_setup))
+[Run Setup] and look at the tags)
 
 ```
 array("geo.bu.edu" =>
@@ -266,28 +273,27 @@ are additional entries to add to the job.sh file generated to
 run the model. This can be used to make sure modules are loaded
 on the HPC cluster before running the actual model.
 
-## Running PEcAn code for modules remotely
+## Running PEcAn code for remotely
 
-You can compile and install the model specific code pieces of
+You do not need to download PEcAn fully on your remote machine. You can compile and install the model specific code pieces of
 PEcAn on the cluster easily without having to install the
-full code base of PEcAn (and all OS dependencies). All of the
-code pieces depend on PEcAn.utils to install this you can
-run the following on the cluster:
+full code base of PEcAn (and all OS dependencies). Use the `git clone ` command to:
 
 ```
-devtools::install_github("pecanproject/pecan", subdir = 'utils')
+devtools::install_github("pecanproject/pecan", subdir = 'base/utils')
 ```
 
 Next we need to install the model specific pieces, this is done
-almost the same:
+almost the same (example for ED2):
 
 ```
 devtools::install_github("pecanproject/pecan", subdir = 'models/ed')
 ```
 
-This should install dependencies required. Following are some
-notes on how to install the model specifics on different HPC
-clusters.
+This should install dependencies required. 
+
+* The following are some notes on how to install the model specifics on different HPC
+clusters*
 
 ### geo.bu.edu
 
@@ -309,7 +315,7 @@ install.packages(c('udunits2', 'lubridate'),
 Finally to install support for both ED and SIPNET:
 
 ```
-devtools::install_github("pecanproject/pecan", subdir = 'utils')
+devtools::install_github("pecanproject/pecan", subdir = 'base/utils')
 devtools::install_github("pecanproject/pecan", subdir = 'models/sipnet')
 devtools::install_github("pecanproject/pecan", subdir = 'models/ed')
 ```
diff --git a/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/04_input_conversion.Rmd b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/04_input_conversion.Rmd
index 850b696ee0b..4c18e371868 100755
--- a/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/04_input_conversion.Rmd
+++ b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/04_input_conversion.Rmd
@@ -17,54 +17,7 @@ Current Meteorological products that are coupled to PEcAn can be found in our [A
 
 Note: Unless you are also adding a new model, you will not need to write a script to convert from PEcAn standard to PEcAn models. Those conversion scripts are written when a model is added and can be found within each model's PEcAn directory.
 
-##### Dimensions:
-
-
-|CF standard-name | units |
-|:------------------------------------------|:------|
-| time | days since 1700-01-01 00:00:00 UTC|
-| longitude | degrees_east|
-| latitude |degrees_north|
-
-General Note: dates in the database should be date-time (preferably with timezone), and datetime passed around in PEcAn should be of type POSIXct.
-
-
-##### The variable names should be `standard_name`
-
-| CF standard-name                          | units | bety         | isimip       | cruncep | narr  | ameriflux |
-|:------------------------------------------|:------|:-------------|:-------------|:--------|:------|:----------|
-| **air_temperature**                       | K     | airT         | tasAdjust    | tair    | air   | TA (C)    |
-| air_temperature_max                       | K     |              | tasmaxAdjust | NA      | tmax  |           |
-| air_temperature_min                       | K     |              | tasminAdjust | NA      | tmin  |           |
-| **air_pressure**                          | Pa    | air_pressure |              |         |       | PRESS (KPa) |
-| mole_fraction_of_carbon_dioxide_in_air    | mol/mol |            |              |         |       | CO2       |
-| moisture_content_of_soil_layer            | kg m-2 |             |              |         |       |           |
-| soil_temperature                          | K     | soilT        |              |         |       | TS1 *(NOT DONE)* |
-| relative_humidity                         | % | relative_humidity | rhurs       | NA      | rhum  | RH        |
-| **specific_humidity**                     | 1 | specific_humidity | NA          | qair    | shum  | CALC(RH)  |
-| water_vapor_saturation_deficit            | Pa    | VPD          |              |         |       | VPD *(NOT DONE)*     |
-| **surface_downwelling_longwave_flux_in_air** | W m-2 | same      | rldsAdjust   | lwdown  | dlwrf | Rgl       |
-| **surface_downwelling_shortwave_flux_in_air**| W m-2 |solar_radiation|rsdsAdjust| swdown  | dswrf | Rg        |
-| surface_downwelling_photosynthetic_photon_flux_in_air | mol m-2 s-1 | PAR |     |         |       | PAR *(NOT DONE)*          |
-| **precipitation_flux**                    |  kg m-2 s-1 | cccc   | prAdjust     | rain    | acpc  | PREC (mm/s)          |
-|                                           | degrees | wind_direction |          |         |       | WD        |
-| wind_speed                                | m/s   | Wspd         |              |         |       | WS        |
-| **eastward_wind**                         | m/s   | eastward_wind |             |         |       | CALC(WS+WD) |
-| **northward_wind**                        | m/s   | northward_wind |            |         |       | CALC(WS+WD) |
-
-* preferred variables indicated in bold
-* wind_direction has no CF equivalent and should not be converted, instead the met2CF functions should convert wind_direction and wind_speed to eastward_wind and northward_wind
-* standard_name is CF-convention standard names
-* units can be converted by udunits, so these can vary (e.g. the time denominator may change with time frequency of inputs)
-* soil moisture for the full column, rather than a layer, is soil_moisture_content
-* A full list of PEcAn standard variable names, units and dimensions can be found here: https://github.com/PecanProject/pecan/blob/develop/base/utils/data/standard_vars.csv
-
-
-For example, in the [MsTMIP-CRUNCEP](https://www.betydb.org/inputs/280) data, the variable `rain` should be `precipitation_rate`.
-We want to standardize the units as well as part of the `met2CF.<product>` step. I believe we want to use the CF "canonical" units but retain the MsTMIP units any time CF is ambiguous about the units.
-
-The key is to process each type of met data (site, reanalysis, forecast, climate scenario, etc) to the exact same standard. This way every operation after that (extract, gap fill, downscale, convert to a model, etc) will always have the exact same inputs. This will make everything else much simpler to code and allow us to avoid a lot of unnecessary data checking, tests, etc being repeated in every downstream function.
-
+*Standards dimesion, names, nad units can be found here:* [Input Standards]
 ##### Adding Single-Site Specific Meteorological Data
 
 Perhaps you have meteorological data specific to one site, with a unique format that you would like to add to PEcAn. Your steps would be to:
@@ -176,7 +129,7 @@ PEcAn.data.atmosphere::met2CF.csv(in.path = in.path,
 ```
 
 
-#### Vegetation Data
+### Vegetation Data
 
 Vegetation data will be required to parameterize your model. In these examples we will go over how to produce a standard initial condition file.
 
@@ -190,32 +143,33 @@ First, you'll need to create a input record in BETY that will have a file record
 
 Once you have created an input record you must take note of the input id of your record. An easy way to take note of this is in the URL of the BETY webpage that shows your input record. In this example we use an input record with the id `1000013064` which can be found at this url: https://psql-pecan.bu.edu/bety/inputs/1000013064# . Note that this is the Boston University BETY database. If you are on a different machine, your url will be different.
 
-With the input id  in hand you can now edit a pecan XML so that the PEcAn function `ic.process` will know where to look in order to process your data. The `inputs` section of your pecan XML will look like this. As of now ic.process is set up to work with the ED2 model so we will use ED2 settings and then grab the intermediary Rds data file that is created as the standard PEcAn file. For your Inputs section you will need to input your input id wherever you see the `source.ic` flag.
+With the input id  in hand you can now edit a pecan XML so that the PEcAn function `ic.process` will know where to look in order to process your data. The `inputs` section of your pecan XML will look like this. As of now ic.process is set up to work with the ED2 model so we will use ED2 settings and then grab the intermediary Rds data file that is created as the standard PEcAn file. For your Inputs section you will need to input your input id wherever you see the `useic` flag.
 ```
 <inputs>
       <css>
         <source>FFT</source>
         <output>css</output>
         <username>pecan</username>
-        <source.id>1000013064</source.id>
+        <id>1000013064</id>
         <useic>TRUE</useic>
-        <meta>
+        <metadata>
           <trk>1</trk>
           <age>70</age>
-        </meta>
+          <area>400</area>
+        </metadata>
       </css>
       <pss>
         <source>FFT</source>
         <output>pss</output>
         <username>pecan</username>
-        <source.id>1000013064</source.id>
+        <id>1000013064</id>
         <useic>TRUE</useic>
       </pss>
       <site>
         <source>FFT</source>
         <output>site</output>
         <username>pecan</username>
-        <source.id>1000013064</source.id>
+        <id>1000013064</id>
         <useic>TRUE</useic>
       </site>
       <met>
@@ -237,6 +191,56 @@ With the input id  in hand you can now edit a pecan XML so that the PEcAn functi
     </inputs>
 ```
 
+This IC workflow also supports generating ensembles of initial conditions from posterior estimates of DBH. To do this the tags below can be inserted to the pecan.xml:
+```
+       <css>
+        <source>PalEON</source>
+        <output>css</output>
+        <id>1000015682</id>
+        <useic>TRUE</useic>
+        <ensemble>20</ensemble>
+        <metadata>
+          <area>1256.637</area>
+          <n.patch>3</n.patch>
+        </metadata>
+      </css>
+```
+Here the `id` should point to a file that has MCMC samples to generate the ensemble from. The number between the `<ensemble>` tag defines the number of ensembles requested. The workflow will populate the settings list `run$inputs` tag with ensemble member information. E.g.:
+```
+  <inputs>
+   <css>
+    <path1>...</path1>
+    <path2>...</path2>
+    <path3>...</path3>
+    ...
+    <pathN>...</pathN>
+   </css>
+   <pss>
+    <path>
+     <path1>...</path1>
+     <path2>...</path2>
+     <path3>...</path3>
+      ...
+     <pathN>...</pathN>
+    </path>
+   </pss>
+   <site>
+    <path>
+     <path1>...</path1>
+     <path2>...</path2>
+     <path3>...</path3>
+      ...
+     <pathN>...</pathN>
+    </path>
+   </site>
+   <met>...</met>
+   <lu>...</lu>
+   <soil>...</soil>
+   <thsum>...</thsum>
+   <veg>...</veg>
+  </inputs>
+```
+
 Once you edit your PEcAn.xml you can than create a settings object using PEcAn functions. Your `pecan.xml` must be in your working directory.
 
 ```
@@ -281,7 +285,7 @@ pool_ic_list2netcdf(input = input, outdir = outdir, siteid = siteid)
 
 You should now have a netcdf file with initial conditions.
 
-#### Soil Data
+### Soil Data
 
 ###### Example 1: Converting Data in hand 
 
@@ -311,4 +315,18 @@ In addition to location-specific soil data, PEcAn can extract soil texture infor
 In the future we aim to extend this extraction to a wider range of soil products.
 
 
+###### Example 3: Extracting soil properties from gSSURGO database
+
+In addition to location-specific soil data, PEcAn can extract soil texture information from the gSSURGO data product. This product needs no installation and it extract soil proeprties for the lower 48 states in U.S. In order to let the pecan know that you're planning to use gSSURGO, you can the following XML tag under input in your pecan xml file.
+
+```<inputs>```
+
+```
+   <soil>
+     <source>gSSURGO</source>
+   </soil>
+```
+```</inputs>```
+
+
 
diff --git a/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/06_data_ingest_workflow.Rmd b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/06_data_ingest_workflow.Rmd
new file mode 100644
index 00000000000..719b6faa592
--- /dev/null
+++ b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/06_data_ingest_workflow.Rmd
@@ -0,0 +1,87 @@
+# Pecan Data Ingest via Web Interface 
+
+This tutorial explains the process of ingesting data into PEcAn via our Data-Ingest Application. In order to ingest data, the users must first select data that they wish to upload. Then, they enter metadata to help PEcAn parse and load the data into the main PEcAn workflow.
+
+# 1. Loading Data
+
+## Selecting Ingest Method
+The Data-Ingest application is capable of loading data from the DataONE data federation and from the user's local machine. The first step in the workflow is therefore to select an upload method. The application defaults to uploading from DataONE. To upload data from a local device, simply select the radio button titled `Local Files `. 
+
+### DataONE Upload Example 
+<br>
+![Select Method](images/data-ingest/D1Ingest-1.gif)
+
+<br>
+The DataONE download feature allows the user to download data at a given doi or DataONE specific package id. To do so, enter the doi or identifier in the `Import From DataONE` field and select `download`. The download process may take a couple of minutes to run depending on the number of files in the dataONE package. This may be a convenient option if the user does not wish to download files directly to their local machine. Once the files have been successfully downloaded from DataONE, they are displayed in a table. Before proceeding to the next step, the user can select a file to ingest by clicking on the corresponding row in the data table. 
+<br> 
+
+## Local Upload Example
+
+<br>
+To upload local files, the user should first select the `Local Files` button. From there, the user can upload files from their local machines by selecting `Browse` or by dragging and dropping files into the text box. The files will begin uploading automatically. From there, the user should select a file to ingest and then select the `Next Step` button. 
+<br>
+After this step, the workflow is identical for both methods. However, please note that if it becomes necessary to switch from loading data via `DataONE` to uploading local files after the first step, please restart the application. 
+<br>
+
+![Drag and Drop](images/data-ingest/Local_loader_sm.gif)
+
+<br>
+![Browse](images/data-ingest/local_browse.gif)
+
+## 2. Creating an Input Record
+Creating an input record requires some basic metadata about the file that is being ingested. Each entry field is briefly explained below. 
+<br> 
+
+  - Site: To link the selected file with a site, the user can scroll or type to search all the sites in PEcAn. See Example: 
+  <br>
+![Choose Site](images/data-ingest/Selectize_Input_sm.gif)
+<br>
+- Parent: To link the selected file with another dataset, type to search existing datasets in the `Parent` field. 
+
+- Name: this field should be autofilled by selecting a file in step 1.
+
+- Format: If the selected file has an existing format name, the user can search and select in the `Format` field. If the selected file's format is not already in pecan, the user can create a new format by selecting `Create New Format`. Once this new format is created, it will automatically populate the `Format` box and the `Current Mimetype` box (See Section 3).
+
+- Mimetype: If the format already exists, select an existing mimetype. 
+
+- Start and End Date and Time: Inputs can be entered manually or by using the user interface. See example
+
+<br>
+![Choose FIle for Ingest](images/data-ingest/DateTime.gif)
+
+  - Notes: Describe the data that is being uploaded. Please include any citations or references. 
+
+## 3. Creating a format record
+If it is necessary to add a new format to PEcAn, the user should fill out the form attached to the `Create New Format` button. The inputs to this form are described below: 
+
+- Mimetype: type to search existing mimetypes. If the mimetype is not in that list, please click on the link `Create New Mimetype` and create a new mimetype via the BETY website.
+
+- New Format Name: Add the name of the new format. Please exclude spaces from the name. Instead please use underscores "_".
+
+- Header: If there is space before the first line of data in the dataset, please select `Yes`
+
+- Skip: The number of lines in the header that should be skipped before the data. 
+
+- Please enter notes that describe the format. 
+
+Example: 
+<br>
+![Create New Format](images/data-ingest/new_format_record.gif)
+
+## 4. Formats_Variables Record
+The final step in the ingest process is to register a formats-variables record. This record links pecan variables with variables from the selected data. 
+
+- Variable: PEcAn variable that is equivalent to variable in selected file.
+
+- Name: The variable name in the imported data need only be specified if it differs from the BETY variable name.
+
+- Unit: Should be in a format parseable by the udunits library and need only be secified if the units of the data in the file differ from the BETY standard.
+
+- Storage Type: Storage type need only be specified if the variable is stored in a format other than would be expected (e.g. if numeric values are stored as quoted character strings). Additionally, storage_type stores POSIX codes that are used to store any time variables (e.g. a column with a 4-digit year would be `%Y`).
+
+- Column Number: Vector of integers that list the column numbers associated with variables in a dataset. Required for text files that lack headers.
+<br>
+![Create New Format](images/data-ingest/D1Ingest-9_sm.gif)
+
+Finally, the path to the ingest data is displayed in the `Select Files` box. 
+
diff --git a/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/D1Ingest-1.gif b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/D1Ingest-1.gif
new file mode 100644
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new file mode 100644
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diff --git a/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/Format-vars1.gif b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/Format-vars1.gif
new file mode 100644
index 00000000000..f230e08b8b2
Binary files /dev/null and b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/Format-vars1.gif differ
diff --git a/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/Local_loader_sm.gif b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/Local_loader_sm.gif
new file mode 100644
index 00000000000..33f248ec2a8
Binary files /dev/null and b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/Local_loader_sm.gif differ
diff --git a/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/Selectize_Input_sm.gif b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/Selectize_Input_sm.gif
new file mode 100644
index 00000000000..e5c0a3786e1
Binary files /dev/null and b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/Selectize_Input_sm.gif differ
diff --git a/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/local_browse.gif b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/local_browse.gif
new file mode 100644
index 00000000000..6f2cff7c150
Binary files /dev/null and b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/local_browse.gif differ
diff --git a/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/new_format_record.gif b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/new_format_record.gif
new file mode 100644
index 00000000000..53e7b0de2cc
Binary files /dev/null and b/book_source/04_advanced_user_guide/02_adding_to_pecan/01_case_studies/images/data-ingest/new_format_record.gif differ
diff --git a/book_source/05_developer_guide/01_setup/01_install_PEcAn/05_compile_PEcAn.Rmd b/book_source/05_developer_guide/01_setup/01_install_PEcAn/05_compile_PEcAn.Rmd
index 40a018734df..ae27682d2f1 100644
--- a/book_source/05_developer_guide/01_setup/01_install_PEcAn/05_compile_PEcAn.Rmd
+++ b/book_source/05_developer_guide/01_setup/01_install_PEcAn/05_compile_PEcAn.Rmd
@@ -21,7 +21,7 @@ git clone https://github.com/PecanProject/pecan.git
 
 # compile pecan
 cd pecan
-./scripts/build.sh --dependencies
+make
 ```
 
 Following will run a small script to setup some hooks to prevent people from using the pecan demo user account to check in any code.
@@ -49,4 +49,4 @@ cp ../pecan/scripts/workflow.R workflow.R
 rm -rf pecan
 ./workflow.R pecan.xml
 ```
-NB: pecan.xml is configured for the virtual machine, you will need to change the <met> field from '/home/carya/' to wherever you installed your 'sites', usually $HOME
\ No newline at end of file
+NB: pecan.xml is configured for the virtual machine, you will need to change the <met> field from '/home/carya/' to wherever you installed your 'sites', usually $HOME
diff --git a/book_source/05_developer_guide/03_git/01_Using-Git.Rmd b/book_source/05_developer_guide/03_git/01_using-git.Rmd
old mode 100755
new mode 100644
similarity index 54%
rename from book_source/05_developer_guide/03_git/01_Using-Git.Rmd
rename to book_source/05_developer_guide/03_git/01_using-git.Rmd
index 1fc68deb848..b579d05f9ec
--- a/book_source/05_developer_guide/03_git/01_Using-Git.Rmd
+++ b/book_source/05_developer_guide/03_git/01_using-git.Rmd
@@ -1,25 +1,14 @@
 ## Using Git
 
-
 This document describes the steps required to download PEcAn, make changes to code, and submit your changes.
 
-* For asking questions, reporting bugs, and requesting features, see our documentation for [reporting issues on Redmine and GitHub](#github-issue) 
-* If you are new to GitHub or to PEcAn, start with the one-time set-up instructions under [Before any work is done](#before-any-work-is-done). Also see the excellent tutorials and references in the [References](Using-Git.md#references) section at the the bottom of this page.
-* To make trivial changes, see [Quick and Easy](Using-Git.md#quick-and-easy)
-* To make changes to the code, start with the [basic workflow](Using-Git.md#basic-workflow). 
-* If you want to submit changes that you've made to be part of PEcAn you'll want to follow [Committing Changes Using Pull Requests](Using-Git.md#committing-changes-using-pull-requests)
-* **To update your local branch**
-
- ```
-cd pecan
-git pull upstream master
-./scripts/build.sh
- ```
+* If you are new to GitHub or to PEcAn, start with the one-time set-up instructions under [Before any work is done]. Also see the excellent tutorials and references in the [Git]) section right below this list and at the bootom in [References].
+* To make trivial changes, see [Quick and Easy].
+* To make a few changes to the code, start with the [Basic Workflow]. 
+* To make substantial changes and/or if plan to contribute over time see [Recommended Workflow: A new branch for each change].                                             
 
 ### Git
 
-Git is a version control software; GitHub is a project-hosting website that is similar to [Redmine](https://ebi-forecast.igb.illinois.edu/redmine/) but easier to use for open and collaborative development.
-
 Git is a free & open source, distributed version control system designed
 to handle everything from small to very large projects with speed and
 efficiency. Every Git clone is a full-fledged repository with complete
@@ -29,42 +18,47 @@ easy to do.
 
 A good place to start is the [GitHub 5 minute illustrated tutorial](https://guides.github.com/introduction/flow/). 
 In addition, there are three fun tutorials for learning git:
-
+  
 * [Learn Git](https://www.codecademy.com/learn/learn-git) is a great web-based interactive tutorial.
-* [LearnGitBranching](http://pcottle.github.com/learnGitBranching/)
+* [LearnGitBranching](https://learngitbranching.js.org/)
 * [TryGit](http://try.github.com).
 
-For additional tutorials and background see [References](Using-Git.md#references)
 
 **URLs** In the rest of the document will use specific URL’s to clone the code.
 There a few URL’s you can use to clone a project, using https, ssh and
 git. You can use either https or git to clone a repository and write to
 it. The git protocol is read-only.
+This document describes the steps required to download PEcAn, make changes to code, and submit your changes.
 
-#### PEcAnProject on GitHub: https://github.com/organizations/PecanProject
 
-* PEcAn source code: 
- * https://github.com/PecanProject/pecan.git
- * git@github.com:PecanProject/pecan.git
-* BETYdb source code:
- * https://github.com/PecanProject/bety.git
- * git@github.com:PecanProject/bety.git
+### PEcAn Project and Github
+                                                                                                                                                                * Organization Repository: https://github.com/organizations/PecanProject                                                                                        * PEcAn source code: https://github.com/PecanProject/pecan.git                                                                                                  * BETYdb source code: https://github.com/PecanProject/bety.git
 * These instructions apply to other repositories too.
+                                                                                                                                                                                                   
+### PEcAn Project Branches
+                                                                                                                                                                We follow branch organization laid out on [this page](http://nvie.com/posts/a-successful-git-branching-model).
+  
+In short, there are three main branches you must be aware of:
+
+* **develop** - Main Branch containing the latest code. This is the main branch you will make changes to. 
+* **master** - Branch containing the latest stable code. DO NOT MAKE CHANGES TO THIS BRANCH. 
+* **release/vX.X.X** - Named branches containing code specific to a release. Only make changes to this branch if you are fixing a bug on a release branch.
 
 #### Milestones, Issues, Tasks
 
 The Milestones, issues, and tasks can be used to organize specific features or research projects. In general, there is a heirarchy:
-
-* milestones (Big picture, "Epic"): contains many issues
-* issues (Specific features / bugs, "Story"): may contain a list of tasks; represent 
+  
+* milestones (Big picture, "Epic"): contains many issues, organized by release.
+* issues (Specific features / bugs, "Story"): may contain a list of tasks; represent
 * task list (to do list, "Tasks"): list of steps required to close an issue, e.g.:
-```
- * [ ] first do this
- * [ ] then this
- * [ ] completed when x and y
+  ```
+* [ ] first do this
+* [ ] then this
+* [ ] completed when x and y
 ```
 
-#### Quick and Easy
+
+### Quick and Easy
 
 The **easiest** approach is to use GitHub's browser based workflow. This is useful when your change is a few lines, if you are editing a wiki, or if the edit is trivial (and won't break the code). The [GitHub documentation is here](https://help.github.com/articles/github-flow-in-the-browser) but it is simple: finding the page or file you want to edit, click "edit" and then the GitHub web application will automatically forking and branch, then allow you to submit a pull request. However, it should be noted that unless you are a member of the PEcAn project that the "edit" button will not be active and you'll want to follow the workflow described below for forking and then submitting a pull request.
 
@@ -72,18 +66,15 @@ The **easiest** approach is to use GitHub's browser based workflow. This is usef
 ### Recommended Git Workflow
 
 
-**Each feature should be in it’s own branch** (for example each redmine
-issue is a branch, names of branches are often the issue in a bug
-tracking system).
+**Each feature should be in its own branch** (for example each issue is a branch, names of branches are often the issue in a bug tracking system).
 
 **Commit and Push Frequency** On your branch, commit **_at minimum once a day before you push changes:_** even better: every time you reach a stopping point and move to a new issue. best: any time that you have done work that you do not want to re-do. Remember, pushing changes to your branch is like saving a draft. Submit a pull request when you are done.
 
-
-#### Before any work is done:
+### Before any work is done:
 
 The first step below only needs to be done once when you first start working on the PEcAn code. The steps below that need to be done to set up PEcAn on your computer, and would need to be repeated if you move to a new computer. If you are working from the PEcAn VM, you can skip the "git clone" since the PEcAn code is already installed. 
 
-Most people will not be able to work in the PEcAn repository directly and will need to create a fork of the PEcAn source code in their own folder. To fork PEcAn into your own github space ([github help: "fork a repo"](https://help.github.com/articles/fork-a-repo)). This forked repository will allow you to create branches and commit changes back to GitHub and create pull requests to the master of PEcAn.
+Most people will not be able to work in the PEcAn repository directly and will need to create a fork of the PEcAn source code in their own folder. To fork PEcAn into your own github space ([github help: "fork a repo"](https://help.github.com/articles/fork-a-repo)). This forked repository will allow you to create branches and commit changes back to GitHub and create pull requests to the develop branch of PEcAn.
 
 The forked repository is the only way for external people to commit code back to PEcAn and BETY. The pull request will start a review process that will eventually result in the code being merged into the main copy of the codebase. See https://help.github.com/articles/fork-a-repo for more information,  especially on how to keep your fork up to date with respect to the original. (Rstudio users should also see [Git + Rstudio](Using-Git.md#git--rstudio), below)
 
@@ -91,167 +82,158 @@ You can setup SSH keys to make it easier to commit cod back to GitHub. This migh
 
 1. Introduce yourself to GIT
 
-        git config --global user.name "FULLNAME"
-        git config --global user.email you@yourdomain.example.com
+`git config --global user.name "FULLNAME"`
+`git config --global user.email you@yourdomain.example.com`
 
-2. Fork PEcAn on GitHub. Goto the PEcAn source code and click on the Fork button in the upper right. This will create a copy of PEcAn in your personal space.
+2. Fork PEcAn on GitHub. Go to the PEcAn source code and click on the Fork button in the upper right. This will create a copy of PEcAn in your personal space.
 
-3. Clone to your local machine 
+3. Clone to your local machine via command line
 
-        git clone git@github.com:<username>/pecan.git
+`git clone git@github.com:<username>/pecan.git`
 
-3. Define upstream repository
- 
-        cd pecan
-        git remote add upstream git@github.com:PecanProject/pecan.git
+If this does not work, try the https method
 
+`git clone https://github.com/PecanProject/pecan.git`
+
+4. Define upstream repository
+
+```
+cd pecan
+git remote add upstream git@github.com:PecanProject/pecan.git
+```
 
 ### During development:
 
 * commit often; 
-* each commit can address 0 or 1 issue; many commits can reference an issue (see [[Link commits to issue|Using-Git#link-commits-to-issues]])
-* ensure that all tests are passing before anything is pushed into master.
-
-#### Basic Workflow
+* each commit can address 0 or 1 issue; many commits can reference an issue
+* ensure that all tests are passing before anything is pushed into develop.
 
-PLEASE DO NOT USE THIS, SEE ADVANCED WORKFLOW!
+### Basic Workflow
 
+This workflow is for educational purposes only. Please use the Recommended Workflow if you plan on contributing to PEcAn. This workflow does not include creating branches, a feature we would like you to use.
 1. Get the latest code from the main repository
 
-        git pull upstream master
+`git pull upstream develop`
 
 2. Do some coding
 
 3. Commit after each chunk of code (multiple times a day)
-        
-        git commit -m "<some descriptive information about what was done; references/fixes gh-X>"
+
+`git commit -m "<some descriptive information about what was done; references/fixes gh-X>"`
 
 4. Push to YOUR Github (when a feature is working, a set of bugs are fixed, or you need to share progress with others)
 
-        git push origin <branchname>
+`git push origin develop`
 
-4. Before submitting code back to the main repository, make sure that code compiles
+5. Before submitting code back to the main repository, make sure that code compiles from the main directory.
 
-        ./scripts/build.sh -c
+`make`
 
-5. submit pull request with a reference to related issue (see [[Link commits to issue|Using-Git#link-commits-to-issues]]); 
-   * also see [github documentation](https://help.github.com/articles/using-pull-requests)
 
-#### Advanced Workflow: A new branch for each change
+6. submit pull request with a reference to related issue; 
+* also see [github documentation](https://help.github.com/articles/using-pull-requests)
 
-1. Make sure you start in master 
 
-        git checkout master
+### Recommended Workflow: A new branch for each change
 
-2. Make sure master is up to date 
+1. Make sure you start in develop 
 
-        git pull upstream master
+`git checkout develop`
 
-2.  Run any tests / make sure that code compiles
+2. Make sure develop is up to date 
 
-* For PEcAn: Build most recent versions of R packages ([`./scripts/build.sh -h` for help)](Installing-PEcAn#update-build-and-check-pecan))
+`git pull upstream develop`
 
-        ./scripts/build.sh
+3. Run the PEcAn MAKEFILE to compile code from the main directory.
 
-* For BETYdb ([see BETY wiki](https://github.com/PecanProject/bety/wiki/Testing#running-the-tests))
+`make`
 
-        rspec
+4. Create a branch and switch to it
 
-3. Create a branch and switch to it
+`git checkout -b <branchname>`
 
-        git checkout -b <branchname>
+5. Work/commit/etc 
 
-4. work/commit/etc 
+`git add <file_that_was_changed.R>`
 
-        git commit -m "<some descriptive information about what was done>"
+`git commit -m "<some descriptive information about what was done>"`
 
-5. Run any tests / make sure that code compiles
+6. Make sure that code compiles and documentation updated. The make document command will run roxygenise. 
 
-For PEcAn:
-        ./scripts/build.sh -c
+`make document`
+`make`
 
-5. Push this branch to your github space 
+7. Push this branch to your github space 
 
-        git push origin <branchname>
+`git push origin <branchname>`
 
-6. submit pull request with [[link commits to issues|Using-Git#link-commits-to-issuess]]; 
-   * also see [explanation in this PecanProject/bety issue](https://github.com/PecanProject/bety/issues/57) and [github documentation](https://help.github.com/articles/using-pull-requests)
+8. submit pull request with [[link commits to issues|Using-Git#link-commits-to-issuess]]; 
+* also see [explanation in this PecanProject/bety issue](https://github.com/PecanProject/bety/issues/57) and [github documentation](https://help.github.com/articles/using-pull-requests)
 
 #### After pull request is merged
 
 1. Make sure you start in master 
 
-        git checkout master
+`git checkout develop`
 
 2. delete branch remotely 
 
-        git push origin --delete <branchname>
+`git push origin --delete <branchname>`
 
 3. delete branch locally 
 
-        git branch -D <branchname>
+`git branch -D <branchname>`
 
 
+#### Fixing a release Branch
 
-#### Link commits to issues
+If you would like to make changes to a release branch, you must follow a different workflow, as the release branch will not contain the latest code on develop and must remain seperate.
 
-You can reference and close issues from comments, pull requests, and commit messages. This should be done when you commit code that is related to or will close/fix an existing issue. 
+1. Fetch upstream remote branches
 
-There are two ways to do this. One easy way is to include the following text in your commit message:
+`git fetch upstream`
 
-* [**Github**](https://github.com/blog/1386-closing-issues-via-commit-messages)
- * to close: "closes gh-xxx" (or syn. close, closed, fixes, fix, fixed)  
- * to reference: just the issue number (e.g. "gh-xxx")
- * avoid "closes #xxx" which will cross-reference Redmine issues 
-* **Redmine**: 
- * to close: "fixes redmine #xxx" (or closes etc.) 
- * to reference: "redmine #xxx"
-* **Bitbucket**: 
- * to close: reference and use web interface!
- * to reference: "re #xxx"
+2. Checkout the correct release branch
 
-Another way is to just add the url to the issue that you are updating. For example, if you are resolving an issue in Redmine, you can simply write the text "resolved by pull request https://github.com/PecanProject/pecan/pull/1" in the comments.
+`git checkout -b release/vX.Y.Z`
 
-### For PEcAn 
+4. Compile Code with make 
 
-```
-./scripts/build.sh -c
-```
+`make`
 
-#### Committing Changes Using Pull Requests
+5. Make changes and commit them
 
-GitHub provides a useful overview of how to submit changes to a project, [Using Pull Requests](https://help.github.com/articles/using-pull-requests).
+`git add <changed_file.R>`
+`git commit -m "Describe changes"`
 
-Once you have added a feature on your local fork of the project that you would like to contribute, these are the steps:
+6. Compile and make roxygen changes
+`make`
+`make document`
 
-* Submit a Pull Request
-* Pull request is reviewed by a member of the PEcAn core group
-* Any comments should be addressed
-* Additional commits are added to the pull request
-* When ready, changes are merged
+7. Commit and push any files that were changed by make document
 
+8. Make a pull request. It is essential that you compare your pull request to the remote release branch, NOT the develop branch.
 
-#### Other Useful Git Commands:
+
+#### Link commits to issues
+
+You can reference and close issues from comments, pull requests, and commit messages. This should be done when you commit code that is related to or will close/fix an existing issue. 
+
+There are two ways to do this. One easy way is to include the following text in your commit message:
+  
+* [**Github**](https://github.com/blog/1386-closing-issues-via-commit-messages)
+* to close: "closes gh-xxx" (or syn. close, closed, fixes, fix, fixed)  
+* to reference: just the issue number (e.g. "gh-xxx") 
 
 
+#### Other Useful Git Commands:
 
 * GIT encourages branching "early and often"
- * First pull from master 
- * Branch before working on feature
- * One branch per feature
- * You can switch easily between branches
- * Merge feature into main line when branch done
-
-            git branch <name of branch>
-            git checkout <name of branch>
-            repeat 
-              write some code
-              commit
-            until done
-
-            git checkout master
-            git merge <name of brach>
-            git push
+* First pull from develop
+* Branch before working on feature
+* One branch per feature
+* You can switch easily between branches
+* Merge feature into main line when branch done
 
 If during above process you want to work on something else, commit all
 your code, create a new branch, and work on new branch. 
@@ -260,35 +242,15 @@ your code, create a new branch, and work on new branch.
 * Delete a branch: `git branch -d <name of branch>`
 * To push a branch git: `push -u origin `<name of branch>`
 * To check out a branch: 
-  ```
-  git fetch origin
-  git checkout --track origin/<name of branch>
-  ```
-
-
-* Get the remote repository locally:
-
-        git clone URL
 
-* To update local repository to latest:
-
-        git pull
-
-* To add new files to the local repository:
-
-        git add <file>
-
-* To commit changes
-
-        git commit <file|folder>
-
-* To update remote repository:
-
-        git push
+```
+git fetch origin
+git checkout --track origin/<name of branch>
+```
 
 * Show graph of commits:
-
-        git log --graph --oneline --all
+  
+`git log --graph --oneline --all`
 
 #### Tags
 
@@ -297,21 +259,21 @@ Git supports two types of tags: lightweight and annotated. For more information
 Lightweight tags are useful, but here we discuss the annotated tags that are used for marking stable versions, major releases, and versions associated with published results. 
 
 The basic command is `git tag`. The `-a` flag means 'annotated' and `-m` is used before a message.  Here is an example:
-
-    git tag -a v0.6 -m "stable version with foo and bar features, used in the foobar publication by Bob"
-
+```  
+  git tag -a v0.6 -m "stable version with foo and bar features, used in the foobar publication by Bob"
+```
 Adding a tag to the a remote repository must be done explicitly with a push, e.g.
-
-    git push v0.6
-    
+```
+git push v0.6
+```
 To use a tagged version, just checkout: 
-
-    git checkout v0.6
-    
+```  
+  git checkout v0.6
+```
 To tag an earlier commit, just append the commit SHA to the command, e.g. 
-
-    git tag -a v0.99 -m "last version before 1.0" 9fceb02
-
+```
+git tag -a v0.99 -m "last version before 1.0" 9fceb02
+```
 
 **Using GitHub** The easiest way to get working with GitHub is by installing the GitHub
 client. For instructions for your specific OS and download of the
@@ -335,11 +297,11 @@ This is a fast way to clone the repository that does not support contributing ne
 
 1.  install Rstudio (www.rstudio.com)
 2.  click (upper right) project
- *   create project
- *   version control
- *   Git - clone a project from a Git Repository
- *   paste https://www.github.com/PecanProject/pecan
- *   choose working dir. for repo
+*   create project
+*   version control
+*   Git - clone a project from a Git Repository
+*   paste https://www.github.com/PecanProject/pecan
+*   choose working dir. for repo
 
 ### For development:
 
@@ -347,37 +309,33 @@ This is a fast way to clone the repository that does not support contributing ne
 2.  create a fork of the PEcAn repository to your own account https://www.github.com/pecanproject/pecan
 3.  install Rstudio (www.rstudio.com)
 4. generate an ssh key 
- * in Rstudio: 
+* in Rstudio: 
   * `Tools -> Options -> Git/SVN -> "create RSA key"`
-  * `View public key -> ctrl+C to copy`
- * in GitHub
-  * go to [ssh settings](https://github.com/settings/ssh)
-  * `-> 'add ssh key' -> ctrl+V to paste -> 'add key'` 
+* `View public key -> ctrl+C to copy`
+* in GitHub
+* go to [ssh settings](https://github.com/settings/ssh)
+* `-> 'add ssh key' -> ctrl+V to paste -> 'add key'` 
 2. Create project in Rstudio
- *  `project (upper right) -> create project -> version control -> Git - clone a project from a Git Repository`
- * paste repository url `git@github.com:<username>/pecan.git>`
- * choose working dir. for repository
-
-References:
------------
-
+*  `project (upper right) -> create project -> version control -> Git - clone a project from a Git Repository`
+* paste repository url `git@github.com:<username>/pecan.git>`
+* choose working dir. for repository
 
-##### Git Documentation
+### References
 
+#### Git Documentation
+  
 * Scott Chacon, ‘Pro Git book’,
 [http://git-scm.com/book](http://git-scm.com/book)
 * GitHub help pages,
 [https://help.github.com](https://help.github.com)/
-* Main GIT page,
+* Main GIT page
 [http://git-scm.com/documentation](http://git-scm.com/documentation)
-* Information about branches,
-[http://nvie.com/posts/a-successful-git-branching-model](http://nvie.com/posts/a-successful-git-branching-model)/
 * Another set of pages about branching,
 [http://sandofsky.com/blog/git-workflow.html](http://sandofsky.com/blog/git-workflow.html)
 * [Stackoverflow highest voted questions tagged "git"](http://stackoverflow.com/questions/tagged/git?sort=votes&pagesize=50)
 
 
-##### GitHub Documentation
+#### GitHub Documentation
 
 When in doubt, the first step is to click the "Help" button at the top of the page.
 
@@ -385,4 +343,4 @@ When in doubt, the first step is to click the "Help" button at the top of the pa
 Scott Chacon (Git evangelist and Ruby developer working on GitHub.com)
 * [GitHub FAQ](https://help.github.com/)
 * [Using Pull Requests](https://help.github.com/articles/using-pull-requests)
-* [SSH Keys](https://help.github.com/articles/generating-ssh-keys)
\ No newline at end of file
+* [SSH Keys](https://help.github.com/articles/generating-ssh-keys)
diff --git a/book_source/05_developer_guide/03_git/02_Github-issues.Rmd b/book_source/05_developer_guide/03_git/02_Github-issues.Rmd
index 33f986cb37e..5cf7fab6057 100755
--- a/book_source/05_developer_guide/03_git/02_Github-issues.Rmd
+++ b/book_source/05_developer_guide/03_git/02_Github-issues.Rmd
@@ -82,7 +82,7 @@ through UI libraries, hardcopy on David’s bookshelf)\
 
 #### Ideally, non-trivial code changes will be linked to an issue and a commit.
 
-This requires creating issues for each task, making small commits, and referencing the issue within your commit message. Issues can be created [on GitHub](https://github.com/PecanProject/pecan/issues/new). These issues can be linked to commits by adding text such as `fixes gh-5` (see [[Using Git During Development|Using-Git#during-development]]).
+This requires creating issues for each task, making small commits, and referencing the issue within your commit message. Issues can be created [on GitHub](https://github.com/PecanProject/pecan/issues/new). These issues can be linked to commits by adding text such as `fixes gh-5`).
 
 Rationale: This workflow is a small upfront investment that reduces error and time spent re-creating and debugging errors. Associating issues and commits, makes it easier to identify why a change was made, and potential bugs that could arise when the code is changed. In addition, knowing which issue you are working on clarifies the scope and objectives of your current task. 
 
diff --git a/book_source/06_reference/01_pecan_standards.Rmd b/book_source/06_reference/01_pecan_standards.Rmd
index 216d5355074..120239d695c 100644
--- a/book_source/06_reference/01_pecan_standards.Rmd
+++ b/book_source/06_reference/01_pecan_standards.Rmd
@@ -5,8 +5,96 @@
 * New formats can be defined on the ['formats' page of BETYdb](http://betydb.org/formats)
 * After creating a new format, the contents should be defined by specifying the BETYdb variable name and the name used in the file/
 
-### Outputs
+### Input Standards
+
+####Meterology Standards
+##### Dimensions:
+
+
+|CF standard-name | units |
+|:------------------------------------------|:------|
+| time | days since 1700-01-01 00:00:00 UTC|
+| longitude | degrees_east|
+| latitude |degrees_north|
+
+General Note: dates in the database should be date-time (preferably with timezone), and datetime passed around in PEcAn should be of type POSIXct.
+
+
+##### The variable names should be `standard_name`
+```{r, echo=FALSE,warning=FALSE,message=FALSE}
+names<-c("<b>air_temperature</b>", "air_temperature_max", "air_temperature_min", "<b>air_pressure</b>", 
+         "mole_fraction_of_carbon_dioxide_in_air", "moisture_content_of_soil_layer", "soil_temperature ",
+         "relative_humidity", "<b>specific_humidity</b>", "water_vapor_saturation_deficit","<b>surface_downwelling_longwave_flux_in_air</b>",
+         "<b>surface_downwelling_shortwave_flux_in_air</b>", "surface_downwelling_photosynthetic_photon_flux_in_air",
+         "<b>precipitation_flux</b>", "  ","wind_speed","<b>eastward_wind</b>", "<b>northward_wind</b>")
+
+units <-c("K","K","K","Pa","mol/mol","kg m-2","K","%","1","Pa","W m-2","W m-2","mol m-2 s-1", "kg m-2 s-1", "degrees", "m/s", "m/s", "m/s")
+
+bety <- c("airT", "","", "air_pressure","","","soilT","relative_humidity","specific_humidity","VPD", "same","solar_radiation","PAR",
+          "cccc", "wind_direction", "Wspd", "eastward_wind", "northward_wind")
+
+isimip <-c("tasAdjust", "tasmaxAdjust", "tasminAdjust","" ,"" ,"" ,"" ,"rhurs","NA", "","rldsAdjust","rsdsAdjust","", "prAdjust","","","","")
+cruncep <- c("tair","NA","NA","","","","","NA","qair","","lwdown","swdown","","rain","","","","")
+narr <- c("air","tmax","tmin","","","","","rhum","shum","","dlwrf","dswrf","","acpc","","","","")
+ameriflux <- c("TA(C)","" ,"" , "PRESS (KPa)","CO2","","TS1(NOT DONE)",
+               "RH","CALC(RH)","VPD(NOT DONE)","Rgl","Rg","PAR(NOT DONE)","PREC","WD","WS","CALC(WS+WD)","CALC(WS+WD)")
+
+in_tab<-cbind(names,units,bety,isimip,cruncep,narr,ameriflux)
+colnames(in_tab)<- c("CF standard-name","units","BETY","Isimip","CRUNCEP","NARR", "Ameriflux")
+install.packages("DT")
+library(DT)
+datatable(in_tab, escape = FALSE,
+              extensions = 'FixedColumns',
+              options = list(
+                dom = 't',
+                scrollX = TRUE,
+                fixedColumns = TRUE
+              ))
+
+```
+
+* preferred variables indicated in bold
+* wind_direction has no CF equivalent and should not be converted, instead the met2CF functions should convert wind_direction and wind_speed to eastward_wind and northward_wind
+* standard_name is CF-convention standard names
+* units can be converted by udunits, so these can vary (e.g. the time denominator may change with time frequency of inputs)
+* soil moisture for the full column, rather than a layer, is soil_moisture_content
+* A full list of PEcAn standard variable names, units and dimensions can be found here: https://github.com/PecanProject/pecan/blob/develop/base/utils/data/standard_vars.csv
+
+
+For example, in the [MsTMIP-CRUNCEP](https://www.betydb.org/inputs/280) data, the variable `rain` should be `precipitation_rate`.
+We want to standardize the units as well as part of the `met2CF.<product>` step. I believe we want to use the CF "canonical" units but retain the MsTMIP units any time CF is ambiguous about the units.
+
+The key is to process each type of met data (site, reanalysis, forecast, climate scenario, etc) to the exact same standard. This way every operation after that (extract, gap fill, downscale, convert to a model, etc) will always have the exact same inputs. This will make everything else much simpler to code and allow us to avoid a lot of unnecessary data checking, tests, etc being repeated in every downstream function.
+
+#### Soils and Vegetation Inputs
+
+##### Soil Data 
+
+Check out the [Soil Data] section on more into on creating a standard soil data file.
+
+##### Vegetation Data
+
+Check Out the [Vegetation Data] section on more info on creating a standard vegetation data file
+
+
+
+### Output Standards
 
 * created by `model2netcdf` functions
 * based on format used by [MsTMIP](http://nacp.ornl.gov/MsTMIP_variables.shtml)
-* Can be seen at [Model Variables]
+* Can be seen at HERE
+
+We originally used the [MsTMIP](http://nacp.ornl.gov/MsTMIP_variables.shtml) conventions. Since then, we've added the PaLEON variable conventions to our standard as well. If a variable isn't in one of those two, we stick to the CF conventions.
+
+```{r, echo=FALSE,warning=FALSE,message=FALSE}
+data("standard_vars", package = "PEcAn.utils")
+install.packages("DT")
+library(DT)
+DT::datatable(standard_vars,
+          extensions = 'FixedColumns',
+            options = list(
+            dom = 't',
+            scrollX = TRUE,
+            fixedColumns = TRUE
+          ))
+```
diff --git a/book_source/06_reference/02_models/template.Rmd b/book_source/06_reference/02_models/01_template.Rmd
similarity index 100%
rename from book_source/06_reference/02_models/template.Rmd
rename to book_source/06_reference/02_models/01_template.Rmd
diff --git a/book_source/06_reference/02_models/ED2-configuration.Rmd b/book_source/06_reference/02_models/ED2-configuration.Rmd
deleted file mode 100755
index 471f874d34e..00000000000
--- a/book_source/06_reference/02_models/ED2-configuration.Rmd
+++ /dev/null
@@ -1,70 +0,0 @@
-## ED2 Configuration
-
-ED2 is configured using 2 files which are placed in the run folder.
-
-* **ED2IN** : template for this file is located at models/ed/inst/ED2IN.\<revision\>. The values in this template that need to be modified are described below and are surrounded with @ symbols.
-* **config.xml** : this file is generated by PEcAn. Some values are stored in the pecan.xml in \<pfts\>\<pft\>\<constants\> section as well as in \<model\> section.
-
-An example of the template can be found in [ED2IN.r82](https://github.com/PecanProject/pecan/blob/master/models/ed/inst/ED2IN.r82)
-
-### ED2IN configuration variables
-
-**@ENSNAME@** : run id of the simulation, used in template for NL%EXPNME
-
-**@START_MONTH@** : start of simulation UTC time, from \<run\>\<start.date\>, used in template for NL%IMONTHA  
-**@START_DAY@** : start of simulation UTC time, from \<run\>\<start.date\>, used in template for NL%IDATEA  
-**@START_YEAR@** : start of simulation UTC time, from \<run\>\<start.date\>, used in template for NL%IYEARA  
-**@END_MONTH@** : end of simulation UTC time, from \<run\>\<end.date\>, used in template for NL%IMONTHZ  
-**@END_DAY@** : end of simulation UTC time, from \<run\>\<end.date\>, used in template for NL%IDATEZ  
-**@END_YEAR@** : end of simulation UTC time, from \<run\>\<end.date\>, used in template for NL%IYEARZ  
-
-**@SITE_LAT@** : site latitude location, from \<run\>\<site\>\<lat\>, used in template for NL%POI_LAT  
-**@SITE_LON@** : site longitude location, from \<run\>\<site\>\<lon\>, used in template for NL%POI_LON  
-
-**@SITE_MET@** : met header location, from \<run\>\<site\>\<met\>, used in template for NL%ED_MET_DRIVER_DB  
-**@MET_START@** : first year of met data, from \<run\>\<site\>\<met.start\>, used in template for NL%METCYC1  
-**@MET_END@** : last year of met data, from \<run\>\<site\>\<met.end\>, used in template for NL%METCYCF  
-
-**@PHENOL_SCHEME@** : phenology scheme, if this variabe is 1 the following 3 fields will be used, otherwise they will be set to empty strings, from \<model\>\<phenol.scheme\>, used in template for NL%IPHEN_SCHEME  
-**@PHENOL_START@** : first year for phenology, from \<model\>\<phenol.start\>, used in template for NL%IPHENYS1 and NL%IPHENYF1  
-**@PHENOL_END@** : last year for phenology, from \<model\>\<phenol.end\>, used in template for NL%IPHENYSF and NL%IPHENYFF  
-**@PHENOL@** : path and prefix of the prescribed phenology data, from \<model\>\<phenol\>, used in template for NL%PHENPATH  
-
-**@SITE_PSSCSS@** :  path and prefix of the previous ecosystem state, from \<model\>\<psscss\>, used in template for NL%SFILIN  
-**@ED_VEG@** : path and prefix of the vegetation database, used only to determine the land/water mask, from \<model\>\<veg\>, used in template for NL%VEG_DATABASE  
-**@ED_SOIL@** : path and prefix of the soil database, used to determine the soil type, from \<model\>\<soil\>, used in template for NL%SOIL_DATABASE  
-**@ED_INPUTS@** : input directory with dataset to initialise chilling degrees and growing degree days, which is used to drive the cold-deciduous phenology, from \<model\>\<inputs\>, used in template for NL%THSUMS_DATABASE  
-
-**@FFILOUT@** : path and prefix for analysis files, generated from \<run\>\<host\>\<outdir\>/run.id/analysis,  used in template for NL%FFILOUT  
-**@SFILOUT@** : path and prefix for history files, generated from \<run\>\<host\>\<outdir\>/run.id/history,  used in template for NL%SFILOUT  
-
-**@CONFIGFILE@** : XML file containing additional parameter settings, this is always "config.xml", used in template for NL%IEDCNFGF  
-
-**@OUTDIR@** :  location where output files are written (**without the runid**), from \<run\>\<host\>\<outdir\>, should not be used.  
-**@SCRATCH@** : local scratch space for outputs, generated `/scratch/\<username\>/run$scratch`, should not be used right now since it only works on ebi-cluster  
-
-**ED Computation HPC**
-
-**TACC lonestar**
-
-```bash
-module load hdf5
-curl -o ED.r82.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.tgz
-tar zxf ED.r82.tgz
-rm ED.r82.tgz
-cd ED.r82/ED/build/bin
-curl -o include.mk.lonestar http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.lonestar
-make OPT=lonestar
-```
-
-**TACC stampede**
-
-```bash
-module load hdf5
-curl -o ED.r82.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.tgz
-tar zxf ED.r82.tgz
-rm ED.r82.tgz
-cd ED.r82/ED/build/bin
-curl -o include.mk.stampede http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.stampede
-make OPT=stampede
-```
diff --git a/book_source/06_reference/02_models/ed.Rmd b/book_source/06_reference/02_models/ed.Rmd
index ca6f030a96b..2e07467a682 100644
--- a/book_source/06_reference/02_models/ed.Rmd
+++ b/book_source/06_reference/02_models/ed.Rmd
@@ -1,26 +1,46 @@
 ## ED
 
-| Model Information ||
-| -- | -- |
-| Home Page | http://moorcroftlab.oeb.harvard.edu/ |
-| Source Code | https://github.com/EDmodel/ED2 |
-| License |  |
-| Authors | Paul Moorcroft, ... |
-| PEcAn Integration | Michael Dietze, Rob Kooper |
+| Model Information |                                      |
+| --                | --                                   |
+| Home Page         | http://moorcroftlab.oeb.harvard.edu/ |
+| Source Code       | https://github.com/EDmodel/ED2       |
+| License           |                                      |
+| Authors           | Paul Moorcroft, ...                  |
+| PEcAn Integration | Michael Dietze, Rob Kooper           |
 
-**Introduction**
+### Introduction
 
 Introduction about ED model
 
-**PEcAn configuration file additions**
-
-Should list the model specific additions to the PEcAn file here
-
-**Model specific input files**
+### PEcAn configuration file additions
+
+The following sections of the PEcAn XML are relevant to the ED model:
+
+- `model`
+  - `id` -- BETY model ID. Each ID corresponds to a different revision of ED (see below)
+  - `revision` -- The revision (a.k.a. release) number of ED (e.g. "r82"). "rgit" indicates the latest code on the ED repository
+  - `ed2in` -- Path and filename of the ED2IN configuration file
+  - `start.date` -- Run start date
+  - `end.date` -- Run end date
+  - `phenol.scheme`
+  - `phenol`
+  - `phenol.start`
+  - `phenol.end`
+  - `ed2in_tags` -- Named list of additional tags in the ED2IN to be modified. These modifications override any of those set by the standard PEcAn workflow.
+  - `jobtemplate`
+  - `prerun`
+  - `postrun`
+  - `binary`
+- `run/site`
+  - `lat` -- Latitude coordinate of site
+  - `lon` -- Longitude coordinate of site
+- `inputs/met/path` -- Path to ED_MET_DRIVER_HEADER file
+
+### Model specific input files
 
 List of inputs required by model, such as met, etc.
 
-**Model configuration files**
+### Model configuration files
 
 ED2 is configured using 2 files which are placed in the run folder.
 
@@ -63,17 +83,17 @@ The ED2IN template can contain the following variables. These will be replaced w
 * **@CONFIGFILE@** : XML file containing additional parameter settings, this is always "config.xml", used in template for NL%IEDCNFGF  
 
 * **@OUTDIR@** :  location where output files are written (**without the runid**), from \<run\>\<host\>\<outdir\>, should not be used.  
-* **@SCRATCH@** : local scratch space for outputs, generated /scratch/\<username\>/run$scratch, should not be used right now since it only works on ebi-cluster  
+* **@SCRATCH@** : local scratch space for outputs, generated /scratch/\<username\>/run\$scratch, should not be used right now since it only works on ebi-cluster  
 
-**Installation notes**
+### Installation notes
 
 This section contains notes on how to compile the model. The notes for the VM might work on other machines or configurations as well.
 
-**VM**
+#### VM
 
-** BU geo**
+#### BU geo
 
-**TACC lonestar**
+#### TACC lonestar
 
 ```bash
 module load hdf5
@@ -85,7 +105,7 @@ curl -o include.mk.lonestar http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk
 make OPT=lonestar
 ```
 
-**TACC stampede**
+#### TACC stampede
 
 ```bash
 module load hdf5
diff --git a/book_source/06_reference/02_models/model_index.Rmd b/book_source/06_reference/02_models/model_index.Rmd
index b1b8ddcad8b..d13909a5507 100644
--- a/book_source/06_reference/02_models/model_index.Rmd
+++ b/book_source/06_reference/02_models/model_index.Rmd
@@ -7,14 +7,14 @@ This section will contain information about all models and output variables that
 | [BioCro] | Yes | Yes | Yes| No |
 | [CLM]| No | No | No| No |
 | [DALEC]| Yes | Yes | Yes| No |
-| [ED]| Yes | Yes | Yes| No |
+| [ED]| Yes | Yes | Yes| Yes |
 | FATES | No | Yes | | No|
 | [GDAY] | No | No | No| No |
 | [LINKAGES] | Yes | Yes | Yes| Yes |
 | [LPJ-GUESS]| Yes | Yes | No | No |
 | [MAESPA]| Yes | Yes | No | No |
 | [PRELES] | Yes | Yes | Partially | No |
-| [Sipnet]| Yes | Yes | Yes| No |
+| [Sipnet]| Yes | Yes | Yes| Yes |
 
 
 **Output Variables**
diff --git a/book_source/06_reference/02_models/variables.Rmd b/book_source/06_reference/02_models/variables.Rmd
deleted file mode 100644
index 55e3382df5e..00000000000
--- a/book_source/06_reference/02_models/variables.Rmd
+++ /dev/null
@@ -1,9 +0,0 @@
-## Model Variables
-
-We originally used the [MsTMIP](http://nacp.ornl.gov/MsTMIP_variables.shtml) conventions. Since, We've added the PaLEON variable conventions to our standard as well. If a variable isn't in one of those two, we stick to the CF conventions.
-```{r, echo=FALSE}
-data("standard_vars", package = "PEcAn.utils")
-install.packages("DT")
-library(DT)
-datatable(standard_vars)
-```
diff --git a/book_source/06_reference/04_docker/01-introduction.Rmd b/book_source/06_reference/04_docker/01-introduction.Rmd
new file mode 100644
index 00000000000..a2c27d20398
--- /dev/null
+++ b/book_source/06_reference/04_docker/01-introduction.Rmd
@@ -0,0 +1,93 @@
+
+# What is Docker?
+
+Docker is a relativly new technology to encapsulate software as a service. This allow for simple distribution of software since all depedencies are installed as well. Unlike traditional VM's, in docker each component will only run a single service/process and is build on top of existing services provided by the host OS (such as disk access, networking, memory managment etc.). To create a complex system such as PEcAn, we take multiple of these components and link them together.
+
+A common term used in docker is that of an image or container. This refers to all the software needed to run a single service, including the service itself, bundled and installed. The difference between an image and a container is that a container is the execution of an image  (in object oriented programming, an image is a class and a container is an instance of the class). When creating docker images a good mental model to follow is to have a single process per container, and have multiple containers together create an application.
+
+For example in the case of BETY we will need at least two processes, the database and the BETY web application. When distributing a VM with the BETY application we will need to create VM with a base OS (in our case this would be Ubuntu), a database (PostgreSQL) and the BETY web-app (ruby). This requires us to install the dependencies and applications. In the case of Docker, we will need a container for the database (standard PostGIS container) as well as the custom BETY container (build on top of the existing Ruby container), both running on a host OS (coreOS for example). When starting BETY we start the PostGIS container first, and next start the BETY container telling it where it can find the PostGIS container. To upgrade we stop the BETY container, download the latest version, tell it to upgrade the database, and start the BETY container. There is no need to install new dependencies for BETY since they are all shipped as part of the container.
+
+The containers that work together to build an application, BETY or PEcAn, is often referred to as a stack. Using docker we can have multiple of these stacks run in  parallel. For example we can have two PEcAn stacks running next to each other. To separate these stacks each of them is given a unique name, and all containers are prefixed with this name. Inside these stacks the containers can talk with each other using the generic names, for example they can use postgres to talk to the postgres database. To prevent different stacks from talking to the wrong container, each stack has its own network. This will only allow those containers in the same network to talk to each other. Finally when starting the stack you can define explicitly what external port maps to what port inside the containers, or let docker pick them. In the case of PEcAn we will automatically connect all containers to the pecan network.
+
+In the case of PEcAn we want to use this ability to ship all dependencies as part of the image to make it easier for the users to download a new model, since the image will contain everything that is needed to run the model as part of PEcAn. If two models depend on different versions of the library we no longer need to worry on how to install these models next to each other and creating issues with the libraries used. Each image will contain only a single model and all libraries needed by that model.
+
+The next section, [architecture](02-architecture.md) will go in more detail on the containers that make up the PEcAn framework and how these containers interact with each other.
+
+## Working with Docker
+
+To run an image you will use the docker command line, for example:
+
+```bash
+docker run \
+	--detach \
+	--rm \
+	--name postgresql \
+	--network pecan \
+	--publish 9876:5432 \
+	--volume ${PWD}/postgres:/var/lib/postgresql/data \
+	mdillon/postgis:9.6-alpine
+```
+
+This will start for example the PostgreSQL+PostGIS container. The options used are:
+
+- `--detach` makes the container run in the background. 
+- `--rm` removes the container when it is finished (make sure to use the volume below).
+- `--name` the name of the container, also the hostname of the container which can be used by other docker containers in the same network inside docker.
+- `--network pecan` the network that the container should be running in, this leverages of network isolation in docker and allows this container to be connected to by others using the postgresql hostname.
+- `--publish` exposes the port to the outside world, this is like ssh, and maps port 9876 to port 5432 in the docker container
+- `--volume` maps a folder on your local machine to the machine in the container. This allows you to save data on your local machine. 
+- `mdillon/postgis:9.6-alpine` is the actual image that will be run, in this case it comes from the group/person mdillon, the container is postgis and the version 9.6-alpine (version 9.6 build on alpine linux).
+
+Other options that might be used:
+
+- `--link` makes it such that two containers can see each other.
+
+
+- `--tty` allocate a pseudo-TTY to send stdout and stderr back to the console.
+- `--interactive` keeps stdin open so the user can interact with the application running.
+- `--env` sets environment variables, these are often used to change the behavior of the docker container.
+
+To see a list of all running containers you can use the following command:
+
+```bash
+docker ps
+```
+
+To see the log files of this container you use the following command (you can either use their name or id as returned by `docker ps`). The -f flag will follow the stdout/stderr from the container, use Ctrl-C to stop following the stdout/stderr.
+
+```bash
+docker logs -f postgresql
+```
+
+To stop a running container use:
+
+```
+docker stop postgresql
+```
+
+Containers that are started without the `--detach` can be stopped by pressing Ctrl-C, if you have started containers in the background they will keep on running until the machine is restarted or the container is stopped using `docker stop`
+
+## Working with docker-compose
+
+In the case of PEcAn we have multiple docker containers that we want to work together. To help with this we can use docker-compose. This will take a file as input that lists all the containers that make up the application and the dependencies between these containers. For example in the case of BETY we need the postgres container as well as the BETY container. 
+
+```yaml
+version: "3"
+services:
+  postgres:
+    image: mdillon/postgis:9.5
+  bety:
+    image: pecan/bety
+    depends_on:
+      - postgres
+```
+
+This simple file allows us to bring up a full BETY application with both database and BETY application. The BETY app will not be brought up until the database container has started.
+
+You can now start this application using:
+
+```
+docker-compose up
+```
+
+This will start the application, and you will see the log files for the 2 different containers.
\ No newline at end of file
diff --git a/book_source/06_reference/04_docker/architecture.Rmd b/book_source/06_reference/04_docker/02-architecture.Rmd
similarity index 93%
rename from book_source/06_reference/04_docker/architecture.Rmd
rename to book_source/06_reference/04_docker/02-architecture.Rmd
index a8294a63754..755896879d1 100644
--- a/book_source/06_reference/04_docker/architecture.Rmd
+++ b/book_source/06_reference/04_docker/02-architecture.Rmd
@@ -1,4 +1,3 @@
-**THIS IS EXPERIMENTAL DO NOT USE THIS IN PRODUCTION SUBJECT TO CHANGE**
 
 # PEcAn Docker Architecture
 
@@ -14,8 +13,8 @@ The PEcAn framework containers consist of multiple unique ways to interact with
 
 - PEcAn shiny hosts the shiny applications developed and will interact with the database to get all information necessary to display
 - PEcAn rstudio is a rstudio environment with the PEcAn libraries preloaded. This allows for prototyping of new algorithms that can be used as part of the PEcAn framework later.
-- PEcAn web allows the user to create a new PEcAn workflow. The workflow is stored in the database, and the models are exectued by the model containers.
-- PEcAn cli will allow the user to give a pecan.xml file that will be executed by the PEcAn framework.  The workflow created from the XML file is stored in the database, and the models are exectued by the model containers.
+- PEcAn web allows the user to create a new PEcAn workflow. The workflow is stored in the database, and the models are executed by the model containers.
+- PEcAn cli will allow the user to give a pecan.xml file that will be executed by the PEcAn framework.  The workflow created from the XML file is stored in the database, and the models are executed by the model containers.
 
 The model containers contain the actual models that are executed as well as small wrappers to make them work in the PEcAn framework. The containers will run the model based on the parameters received from the message bus and convert the outputs back to the standard PEcAn output format. Once the container is finished processing a message it will immediatly get the next message and start processing it.
 
diff --git a/book_source/06_reference/04_docker/03-quickstart.Rmd b/book_source/06_reference/04_docker/03-quickstart.Rmd
new file mode 100644
index 00000000000..6b58036f27f
--- /dev/null
+++ b/book_source/06_reference/04_docker/03-quickstart.Rmd
@@ -0,0 +1,78 @@
+# Quickstart for Docker and PEcAn.
+
+This is a short documentation on how to start with Docker and PEcAn. This will not go into much detail about about how to use docker.
+
+## Install Docker
+
+You will need to install docker first. See https://www.docker.com/community-edition#/download
+
+## Running PEcAn
+
+We will use a yaml file to describe the containers that we make up, This yaml file is called [docker-compose.yml](https://github.com/PecanProject/pecan/blob/master/docker-compose.yml). Before you get started you will need to download this file first. Place this file somewhere on your machine and cd to the folder that contains this file.
+
+Next we will start the docker containers to start Docker. Since both BETY and PEcAn depend on a populated database we will first start the database and populate it with some data. This only needs to be done once, if this is done already, you can skip this step and go to the next step
+
+```bash
+docker-compose -p pecan up -d postgres
+docker run -ti --rm \
+	--network pecan_pecan \
+	hub.ncsa.illinois.edu/pecan/bety:latest initialize
+docker run -ti --rm \
+	--network pecan_pecan \
+    --volume pecan_pecan:/data \
+    hub.ncsa.illinois.edu/pecan/data:develop
+```
+
+If this is finished (or you had done this in the past), we can start the full stack:
+
+```bash
+docker-compose -p pecan up -d
+```
+
+This will start all the containers marked green in the architecture diagram. Once this is done you have a working instance of PEcAn. Following is a list of URL's you can visit
+
+| URL                          | Service                                               |
+| ---------------------------- | ----------------------------------------------------- |
+| http://localhost:8000/pecan/ | PEcAn web GUI                                         |
+| http://localhost:8000/bety/  | BETY web application                                  |
+| http://localhost:8000/minio/ | File browser (username carya, password illinois)      |
+| http://localhost:8000/       | RabbitMQ (username guest, password guest)             |
+| http://localhost:8001/       | Træfik, webserver shows mapping from url to container |
+
+## Testing PEcAn
+
+To test PEcAn you can use the following curl statement, or use the webpage to submit a request:
+
+```bash
+curl -v -X POST \
+    -F 'hostname=docker' \
+    -F 'modelid=5000000002' \
+    -F 'sitegroupid=1' \
+    -F 'siteid=772' \
+    -F 'sitename=Niwot Ridge Forest/LTER NWT1 (US-NR1)' \
+    -F 'pft[]=temperate.coniferous' \
+    -F 'start=2004/01/01' \
+    -F 'end=2004/12/31' \
+    -F 'input_met=5000000005' \
+    -F 'email=' \
+    -F 'notes=' \
+    'http://localhost:8000/pecan/04-runpecan.php'
+```
+
+This should return some text with in there `Location:` this is shows the workflow id, you can prepend http://localhost:8000/pecan/ to the front of this, for example: http://localhost:8000/pecan/05-running.php?workflowid=99000000001. Here you will be able to see the progress of the workflow.
+
+To see what is happening behind the scenes you can use look at the log file of the specific docker containers, once of interest are `pecan_executor_1` this is the container that will execute a single workflow and `pecan_sipnet_1` which executes the sipnet mode. To see the logs you use `docker logs pecan_executor_1` Following is an example output:
+
+```
+2018-06-13 15:50:37,903 [MainThread     ] INFO    : pika.adapters.base_connection - Connecting to 172.18.0.2:5672
+2018-06-13 15:50:37,924 [MainThread     ] INFO    : pika.adapters.blocking_connection - Created channel=1
+2018-06-13 15:50:37,941 [MainThread     ] INFO    : root -  [*] Waiting for messages. To exit press CTRL+C
+2018-06-13 19:44:49,523 [MainThread     ] INFO    : root - b'{"folder": "/data/workflows/PEcAn_99000000001", "workflowid": "99000000001"}'
+2018-06-13 19:44:49,524 [MainThread     ] INFO    : root - Starting job in /data/workflows/PEcAn_99000000001.
+2018-06-13 19:45:15,555 [MainThread     ] INFO    : root - Finished running job.
+```
+
+This shows that the executor connects to RabbitMQ, waits for messages. Once it picks up a message it will print the message, and execute the workflow in the folder passed in with the message. Once the workflow (including any model executions) is finished it will print Finished. The log file for `pecan_sipnet_1` is very similar, in this case it runs the `job.sh` in the run folder.
+
+To run multiple executors in parallel you can duplicate the executor section in the docker-compose file and just rename it from executor to executor1 and executor2 for example. The same can be done for the models. To make this easier it helps to deploy the containers using kubernetes allowing to easily scale up and down the containers.
+
diff --git a/book_source/06_reference/04_docker/04-models.Rmd b/book_source/06_reference/04_docker/04-models.Rmd
new file mode 100644
index 00000000000..d4b6c8a48a5
--- /dev/null
+++ b/book_source/06_reference/04_docker/04-models.Rmd
@@ -0,0 +1,160 @@
+
+# Dockerfiles for Models
+
+In general we try to minimize the size of the images. To be able to do this we split the process of creating the building of the model images into two pieces (or leverage of an image that exists from the original model developers). If you look at the example Dockerfile you will see that there are 2 sections, the first section will build the model binary, the second section will build the actual PEcAn model, which copies the binary from the first section.
+
+This is an example of how the ED2 model is build. This will install all the packages needed to build ED2 model, gets the latest version from GitHub and builds the model.
+
+The second section will create the actual model executor. This will leverage the PEcAn executor image that has PEcAn already installed as well as the python code to listen for messages and run the actual model code. This will install some additional packages needed by the model binary (more about that below) as well as set the `MODEL_TYPE` and `MODEL_VERSION` variables. These variables will be used to specify the queue that the model will listen on for any execution requests.
+
+It is important that the `MODEL_TYPE` and `MODEL_VERSION` match what is in the BETY database. The PEcAn code will use what is in the BETY database to send out a message to a specfic worker queue, if you do not set these variables correctly your model executor will pick up messages for the wrong model.
+
+To build the docker image, we use a Dockerfile (see example below) and run the following command. This command will expect the Dockerfile.ed2 to live in the current folder. It will also copy the content of the current folder and make it available to the build process (in this example we do not need any additional files). The image will be named pecan/model-ed2, since we do not specify the exact version it will be atomically be named `pecan/model-ed2:latest`.
+
+````bash
+docker build \
+	--tag pecan/model-ed2 \
+	--file Dockerfile.ed2 \
+	.
+````
+
+Example of a Dockerfile, in this case to build the ED2 model.
+
+```dockerfile
+# ----------------------------------------------------------------------
+# FIRST STAGE : BUILD MODEL BINARY
+# ----------------------------------------------------------------------
+FROM debian:testing as model-binary
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+
+# install dependencies
+RUN apt-get update \
+    && apt-get install -y \
+       build-essential \
+       curl \
+       gfortran \
+       git \
+       libhdf5-dev \
+       libopenmpi-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# download, unzip and build ed2
+WORKDIR /src
+RUN git clone https://github.com/EDmodel/ED2.git \
+    && cd ED2/ED/build \
+    && curl -o make/include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.Linux \
+    && if [ "${MODEL_VERSION}" != "git" ]; then git checkout ${MODEL_VERSION}; fi \
+    && ./install.sh -g -p VM
+
+########################################################################
+
+# ----------------------------------------------------------------------
+# SECOND STAGE : BUILD PECAN FOR MODEL
+# ----------------------------------------------------------------------
+FROM pecan/executor:latest
+
+# ----------------------------------------------------------------------
+# INSTALL MODEL SPECIFIC PIECES
+# ----------------------------------------------------------------------
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+       libgfortran5 \
+       libopenmpi3 \
+    && rm -rf /var/lib/apt/lists/*
+
+# ----------------------------------------------------------------------
+# SETUP FOR SPECIFIC MODEL
+# ----------------------------------------------------------------------
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+
+# variables to store in docker image
+ENV APPLICATION="./job.sh" \
+    MODEL_TYPE="ED2" \
+    MODEL_VERSION="${MODEL_VERSION}" \
+    RABBITMQ_QUEUE="${MODEL_TYPE}_${MODEL_VERSION}"
+
+# COPY model binary
+COPY --from=model-binary /src/ED2/ED/build/ed_2.1-opt /usr/local/bin/ed2.${MODEL_VERSION}
+```
+
+Once the model has build and is working we can add it to the PEcAn stack and be able to use this model in the web interface. There are two methods to start this new model. First, we can add it to the `docker-compose.yml` file and start the container using `docker-compose -p pecan -d up`.
+
+```yaml
+  sipnet:
+    image: pecan/model-ed2
+    networks:
+      - pecan
+    volumes:
+      - pecan:/data
+    depends_on:
+       - rabbitmq
+    restart: unless-stopped
+```
+
+Alternatively we can start the container manually using the following command.
+
+```bash
+docker run \
+	--detach \
+	--rm \
+	--name pecan-ed2 \
+	--networks pecan_pecan \
+	--volume pecan_pecan:/data
+	pecan/model-ed2
+```
+
+## Common problems
+
+Following are some solutions for common problems that you might encounter when building the docker images for a model.
+
+### Debugging missing libraries
+
+When building the model binary it might require specific libraries to be installed. In the second stage the model binary is copied into a new image, which could result in the binary missing specific libraries. In the case of the ED2 model the following was used to find the libraries that are needed to be installed (libgfortran5 and libopenmpi3).
+
+The first step is to build the model using the Dockerfile (in this case the ap-get install was missing in the second stage).
+
+
+```
+Step 5/9 : RUN git clone https://github.com/EDmodel/ED2.git     && cd ED2/ED/build     && curl -o make/include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s`     && if [ "${MODEL_VERSION}" != "git" ]; then git checkout ${MODEL_VERSION}; fi     && ./install.sh -g -p VM
+... LOTS OF OUTPUT ...
+make[1]: Leaving directory '/src/ED2/ED/build/bin-opt-E'
+Installation Complete.
+Removing intermediate container a53eba9a8fc1
+ ---> 7f23c6302130
+Step 6/9 : FROM pecan/executor:latest
+ ---> f19d81b739f5
+... MORE OUTPUT ...
+Step 9/9 : COPY --from=model-binary /src/ED2/ED/build/ed_2.1-opt /usr/local/bin/ed2.${MODEL_VERSION}
+ ---> 07ac841be457
+Successfully built 07ac841be457
+Successfully tagged pecan/pecan-ed2:latest
+```
+
+At this point we have created a docker image with the binary and all PEcAn code that is needed to run the model. Some models (especially those build as native code) might be missing additional packages that need to be installed in the docker image. To see if all libraries are installed for the binary.
+
+```bash
+> docker run -ti --rm pecan/pecan-ed2 /bin/bash
+root@8a95ee8b6b47:/work# ldd /usr/local/bin/ed2.git  | grep "not found"
+    libmpi_usempif08.so.40 => not found
+    libmpi_usempi_ignore_tkr.so.40 => not found
+    libmpi_mpifh.so.40 => not found
+    libmpi.so.40 => not found
+    libgfortran.so.5 => not found
+```
+
+Start the build container again (this is the number before the line FROM pecan/executor:latest, 7f23c6302130 in the example), and find the missing libraries listed above (for example libmpi_usempif08.so.40):
+
+```bash
+> docker run --rm -ti 7f23c6302130
+root@e716c63c031f:/src# dpkg -S libmpi_usempif08.so.40
+libopenmpi3:amd64: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so.40.10.1
+libopenmpi3:amd64: /usr/lib/x86_64-linux-gnu/libmpi_usempif08.so.40.10.1
+libopenmpi3:amd64: /usr/lib/x86_64-linux-gnu/libmpi_usempif08.so.40
+```
+
+This shows the pages is libopenmpi3 that needs to be installed, do this for all missing packages, modify the Dockerfile and rebuild. Next time you run the ldd command there should be no more packages being listed.
\ No newline at end of file
diff --git a/book_source/06_reference/04_docker/introduction.Rmd b/book_source/06_reference/04_docker/introduction.Rmd
deleted file mode 100644
index f2a37b9df22..00000000000
--- a/book_source/06_reference/04_docker/introduction.Rmd
+++ /dev/null
@@ -1,14 +0,0 @@
-**THIS IS EXPERIMENTAL DO NOT USE THIS IN PRODUCTION SUBJECT TO CHANGE**
-
-# What is Docker?
-
-Docker is a relativly new technology to encapsulate software as a service. This allow for simple distribution of software since all depedencies are installed as well. Unlike traditional VM's, in docker each component will only run a single service/process and is build on top of existing services provided by the host OS (such as disk access, networking, memory managment etc.). To create a complex system such as PEcAn, we take multiple of these components and link them together.
-
-A common term used in docker is that of an image or container. This refers to all the software needed to run a single service, including the service itself, bundled and installed. The difference between an image and a container is that a container is the execution of an image  (in object oriented programming, an image is a class and a container is an instance of the class). When creating docker images a good mental model to follow is to have a single process per container, and have multiple containers together create an application.
-
-For example in the case of BETY we will need at least two processes, the database and the BETY web application. When distributing a VM with the BETY application we will need to create VM with a base OS (in our case this would be Ubuntu), a database (PostgreSQL) and the BETY webapp (ruby). This requires us to install the dependencies and applications. In the case of Docker, we will need a container for the database (standard postgis container) as well as the custom BETY container (build on top of the exising Ruby container), both running on a host OS (coreOS for example). When starting BETY we start the postgis container first, and next start the BETY container telling it where it can find the postgis container. To upgrade we stop the BETY container, download the latest version, tell it to upgrade the database, and start the BETY container. There is no need to install new dependencies for BETY since they are all shipped as part of the container.
-
-In the case of PEcAn we want to use this ability to ship all dependencies as part of the image to make it easier for the users to download a new model, since the image will contain everything that is needed to run the model as part of PEcAn. If two models depend on different versions of the library we no longer need to worry on how to install these models next to each other and creating issues with the libraries used. Each image will contain only a single model and all libraries needed by that model.
-
-The next section, [architecture](architecture.md) will go in more detail on the containers that make up the PEcAn framework and how these containers interact with each other.
-
diff --git a/book_source/06_reference/04_docker/models.Rmd b/book_source/06_reference/04_docker/models.Rmd
deleted file mode 100644
index 26e7de8765f..00000000000
--- a/book_source/06_reference/04_docker/models.Rmd
+++ /dev/null
@@ -1,57 +0,0 @@
-**THIS IS EXPERIMENTAL DO NOT USE THIS IN PRODUCTION SUBJECT TO CHANGE**
-
-# Dockerfiles for Models
-
-Each model will be disitrbuted as a docker container. These docker containers will contain the model, as well as some additional code to convert the output from the model to the standard PEcAn output, and code to connect to the message bus and receive messages.
-
-Most of these dockerfiles will be the same and will compile the model in one container, copy the resulting binary and any additional files needed to a second container and add all PEcAn pieces needed. This process will reduce the size of the final image.
-
-Each of these docker images will be ready to run the model given an input file and produce outputs that conform to PEcAn. Each container will contain a small script that will execute the binary, check the model exit code, convert the model output to PEcAn output and quit. The conversion from the model specific output to the PEcAn output is done by calling the  model2netcdf. This code will assume the site is located at lat=0, lon=0. To set this you can start the docker process with `-e "SITE_LAT=35.9782" -e "SITE_LON=-79.0942"`. The following variables can be set:
-
-- `SITE_LAT`  : Latitutude of the site, written in output files, default is 0
-- `SITE_LON` : Longitude of the site, written in output files, default is 0
-- `START_DATE` : Start date of the model to be executed.
-- `END_DATE`  : End date of the model to be executed.
-- `DELETE_RAW` : Should the model output be deleted, default is no.
-- `OVERWRITE`  : Should any results be overwritten
-
-Following environment variables are only for information purpose and should not be changed:
-- `MODEL` : The name of the model, used in the script to run the model
-- `BINARY` : Location of the acutual binary, used in the script to run the model
-- `OUTDIR` : Location where data is, in this case /work
-- `PECAN_VERSION` : Version of PEcAn used to compile, default is develop
-
-## SIPNET
-
-The folllowing command will build sipnet v136 for PEcAn using the branch that is currently checked out.
-
-```bash
-docker build \
-	--build-arg MODEL_VERSION=136 \
-	--build-arg PECAN_VERSION=$(git rev-parse --abbrev-ref HEAD) \
-	--tag pecan/pecan-sipnet:136 \
-	--file docker/Dockerfile.sipnet \
-	.
-```
-
-Once the process is finished you can push (upload) the created image to docker hub. It will use the tag to place the image. In this case the image will be placed in the pecan project as the pecan-sipnet repository and tagged with 136. To do this you can use:
-
-```bash
-# do this only once
-docker login
-# push image
-docker push pecan/pecan-sipnet:136
-```
-
-Once the image is pushed to dockerhub anybody can run the model. If you have not already downloaded the docker container the run command will download the image. Next it will run the image and will execute either the default command or the comman line given to the container. In the following example the default command is executed which will run the model and generate the PEcAn output files.
-
-```bash
-# get test data (only need to do this once)
-curl -o sipnet.data.zip http://isda.ncsa.illinois.edu/~kooper/PEcAn/sipnet/sipnet.data.zip
-unzip sipnet.data.zip
-# cleanup if you rerun
-rm -f sipnet.data/{*.nc*,DONE,ERROR,sipnet.out,std*.log}
-# run the actual model
-docker run -t -i --rm -v ${PWD}/sipnet.data:/work pecan/pecan-sipnet:136
-```
-
diff --git a/book_source/06_reference/04_docker/pecan-docker.png b/book_source/06_reference/04_docker/pecan-docker.png
index 54ac980b95c..eb44a892899 100644
Binary files a/book_source/06_reference/04_docker/pecan-docker.png and b/book_source/06_reference/04_docker/pecan-docker.png differ
diff --git a/book_source/index.Rmd b/book_source/index.Rmd
index c83a537608b..38ec10e4343 100644
--- a/book_source/index.Rmd
+++ b/book_source/index.Rmd
@@ -24,7 +24,7 @@ link-citations: yes
 
 [PEcAn Website](http://pecanproject.github.io/)
 
-[Public Chat Room](https://gitter.im/PecanProject/pecan)
+[Public Chat Room](https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE)
 
 [Github Repository](https://github.com/PecanProject/pecan)
 
diff --git a/docker-compose.yml b/docker-compose.yml
index 3f087eed7eb..76aa18b992e 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -1,76 +1,146 @@
-version: '3'
-
-networks:
-  net1:
-    driver: bridge
+version: "3"
 
 services:
-  postgres:
-    image: 'mdillon/postgis:9.4'
+
+  # webserver to handle all traffic to bety/pecan/rabbitmq
+  traefik:
+    image: traefik:latest
     networks:
-      net1:
-        aliases:
-          - pg
+      - pecan
+    command: --api --web --docker --docker.domain=traefik --logLevel=INFO #--docker.exposedbydefault=false
     ports:
-      - '5432:5432'
+      - "8000:80"     # The HTTP port
+      - "8001:8080" # The Web UI (enabled by --api)
+    volumes:
+      - /dev/null:/traefik.toml
+      - /var/run/docker.sock:/var/run/docker.sock # So that Traefik can listen to the Docker events
+    restart: unless-stopped
+
+  # webserver to handle all traffic to bety/pecan/rabbitmq
+  minio:
+    image: minio/minio
+    networks:
+      - pecan
+    command: server /data
+    #ports:
+    #  - "9000:9000"     # The HTTP port
     environment:
-      - PGDATA=/var/lib/postgresql/data/pgdata
+      - MINIO_ACCESS_KEY=carya
+      - MINIO_SECRET_KEY=illinois
+    volumes:
+      - pecan:/data
+    labels:
+      - "traefik.enable=true"
+      - "traefik.port=9000"
+      - "traefik.frontend.rule=PathPrefix:/minio/"
+      - "traefik.backend=minio"
+    restart: unless-stopped
+
+  # postgresql + postgis to hold all the data
+  postgres:
+    image: mdillon/postgis:9.5
+    networks:
+      - pecan
+    # ports:
+    #   - 8002:5432
+    volumes:
+      - postgres:/var/lib/postgresql/data
+    restart: unless-stopped
+
+  # rabbitmq to connect to extractors
+  rabbitmq:
+    image: rabbitmq:management
+    networks:
+      - pecan
+    # ports:
+    #   - 5672
+    #   - 8003:15672
     volumes:
-      - /home/skywalker/pgdata:/var/lib/postgresql/data/pgdata
+      - rabbitmq:/var/lib/rabbitmq
+    labels:
+      - "traefik.enable=true"
+      - "traefik.port=15672"
+      - "traefik.frontend.rule=PathPrefix:/"
+      - "traefik.backend=rabbitmq"
+    restart: unless-stopped
 
+  # BETY rails frontend to the database
   bety:
-    depends_on:
-      - postgres
-    image: 'pecan/bety:latest'
+    image: pecan/bety:${BETY:-latest}
     networks:
-       net1:
-        aliases:
-          - bety
-    ports:
-      - '3000:3000'
+      - pecan
+    # ports:
+    #   - 8004:8000
     environment:
-      - PG_PORT_5432_TCP_ADDR=pg
-      - PG_PORT_5432_TCP_PORT=5432
+      - UNICORN_WORKER_PROCESSES=1
+      - SECRET_KEY_BASE=1208q7493e8wfhdsohfo9ewhrfiouaho908ruq30oiewfdjspadosuf08q345uwrasdy98t7q243
+      - RAILS_RELATIVE_URL_ROOT=/bety
+    depends_on:
+      - postgres
+    labels:
+      - "traefik.enable=true"
+      - "traefik.frontend.rule=PathPrefix:/bety/"
+      - "traefik.backend=bety"
+    restart: unless-stopped
 
-  pecan-core:
+  # PEcAn web front end, this is just the PHP code
+  web:
+    image: pecan/web:${PECAN:-latest}
+    networks:
+      - pecan
+    # ports:
+    #   - 8005:80
+    volumes:
+      - pecan:/data
+      - pecan:/var/www/html/pecan/data
     depends_on:
        - postgres
-       - bety
-    build:
-      context: .
-      dockerfile: Dockerfile
-    image: amanskywalker/pecan-dev:0.1
+       - rabbitmq
+    labels:
+      - "traefik.enable=true"
+      - "traefik.frontend.rule=PathPrefix:/pecan/"
+      - "traefik.backend=pecan"
+    restart: unless-stopped
+
+  # PEcAn executor, executes jobs launched from web
+  executor:
+    image: pecan/executor:${PECAN:-latest}
     networks:
-       net1:
-        aliases:
-          - pecan-core
-    environment:
-      - PG_HOST=pg
-      - PG_PORT=5432
-      - PG_USER=bety
-      - PG_PASSWORD=bety
-      - PG_DATABASE_NAME=bety
+      - pecan
+    hostname: docker
     volumes:
-      - /home/skywalker/pecandata:/pecandata
-
-  pecan-web:
+      - pecan:/data
     depends_on:
        - postgres
-       - bety
-    build:
-      context: ./docker
-      dockerfile: Dockerfile
+       - rabbitmq
+    restart: unless-stopped
+
+  # PEcAn sipnet model runner
+  sipnet:
+    image: pecan/model-sipnet:136
     networks:
-       net1:
-        aliases:
-          - pecan-web
-    ports:
-      - '8080:80'
-    environment:
-      - PG_HOST=pg
-      - PG_PORT=5432
-      - PG_USER=bety
-      - PG_PASSWORD=bety
-      - PG_DATABASE_NAME=bety
+      - pecan
     volumes:
-      - /home/skywalker/pecandata:/pecandata
+      - pecan:/data
+    depends_on:
+       - rabbitmq
+    restart: unless-stopped
+
+  # PEcAn sipnet model runner
+  ed2:
+    image: pecan/model-ed2:git
+    networks:
+      - pecan
+    volumes:
+      - pecan:/data
+    depends_on:
+       - rabbitmq
+    restart: unless-stopped
+
+networks:
+  pecan:
+
+volumes:
+  postgres:
+  rabbitmq:
+  pecan:
diff --git a/docker.sh b/docker.sh
new file mode 100755
index 00000000000..bfd1fffb915
--- /dev/null
+++ b/docker.sh
@@ -0,0 +1,69 @@
+#!/bin/bash
+
+set -e
+cd $(dirname $0)
+
+DEBUG=${DEBUG:-""}
+DEPEND=${DEPEND:-""}
+
+# --------------------------------------------------------------------------------
+# PECAN BUILD SECTION
+# --------------------------------------------------------------------------------
+
+# some git variables
+PECAN_GIT_BRANCH="$(git rev-parse --abbrev-ref HEAD)"
+PECAN_GIT_CHECKSUM="$(git log --pretty=format:%H -1)"
+PECAN_GIT_DATE="$(git log --pretty=format:%ad -1)"
+
+# get version number
+VERSION=${VERSION:-"$(awk '/Version:/ { print $2 }' base/all/DESCRIPTION)"}
+
+echo "Building PEcAn"
+echo " PECAN_VERSION      : ${VERSION}"
+echo " PECAN_GIT_BRANCH   : ${PECAN_GIT_BRANCH}"
+echo " PECAN_GIT_DATE     : ${PECAN_GIT_DATE}"
+echo " PECAN_GIT_CHECKSUM : ${PECAN_GIT_CHECKSUM}"
+echo ""
+
+# not building dependencies image, following command will build this
+if [ "${DEPEND}" == "" ]; then
+    echo "# docker image for dependencies is not build by default."
+    echo "# this image takes a long time to build. To build this"
+    echo "# image run DEPEND=1 $0"
+else
+    ${DEBUG} docker build \
+        --tag pecan/depends:latest \
+        --file docker/base/Dockerfile.depends . | tee docker/base/build.depends.log
+fi
+echo ""
+
+# build images in this specific order. Images are tagged with latest so other
+# docker images build in this script will use that specifc build.
+for i in base executor web data; do
+    rm -f build.${i}.log
+    ${DEBUG} docker build \
+        --build-arg PECAN_VERSION="${VERSION}" \
+        --build-arg PECAN_GIT_BRANCH="${PECAN_GIT_BRANCH}" \
+        --build-arg PECAN_GIT_CHECKSUM="${PECAN_GIT_CHECKSUM}" \
+        --build-arg PECAN_GIT_DATE="${PECAN_GIT_DATE}" \
+        --tag pecan/${i}:latest \
+        --file docker/base/Dockerfile.${i} . | tee docker/base/build.${i}.log
+done
+
+# --------------------------------------------------------------------------------
+# MODEL BUILD SECTION
+# --------------------------------------------------------------------------------
+
+# build sipnet 136
+rm -f build.sipnet.log
+${DEBUG} docker build \
+    --build-arg MODEL_VERSION="136" \
+    --tag pecan/model-sipnet-136:latest \
+    --file docker/models/Dockerfile.sipnet . | tee docker/models/build.sipnet.log
+
+# build ed2 latest
+rm -f build.ed2.log
+${DEBUG} docker build \
+    --build-arg MODEL_VERSION="git" \
+    --tag pecan/model-ed2-git:latest \
+    --file docker/models/Dockerfile.ed2 . | tee docker/models/build.ed2.log
diff --git a/docker/Dockerfile b/docker/Dockerfile
deleted file mode 100644
index f94caf4d4e2..00000000000
--- a/docker/Dockerfile
+++ /dev/null
@@ -1,37 +0,0 @@
-# Dockerfile for the pecan web
-FROM amanskywalker/pecan-dev:0.1
-MAINTAINER Aman Kumar (ak47su30@gmail.com)
-
-# copy the installation script inside the container
-ADD . /build
-
-# Set script mod +x for preprocessors
-RUN chmod 750 /build/*.sh
-
-# Run the OS System setup script
-RUN /build/system_services.sh
-
-# run update machine to update machine
-RUN /build/update_machine.sh
-
-# install pecan web
-RUN /build/install_pecan_web.sh
-
-# simple scripts to do the startup task
-RUN mkdir -p /etc/my_init.d
-COPY apache2/startup.sh /etc/my_init.d/startup.sh
-RUN chmod +x /etc/my_init.d/startup.sh
-
-# adding demons of apache2
-RUN mkdir -p /etc/service/rserver ; sync
-COPY apache2/runserver.sh /etc/service/rserver/run
-RUN chmod +x /etc/service/rserver/run
-
-# add the pecan-web configuration
-COPY web/config.docker.php /home/carya/pecan/web/config.php
-
-# Clean up APT when done.
-RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /build/*
-
-# startup
-CMD ["/sbin/my_init"]
diff --git a/docker/Dockerfile.pecan-maespa b/docker/Dockerfile.pecan-maespa
new file mode 100644
index 00000000000..d674460819c
--- /dev/null
+++ b/docker/Dockerfile.pecan-maespa
@@ -0,0 +1,31 @@
+# ----------------------------------------------------------------------
+# BUILD MAESPA BINARY
+# ----------------------------------------------------------------------
+FROM debian as maespa-binary
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+
+# install dependencies
+RUN apt-get update \
+    && apt-get install -y \
+       gfortran \
+       git \
+       make \
+    && rm -rf /var/lib/apt/lists/*
+
+# download, unzip and build sipnet
+WORKDIR /src
+RUN git clone https://bitbucket.org/remkoduursma/maespa.git \
+    && cd /src/maespa \
+    && make
+
+########################################################################
+
+# ----------------------------------------------------------------------
+# BUILD PECAN FOR MODEL
+# ----------------------------------------------------------------------
+FROM pecan/pecan-cli:latest
+MAINTAINER Rob Kooper <kooper@illinois.edu>
+
+COPY --from=maespa-binary /src/maespa/maespa.out /usr/local/bin/maespa
diff --git a/docker/Dockerfile.sipnet b/docker/Dockerfile.sipnet
deleted file mode 100644
index f2f2b2eec08..00000000000
--- a/docker/Dockerfile.sipnet
+++ /dev/null
@@ -1,114 +0,0 @@
-# ----------------------------------------------------------------------
-# BUILD SIPNET BINARY
-# ----------------------------------------------------------------------
-FROM debian as sipnet-binary
-
-# Some variables that can be used to set control the docker build
-ARG MODEL_VERSION=136
-
-# install dependencies
-RUN apt-get update \
-    && apt-get install -y \
-       curl \
-       gcc \
-       make \
-    && rm -rf /var/lib/apt/lists/*
-
-# download, unzip and build sipnet
-WORKDIR /src
-RUN curl -o sipnet_r136.tar.gz http://isda.ncsa.illinois.edu/~kooper/PEcAn/sipnet/sipnet_r${MODEL_VERSION}.tar.gz \
-    && tar zxf sipnet_r${MODEL_VERSION}.tar.gz \
-    && cd sipnet_r${MODEL_VERSION} \
-    && make \
-    && mv sipnet /src
-
-########################################################################
-
-# ----------------------------------------------------------------------
-# BUILD PECAN FOR MODEL
-# ----------------------------------------------------------------------
-FROM r-base
-
-# ----------------------------------------------------------------------
-# SETUP FOR BUILD
-# ----------------------------------------------------------------------
-
-WORKDIR /work
-
-# start job when starting container
-CMD /usr/local/bin/runcmd.R
-
-# Some variables that can be used to set control the docker build
-ARG PECAN_VERSION=develop
-ARG MODEL_VERSION=136
-
-# ----------------------------------------------------------------------
-# REQUIREMENTS FOR MOST MODELS
-# ----------------------------------------------------------------------
-
-# INSTALL DEVTOOLS
-RUN apt-get update \
-    && apt-get install -y \
-        libcurl4-gnutls-dev \
-        libssh2-1-dev \
-        libssl-dev \
-    && Rscript --vanilla -e "install.packages('devtools', repos='http://cran.rstudio.com/'); q(status=as.integer(!'devtools' %in% installed.packages()))"
-
-# COPY runcmd
-COPY docker/runcmd.R /usr/local/bin
-
-# INSTALL PEcAn.logger
-COPY base/logger /src/logger/
-RUN Rscript --vanilla -e  "devtools::install_local('/src/logger'); q(status=as.integer(!'PEcAn.logger' %in% installed.packages()))" 
-
-# INSTALL PEcAn.remote
-COPY base/remote /src/remote/
-RUN Rscript --vanilla -e  "devtools::install_local('/src/remote'); q(status=as.integer(!'PEcAn.remote' %in% installed.packages()))" 
-
-# INSTALL PEcAn.utils
-COPY base/utils /src/utils/
-RUN apt-get install -y \
-        jags \
-        libnetcdf-dev \
-        libudunits2-dev \
-        libxml2-dev \
-    && Rscript --vanilla -e  "devtools::install_local('/src/utils'); q(status=as.integer(!'PEcAn.utils' %in% installed.packages()))" 
-
-# INSTALL PEcAn.DB
-COPY base/db /src/db/
-RUN Rscript --vanilla -e  "devtools::install_local('/src/db'); q(status=as.integer(!'PEcAn.DB' %in% installed.packages()))" 
-
-# INSTALL PEcAn.data.atmosphere
-COPY modules/data.atmosphere /src/data.atmosphere/
-RUN Rscript --vanilla -e  "devtools::install_local('/src/data.atmosphere'); q(status=as.integer(!'PEcAn.data.atmosphere' %in% installed.packages()))" 
-
-# ----------------------------------------------------------------------
-# SIPNET
-# ----------------------------------------------------------------------
-
-# COPY sipnet binary
-COPY --from=sipnet-binary /src/sipnet /usr/local/bin
-
-# INSTALL PEcAn.SIPNET
-COPY models/sipnet /src/sipnet/
-RUN Rscript --vanilla -e  "devtools::install_local('/src/sipnet'); q(status=as.integer(!'PEcAn.SIPNET' %in% installed.packages()))" 
-
-# CLEANUP
-RUN rm -rf /var/lib/apt/lists/*
-
-# ----------------------------------------------------------------------
-# ENVIRONMENT VARIABLES THAT CONTROL RUNS
-# ----------------------------------------------------------------------
-
-# The custom part for the model
-ENV PECAN_VERSION=${PECAN_VERSION} \
-    MODEL=sipnet \
-    MODEL_VERSION=${MODEL_VERSION} \
-    BINARY=/usr/local/bin/sipnet \
-    OUTDIR=/work \
-    SITE_LAT=0 \
-    SITE_LON=0 \
-    START_DATE= \
-    END_DATE= \
-    DELETE_RAW=FALSE \
-    OVERWRITE=FALSE
diff --git a/docker/add-data.sh b/docker/add-data.sh
new file mode 100644
index 00000000000..260bfcb36ae
--- /dev/null
+++ b/docker/add-data.sh
@@ -0,0 +1,241 @@
+#!/bin/bash
+
+FQDN="docker"
+DATADIR="/data"
+PSQL="psql -U bety -h postgres -d bety -q -t -c"
+
+# docker run --rm -ti --network pecan_pecan -v pecan_pecan:/data pecan/data:latest
+
+# load helper functions and set FQDN and PSQL
+. $( dirname $0 )/add.util.sh
+
+echo "######################################################################"
+echo "CREATE FOLDERS"
+echo "######################################################################"
+mkdir -p /data/workflows /data/dbfiles
+chown 33 /data/workflows /data/dbfiles
+
+echo "######################################################################"
+echo "REGISTER MODELS"
+echo "######################################################################"
+
+# Add models (all these are assumed to be local or $FQDN)
+# 1 : name of the model, shown in web interface
+# 2 : type of model (ED2, SIPNET, BIOCRO, DALEC, ...)
+# 3 : model revision number
+# 4 : name of executable, without the path
+# 5 : optionally path to executable
+addModelFile "${FQDN}" "ED2.2"     "ED2"      "46"  "ed2.46"       "/usr/local/bin"
+addModelFile "${FQDN}" "ED2.2"     "ED2"      "82"  "ed2.82"       "/usr/local/bin"
+addModelFile "${FQDN}" "ED2.2"     "ED2"      "git" "ed2.git"      "/usr/local/bin"
+addModelFile "${FQDN}" "SIPNET"    "SIPNET"   "unk" "sipnet.unk"   "/usr/local/bin"
+addModelFile "${FQDN}" "SIPNET"    "SIPNET"   "136" "sipnet.136"   "/usr/local/bin"
+addModelFile "${FQDN}" "DALEC"     "DALEC"    ""    "dalec_seqMH"  "/usr/local/bin"
+addModelFile "${FQDN}" "Linkages"  "LINKAGES" "git" "linkages.git" "/usr/local/bin"
+addModelFile "${FQDN}" "MAESPA"    "MAESPA"   "git" "maespa.git"   "/usr/local/bin"
+addModelFile "${FQDN}" "LPJ-GUESS" "LPJGUESS" "3.1" "guess.3.1"    "/usr/local/bin"
+addModelFile "${FQDN}" "GDAY(Day)" "GDAY"     ""    "gday"         "/usr/local/bin"
+
+# special case for PRELES
+addModelFile "${FQDN}" "Preles"   "PRELES"   ""          "true"           "/bin"
+
+# special case for R models
+addModelFile "${FQDN}" "BioCro"   "BIOCRO"   "git"       "biocro.Rscript" "/usr/local/lib/R/site-library/PEcAn.BIOCRO"
+addModelFile "${FQDN}" "BioCro"   "BIOCRO"   "0.95"      "biocro.Rscript" "/usr/local/lib/R/site-library/PEcAn.BIOCRO"
+addModelFile "${FQDN}" "BioCro"   "BIOCRO"   "1.0"       "biocro.Rscript" "/usr/local/lib/R/site-library/PEcAn.BIOCRO"
+
+addModelFile "${FQDN}" "LINKAGES" "LINKAGES" "R_version" ""               "/usr/local/lib/R/site-library/linkages"
+
+# to add remote files
+#addModelFile "geo.bu.edu" "ED2" "ED2" "git" "ed_2.1-opt" "/home/dietze/ED2.git/ED/build"
+
+echo "######################################################################"
+echo "DOWNLOAD DATA"
+echo "######################################################################"
+cd ${DATADIR}
+
+if [ ! -e ${DATADIR}/sites ]; then
+  curl -s -o sites.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/sites.tgz
+  tar zxf sites.tgz
+  sed -i -e "s#/home/kooper/Projects/EBI#${DATADIR}#" sites/*/ED_MET_DRIVER_HEADER
+  rm sites.tgz
+fi
+
+if [ ! -e ${DATADIR}/inputs ]; then
+  curl -s -o inputs.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/inputs.tgz
+  tar zxf inputs.tgz
+  rm inputs.tgz
+fi
+
+if [ ! -e ${DATADIR}/lpj-guess/cru_1901_2006.bin ]; then
+  if [ ! -d ${DATADIR}/lpj-guess ]; then
+    mkdir ${DATADIR}/lpj-guess
+  fi
+  curl -s -o ${DATADIR}/lpj-guess/cru_1901_2006.bin http://isda.ncsa.illinois.edu/~kooper/PEcAn/data/cru_1901_2006.bin
+fi
+
+if [ ! -e ${DATADIR}/plot ]; then
+  curl -s -o plot.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/plot.tgz
+  tar zxf plot.tgz
+  rm plot.tgz
+fi
+
+if [ ! -e ${DATADIR}/sites/Santarem_Km83 ]; then
+  curl -s -o Santarem_Km83.zip http://isda.ncsa.illinois.edu/~kooper/EBI/Santarem_Km83.zip
+  unzip -q -d sites Santarem_Km83.zip
+  sed -i -e "s#/home/pecan#${DATADIR}#" sites/Santarem_Km83/ED_MET_DRIVER_HEADER
+  rm Santarem_Km83.zip
+fi
+
+if [ ! -e ${DATADIR}/testrun.s83 ]; then
+  curl -s -o testrun.s83.zip http://isda.ncsa.illinois.edu/~kooper/EBI/testrun.s83.zip
+  unzip -q testrun.s83.zip
+  sed -i -e "s#/home/pecan#${DATADIR}#" testrun.s83/ED2IN
+  rm testrun.s83.zip
+fi
+
+if [ ! -e ${DATADIR}/ed2ws.harvard ]; then
+  curl -s -o ed2ws.harvard.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ed2ws.harvard.tgz
+  tar zxf ed2ws.harvard.tgz
+  mkdir ed2ws.harvard/analy ed2ws.harvard/histo
+  sed -i -e "s#/home/pecan#${DATADIR}#g" ed2ws.harvard/input_harvard/met_driver/HF_MET_HEADER ed2ws.harvard/ED2IN ed2ws.harvard/*.r
+  rm ed2ws.harvard.tgz
+fi
+
+if [ ! -e ${DATADIR}/testrun.PDG ]; then
+  curl -s -o testrun.PDG.zip http://isda.ncsa.illinois.edu/~kooper/EBI/testrun.PDG.zip
+  unzip -q testrun.PDG.zip
+  sed -i -e "s#/home/pecan#${DATADIR}#" testrun.PDG/Met/PDG_MET_DRIVER testrun.PDG/Template/ED2IN
+  sed -i -e 's#/n/scratch2/moorcroft_lab/kzhang/PDG/WFire_Pecan/##' testrun.PDG/Template/ED2IN
+  rm testrun.PDG.zip
+fi
+
+if [ ! -e ${DATADIR}/create_met_driver ]; then
+  curl -s -o create_met_driver.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/create_met_driver.tar.gz
+  tar zxf create_met_driver.tar.gz
+  rm create_met_driver.tar.gz
+fi
+
+echo "######################################################################"
+echo "REGISTER DATA"
+echo "######################################################################"
+
+# load helper functions and set FQDN and PSQL
+. ${DIRNAME}/add.util.sh
+
+# subfolders in datadir
+SITES="$DATADIR/sites"
+DALEC="$DATADIR/dalec_EnKF_pub/input_data"
+ED_INPUT="$DATADIR/ed_inputs"
+FAO_INPUT="$DATADIR/faoOLD"
+OGE2_INPUT="$DATADIR/oge2OLD"
+LPJ_GUESS="$DATADIR/lpj-guess"
+
+# ED inputs
+addInput "1118" "41" "1800-01-01 05:50:36" "1999-01-01 06:00:00" # 294
+addInputFile "${FQDN}" "${INPUT_ID}" "" "${ED_INPUT}/glu"
+addInput "1118" "42" "" "" # 295
+addInputFile "${FQDN}" "${INPUT_ID}" "" "${ED_INPUT}"
+addInput "1118" "43" "" "" # 296
+addInputFile "${FQDN}" "${INPUT_ID}" "OGE2_" "${OGE2_INPUT}"
+addInput "1118" "44" "" "" # 297
+addInputFile "${FQDN}" "${INPUT_ID}" "FAO_" "${FAO_INPUT}"
+
+# LPJ-GUESS inputs
+addInput "1118" "1000000020" "" "" # 1000000903
+addInputFile "${FQDN}" "${INPUT_ID}" "cru_1901_2006.bin" "${LPJ_GUESS}"
+
+# [76] EBIFARM
+addInput "76" "10" "" "" # 5
+addInputFile "${FQDN}" "${INPUT_ID}" "ebifarm.lat40.0lon-88.0.site" "${SITES}/ebifarm"
+addInput "76" "11" "" "" # 6
+addInputFile "${FQDN}" "${INPUT_ID}" "ebifarm.lat40.0lon-88.0.css" "${SITES}/ebifarm"
+addInput "76" "12" "2004-01-01 00:00:00" "2009-12-31 23:59:59" # 7
+addInputFile "${FQDN}" "${INPUT_ID}" "ED_MET_DRIVER_HEADER" "${SITES}/ebifarm"
+addInput "76" "15" "" "" # 8
+addInputFile "${FQDN}" "${INPUT_ID}" "ebifarm.lat40.0lon-88.0.pss" "${SITES}/ebifarm"
+
+# [758] HARVARD
+addInput "758" "12" "1991-01-01 06:00:00" "2006-12-31 06:00:00" # 82
+addInputFile "${FQDN}" "${INPUT_ID}" "ED_MET_DRIVER_HEADER" "${SITES}/harvard_ems"
+addInput "758" "16" "1991-01-01 06:00:00" "2006-12-31 06:00:00" # 83
+addInputFile "${FQDN}" "${INPUT_ID}" "US-Ha1forcing.nc" "${SITES}/harvard_ems"
+addInput "758" "10" "" "" # 136 ~
+addInputFile "${FQDN}" "${INPUT_ID}" "harvard.NACP.lat42.5lon-72.5.site" "${SITES}/harvard_ems"
+addInput "758" "11" "" "" # 138
+addInputFile "${FQDN}" "${INPUT_ID}" "harvard.NACP.lat42.5lon-72.5.css" "${SITES}/harvard_ems"
+addInput "758" "15" "" "" # 137
+addInputFile "${FQDN}" "${INPUT_ID}" "harvard.NACP.lat42.5lon-72.5.pss" "${SITES}/harvard_ems"
+
+# [676] Willow Creek
+addInput "676" "24" "1998-01-01" "2006-12-31"
+addInputFile "${FQDN}" "${INPUT_ID}" "wcr.clim" "${SITES}/willow"
+addInput "676" "12" "1998-01-01 06:00:00" "2006-12-31 06:00:00" # 134
+addInputFile "${FQDN}" "${INPUT_ID}" "ED_MET_DRIVER_HEADER" "${SITES}/willow"
+addInput "676" "16" "1998-01-01 06:00:00" "2006-12-31 06:00:00" # 135
+addInputFile "${FQDN}" "${INPUT_ID}" "US-WCrforcing.nc" "${SITES}/willow"
+addInput "676" "10" "1998-01-01 06:00:00" "2006-12-31 06:00:00" # 171
+addInputFile "${FQDN}" "${INPUT_ID}" "WCr.NACP.lat45.5lon-90.5.site" "${SITES}/willow"
+addInput "676" "11" "1998-01-01 06:00:00" "2006-12-31 06:00:00" # 169
+addInputFile "${FQDN}" "${INPUT_ID}" "WCr.NACP.lat45.5lon-90.5.css" "${SITES}/willow"
+addInput "676" "15" "1998-01-01 06:00:00" "2006-12-31 06:00:00" # 170
+addInputFile "${FQDN}" "${INPUT_ID}" "WCr.NACP.lat45.5lon-90.5.pss" "${SITES}/willow"
+
+# [676] Willow Creek updated by Shawn
+addInput "676" "10" "1998-01-01 06:00:00" "2006-12-31 06:00:00" # 171
+addInputFile "${FQDN}" "${INPUT_ID}" "US-WCr.Inv.lat45.5lon-90.site" "${SITES}/willow"
+addInput "676" "11" "1998-01-01 06:00:00" "2006-12-31 06:00:00" # 169
+addInputFile "${FQDN}" "${INPUT_ID}" "US-WCr.Inv.lat45.5lon-90.css" "${SITES}/willow"
+addInput "676" "15" "1998-01-01 06:00:00" "2006-12-31 06:00:00" # 170
+addInputFile "${FQDN}" "${INPUT_ID}" "US-WCr.Inv.lat45.5lon-90.pss" "${SITES}/willow"
+
+# [622] Sylvania
+addInput "622" "24" "2001-01-01" "2006-12-31"
+addInputFile "${FQDN}" "${INPUT_ID}" "syl.clim" "${SITES}/sylvana"
+addInput "622" "12" "2001-01-01 06:00:00" "2006-12-31 06:00:00" # 132
+addInputFile "${FQDN}" "${INPUT_ID}" "ED_MET_DRIVER_HEADER" "${SITES}/sylvana"
+addInput "622" "16" "2001-01-01 06:00:00" "2006-12-31 06:00:00" # 133
+addInputFile "${FQDN}" "${INPUT_ID}" "US-Syvforcing.nc" "${SITES}/sylvana"
+addInput "622" "10" "2001-01-01 06:00:00" "2006-12-31 06:00:00" # 177
+addInputFile "${FQDN}" "${INPUT_ID}" "Syl.NACP.lat46.5lon-89.5.site" "${SITES}/sylvana"
+addInput "622" "11" "2001-01-01 06:00:00" "2006-12-31 06:00:00" # 175
+addInputFile "${FQDN}" "${INPUT_ID}" "Syl.NACP.lat46.5lon-89.5.css" "${SITES}/sylvana"
+addInput "622" "15" "2001-01-01 06:00:00" "2006-12-31 06:00:00" # 176
+addInputFile "${FQDN}" "${INPUT_ID}" "Syl.NACP.lat46.5lon-89.5.pss" "${SITES}/sylvana"
+
+# [678] Park Falls (WLEF US-PFa)
+addInput "678" "24" "1997-01-01" "2005-12-31"
+addInputFile "${FQDN}" "${INPUT_ID}" "lef.clim" "${SITES}/parkfalls"
+addInput "678" "12" "1995-01-01 06:00:00" "2005-12-31 06:00:00" # 130
+addInputFile "${FQDN}" "${INPUT_ID}" "ED_MET_DRIVER_HEADER" "${SITES}/parkfalls"
+addInput "678" "16" "1995-01-01 06:00:00" "2005-12-31 06:00:00" # 131
+addInputFile "${FQDN}" "${INPUT_ID}" "US-PFaforcing.nc" "${SITES}/parkfalls"
+
+# [679] Lost Creek
+addInput "679" "24" "2001-01-01" "2006-12-31"
+addInputFile "${FQDN}" "${INPUT_ID}" "lcr.clim" "${SITES}/lostcreek"
+addInput "679" "12" "2000-01-01 06:00:00" "2006-12-31 06:00:00" # 92
+addInputFile "${FQDN}" "${INPUT_ID}" "ED_MET_DRIVER_HEADER" "${SITES}/lostcreek"
+addInput "679" "16" "2000-01-01 06:00:00" "2006-12-31 06:00:00" # 93
+addInputFile "${FQDN}" "${INPUT_ID}" "US-Losforcing.nc" "${SITES}/lostcreek"
+
+# [772] NIWOT
+addInput "772" "24" "2002-01-01" "2005-12-31"
+addInputFile "${FQDN}" "${INPUT_ID}" "niwot.clim" "${SITES}/niwot"
+addInput "772" "24" "1999-01-01" "2003-12-31"
+addInputFile "${FQDN}" "${INPUT_ID}" "US-NR1.clim" "${SITES}/niwot"
+addInput "772" "12" "1998-01-01 06:00:00" "2008-01-01 05:00:00" # 112
+addInputFile "${FQDN}" "${INPUT_ID}" "ED_MET_DRIVER_HEADER" "${SITES}/niwot"
+addInput "772" "16" "1998-01-01 06:00:00" "2007-12-31 06:00:00" # 113
+addInputFile "${FQDN}" "${INPUT_ID}" "US-NR1forcing.nc" "${SITES}/niwot"
+addInput "772" "10" "1998-01-01 06:00:00" "2007-12-31 06:00:00" # 188
+addInputFile "${FQDN}" "${INPUT_ID}" "NR1.NACP.lat40.5lon-105.5.site" "${SITES}/niwot"
+addInput "772" "11" "1998-01-01 06:00:00" "2007-12-31 06:00:00" # 186
+addInputFile "${FQDN}" "${INPUT_ID}" "NR1.NACP.lat40.5lon-105.5.css" "${SITES}/niwot"
+addInput "772" "15" "1998-01-01 06:00:00" "2007-12-31 06:00:00" # 187
+addInputFile "${FQDN}" "${INPUT_ID}" "NR1.NACP.lat40.5lon-105.5.pss" "${SITES}/niwot"
+
+# [766] Metolius
+addFormat "text/plain" "DALEC meteorology"
+addInput "766" "${FORMAT_ID}" "1999-01-01" "2003-12-31"
+addInputFile "${FQDN}" "${INPUT_ID}" "dalec_drivers.OREGON.no_obs.dat" "${DALEC}/oregon"
diff --git a/docker/apache2/runserver.sh b/docker/apache2/runserver.sh
deleted file mode 100644
index 008a2465425..00000000000
--- a/docker/apache2/runserver.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-
-exec /etc/init.d/apache2 start
diff --git a/docker/apache2/startup.sh b/docker/apache2/startup.sh
deleted file mode 100644
index ca232920ba2..00000000000
--- a/docker/apache2/startup.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-
-set -e
-
-if [ -f /etc/configured ]; then
-  echo 'already configured'
-else
-  #code that need to run only one time ....
-  update-locale
-  date > /etc/configured
-fi
diff --git a/docker/base/Dockerfile.base b/docker/base/Dockerfile.base
new file mode 100644
index 00000000000..0013ad691e5
--- /dev/null
+++ b/docker/base/Dockerfile.base
@@ -0,0 +1,34 @@
+FROM pecan/depends
+MAINTAINER Rob Kooper <kooper@illinois.edu>
+
+# ----------------------------------------------------------------------
+# PEcAn installation from local source
+# ----------------------------------------------------------------------
+# copy folders
+COPY Makefile /pecan/
+COPY base     /pecan/base/
+COPY modules  /pecan/modules/
+COPY models   /pecan/models/
+
+RUN cd /pecan && make
+
+# COPY WORKFLOW
+WORKDIR /work
+COPY web/workflow.R /work/
+
+# COMMAND TO RUN
+CMD Rscript --vanilla workflow.R | tee workflow.Rout
+
+# ----------------------------------------------------------------------
+# PEcAn version information
+# ----------------------------------------------------------------------
+ARG PECAN_VERSION="develop"
+ARG PECAN_GIT_BRANCH="unknown"
+ARG PECAN_GIT_CHECKSUM="unknown"
+ARG PECAN_GIT_DATE="unknown"
+
+# variables to store in docker image
+ENV PECAN_VERSION=${PECAN_VERSION} \
+    PECAN_GIT_BRANCH=${PECAN_GIT_BRANCH} \
+    PECAN_GIT_CHECKSUM=${PECAN_GIT_CHECKSUM} \
+    PECAN_GIT_DATE=${PECAN_GIT_DATE}
diff --git a/docker/base/Dockerfile.data b/docker/base/Dockerfile.data
new file mode 100644
index 00000000000..2fa935d8285
--- /dev/null
+++ b/docker/base/Dockerfile.data
@@ -0,0 +1,13 @@
+FROM ubuntu
+MAINTAINER Rob Kooper <kooper@illinois.edu>
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        curl \
+        postgresql-client \
+        unzip \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /work
+COPY docker/add-data.sh scripts/add.util.sh /work/
+CMD bash /work/add-data.sh
diff --git a/docker/base/Dockerfile.depends b/docker/base/Dockerfile.depends
new file mode 100644
index 00000000000..ddf261bdce0
--- /dev/null
+++ b/docker/base/Dockerfile.depends
@@ -0,0 +1,48 @@
+# ----------------------------------------------------------------------
+# PECAN FOR MODEL BASE IMAGE
+# ----------------------------------------------------------------------
+FROM r-base
+MAINTAINER Rob Kooper <kooper@illinois.edu>
+
+# ----------------------------------------------------------------------
+# INSTALL BINARY/LIBRARY DEPENDENCIES
+# ----------------------------------------------------------------------
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        jags \
+        libcurl4-gnutls-dev \
+        libgdal-dev \
+        libnetcdf-dev \
+        libpq-dev \
+        librdf0-dev \
+        libssh2-1-dev \
+        libssl-dev \
+        libudunits2-dev \
+        libxml2-dev \
+        time
+
+# ----------------------------------------------------------------------
+# INSTALL DEV TOOLS AND PACKAGES FROM GITHUB NEEDED BUILD PECAN
+# ----------------------------------------------------------------------
+RUN Rscript --vanilla -e "install.packages('devtools', repos='http://cran.rstudio.com/'); q(status=as.integer(!'devtools' %in% rownames(installed.packages())))" \
+    && Rscript --vanilla -e "install.packages('testthat', repos='http://cran.rstudio.com/'); q(status=as.integer(!'testthat' %in% rownames(installed.packages())))" \
+    && Rscript --vanilla -e "install.packages('roxygen2', repos='http://cran.rstudio.com/'); q(status=as.integer(!'roxygen2' %in% rownames(installed.packages())))" \
+    && Rscript --vanilla -e "devtools::install_github('ropensci/geonames'); q(status=as.integer(!'geonames' %in% rownames(installed.packages())))" \
+    && Rscript --vanilla -e "devtools::install_github('ropenscilabs/nneo'); q(status=as.integer(!'nneo' %in% rownames(installed.packages())))" \
+    && Rscript --vanilla -e "devtools::install_github('rforge/reddyproc/pkg/REddyProc'); q(status=as.integer(!'REddyProc' %in% rownames(installed.packages())))"
+    
+# ----------------------------------------------------------------------
+# INSTALL R PACKAGES NEED TO BUILD PEcAn
+# NOT installing: PEcAn.* BioCro linkages Maeswrap Rpreles
+# Currently these will be installed automatically by make later
+# ----------------------------------------------------------------------
+RUN for p in abind BayesianTools car coda dataone datapack data.table DBI dbplyr doParallel dplR dplyr earth ellipse fields foreach getPass ggmap ggplot2 glue grid gridExtra hdf5r here httr IDPmisc jsonlite knitr lattice lubridate magic magrittr maps maptools MASS mclust MCMCpack methods mgcv minpack.lm mlegp mockery mvtnorm ncdf4 nimble nneo parallel PeriodicTable plotly plotrix plyr png progress purrr pwr randtoolbox raster rcrossref RCurl REddyProc redland reshape2 rgdal rjags rjson rlang RMySQL rnoaa RPostgreSQL RSQLite scales shiny shinycssloaders shinydashboard shinyFiles shinyjs SimilarityMeasures sp stringi stringr testthat tibble tidyr tidyverse tools traits truncnorm udunits2 XML xtable zoo; do \
+      echo "# ----------------------------------------------------------------------"; \
+      echo "# INSTALLING ${p}"; \
+      echo "# ----------------------------------------------------------------------"; \
+      Rscript --vanilla -e " \
+      if(!'${p}' %in% rownames(installed.packages())) { \
+        install.packages('${p}', repos='http://cran.rstudio.com/'); \
+        q(status=as.integer(!'${p}' %in% rownames(installed.packages()))) \
+      }" || (echo "FAILED TO INSTALL ${p}"; exit 1); \
+    done
diff --git a/docker/base/Dockerfile.executor b/docker/base/Dockerfile.executor
new file mode 100644
index 00000000000..bb089524f38
--- /dev/null
+++ b/docker/base/Dockerfile.executor
@@ -0,0 +1,22 @@
+# ----------------------------------------------------------------------
+# PECAN FOR MODEL BASE IMAGE
+# ----------------------------------------------------------------------
+FROM pecan/base
+MAINTAINER Rob Kooper <kooper@illinois.edu>
+
+# variables to store in docker image
+ENV RABBITMQ_URI=amqp://guest:guest@rabbitmq/%2F \
+    RABBITMQ_QEUEUE="pecan" \
+    APPLICATION="R CMD BATCH workflow.R"
+
+# ----------------------------------------------------------------------
+# SETUP FOR PYTHON CODE
+# ----------------------------------------------------------------------
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends python3-pip \
+    && pip3 install pika \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /work
+COPY docker/receiver.py docker/sender.py /work/
+CMD python3 /work/receiver.py
diff --git a/docker/base/Dockerfile.web b/docker/base/Dockerfile.web
new file mode 100644
index 00000000000..1030ead82bc
--- /dev/null
+++ b/docker/base/Dockerfile.web
@@ -0,0 +1,37 @@
+FROM php:apache
+MAINTAINER Rob Kooper <kooper@illinois.edu>
+
+# ----------------------------------------------------------------------
+# install rabbitmq and postgresql extentions
+# ----------------------------------------------------------------------
+RUN apt-get update \
+    && apt-get install -y \
+        libpq-dev \
+        librabbitmq-dev \
+    && rm -rf /var/lib/apt/lists/* \
+    && docker-php-ext-install -j$(nproc) pdo pdo_pgsql \
+    && pecl install amqp \
+    && docker-php-ext-enable amqp \
+    && mkdir -p /data/workflows /data/dbfiles \
+    && chown www-data /data/workflows /data/dbfiles
+
+# ----------------------------------------------------------------------
+# copy webpages
+# ----------------------------------------------------------------------
+COPY documentation/index_vm.html /var/www/html/index.html
+COPY web /var/www/html/pecan/
+COPY docker/config.docker.php /var/www/html/pecan/config.php
+
+# ----------------------------------------------------------------------
+# PEcAn version information
+# ----------------------------------------------------------------------
+ARG PECAN_VERSION="develop"
+ARG PECAN_GIT_BRANCH="unknown"
+ARG PECAN_GIT_CHECKSUM="unknown"
+ARG PECAN_GIT_DATE="unknown"
+
+# variables to store in docker image
+ENV PECAN_VERSION=${PECAN_VERSION} \
+    PECAN_GIT_BRANCH=${PECAN_GIT_BRANCH} \
+    PECAN_GIT_CHECKSUM=${PECAN_GIT_CHECKSUM} \
+    PECAN_GIT_DATE=${PECAN_GIT_DATE}
diff --git a/docker/bin/my_init b/docker/bin/my_init
deleted file mode 100644
index ccf79a7711b..00000000000
--- a/docker/bin/my_init
+++ /dev/null
@@ -1,189 +0,0 @@
-#!/bin/bash
-export LC_ALL=C TERM="xterm"
-
-trap 'shutdown_runit_services' INT TERM
-
-# variables
-env > /etc/envvars
-temp_var=$@
-FILES=/etc/container_environment/*
-runsvdir_PID=
-
-# functions
-
-# importing the environment variables from image
-import_envvars () {
-
- clear_existing_environment=${1:-true}
- override_existing_environment=${2:-true}
-
- for file in $FILES
- do
-    FILE=`basename $file`
-    if [ $override_existing_environment = true ] || !( env | grep -q $FILE)
-    then
-      export eval $FILE=`cat $file`
-    fi
- done
-}
-
-# exporting the environment variables to the image
-export_envvars () {
- to_dir=${1:-true}
- no_record="HOME USER GROUP UID GID SHELL SHLVL PWD"
- # to begin .json and.sh files
-  echo -n "{" > /etc/container_environment.json
-  echo -n "" > /etc/container_environment.sh
-  # saving variables into file. individual file by variable.
- env | while read -r line
- do
-  a=`expr index "$line" \=`
-  b=$((a-1))
-  file_name=${line:0:$b}
-  file_val=${line:$a}
-  if echo "$no_record" | grep -q "$file_name"
-  then
-   continue
-  else
-    # write to files
-    if [ $to_dir = true ] ; then echo $file_val > /etc/container_environment/$file_name ; fi
-   # write to .sh file
-    echo "export"  $file_name"='"$file_val"'" >> /etc/container_environment.sh
-   # write to .json file
-    echo -n "\""$file_name"\":\""$file_val"\"," >> /etc/container_environment.json
-  fi
- done
-    # adding } to closed the .json file
-    echo -e "\b}" >> /etc/container_environment.json
-}
-
-# function to run the command
-run_command () {
-   if [ -x $1 ]; then
-        echo >&2 "*** Running: $1"
-        $1
-        retval=$?
-        if [ $retval != 0 ];
-        then
-            echo >&2 "*** Failed with return value: $retval"
-            exit $retval
-         else
-            import_envvars
-            export_envvars false
-        fi
-    fi
-}
-
-# function to run the startup scripts
-run_startup_files() {
-   # running /etc/my_init.d/
-   echo "Starting pre-service scritps in /etc/my_init.d"
-   for script in /etc/my_init.d/*
-    do
-     run_command $script
-   done
-
-   echo "starting rc.local scritps"
-   run_command /etc/rc.local
-}
-
-
-# function to start cron jobs
-start_runit () {
-   echo "Booting runit daemon..."
-   /usr/bin/runsvdir -P /etc/service 'log:.........................................................................................................' &
-   runsvdir_PID=$!
-   echo "Process runsvdir running with PID $runsvdir_PID"
-}
-
-# function to shutdown corn jobs
-shutdown_runit_services() {
-   # need to check if runit service is runnung before shutdown ..
-   echo "Begin shutting down runit services..."
-   /usr/bin/sv down /etc/service/*
-   # need to give some time and check if service is down if time greater than allow them force exit
-   count=1
-   while [ $(/usr/bin/sv status /etc/service/* | grep -c "^run:") != 0 ]
-   do
-     sleep 1
-     count=`expr $count + 1`
-     if [ $count -gt 10 ]; then break ; fi
-   done
-   exit 0
-}
-
-# message to echo things to user
-message () {
-  echo "usage: my_init [-h|--help] [--skip-startup-files] [--skip-runit] [-- MAIN_COMMAND ]"
-  echo "optional arguments:"
-  echo "  -h, --help            show this help message and exit"
-  echo "  --skip-startup-files  Skip running /etc/my_init.d/* and /etc/rc.local"
-  echo "  --skip-runit          Do not run runit services"
-  echo "  --quiet               Only print warnings and errors"
-}
-
-# import & export env
-import_envvars false false
-export_envvars
-
-
-# condition for --help
-if [ `echo $temp_var | grep -c "\-\-help" ` -gt 0 ] || [ `echo $temp_var | grep -c "\-h" ` -gt 0 ] ; then
-  message
-  exit 0
-fi
-
-# condition for --quiet
-if ! [ `echo $temp_var | grep -c "\-\-quiet" ` -gt 0 ] ; then
-   :
- else
-   temp_var=$(echo $temp_var|sed "s/--quiet//")
-   echo "--quiet still need to be implememted"
-fi
-
-# condition for --skip-startup-files
-if ! [ `echo $temp_var | grep -c "\-\-skip-startup-files" ` -gt 0 ] ; then
-   run_startup_files
- else
-   temp_var=$(echo $temp_var|sed "s/--skip-startup-files//")
-fi
-
-# condition for --skip-runit
-if ! [ `echo $temp_var | grep -c "\-\-skip-runit" ` -gt 0 ] ; then
-   start_runit
- else
-   temp_var=$(echo $temp_var|sed "s/--skip-runit//")
-   if  [ `echo $temp_var | grep -c "\-\- " ` -gt 0 ] ; then
-     temp_var=$(echo $temp_var|sed "s/--//")
-     exec $temp_var
-     exit 0
-    else
-      echo "Need to add command to do something:  -- command"
-      echo
-      message
-      exit 0
-   fi
-fi
-
-if  [ `echo $temp_var | grep -c "\-\- " ` -gt 0 ] ; then
-temp_var=$(echo $temp_var|sed "s/--//")
- if ! [ "$temp_var" = "" ] ; then
-     # need to check if all service are online before executing command
-     count=1
-     while [ $(/sbin/sv status /etc/service/* | grep -c "^down:") != 0 ]
-      do
-       sleep 1
-       count=`expr $count + 1`
-       if [ $count -gt 10 ]; then break ; fi
-      done
-     exec $temp_var
-     shutdown_runit_services
- else
-  echo "Need to add command to do something: -- command "
-  echo
-  message
-  shutdown_runit_services
- fi
-fi
-
-wait
diff --git a/docker/web/config.docker.php b/docker/config.docker.php
similarity index 72%
rename from docker/web/config.docker.php
rename to docker/config.docker.php
index 46e3900378d..e8d85fe47ba 100644
--- a/docker/web/config.docker.php
+++ b/docker/config.docker.php
@@ -2,27 +2,11 @@
 
 # Information to connect to the BETY database
 $db_bety_type="pgsql";
-$db_bety_hostname="pg";
-$db_bety_port="5432";
-$db_bety_username="postgres";
+$db_bety_hostname="postgres";
+$db_bety_username="bety";
 $db_bety_password="bety";
 $db_bety_database="bety";
 
-// under development code to get the data from the environment variables
-// $db_bety_hostname=getenv('PG_HOST');
-// $db_bety_port=getenv('PG_PORT');
-// $db_bety_username=getenv('PG_USER');
-// $db_bety_password=getenv('PG_PASSWORD');
-// $db_bety_database=getenv('PG_DATABASE_NAME');
-
-# use only for debuging
-#var_dump($db_bety_type);
-#var_dump($db_bety_hostname);
-#var_dump($db_bety_port);
-#var_dump($db_bety_username);
-#var_dump($db_bety_password);
-#var_dump($db_bety_database);
-
 # Information to connect to the FIA database
 # leave this blank if you do not have the FIA database installed.
 $db_fia_type="pgsql";
@@ -36,6 +20,14 @@
 $browndog_username="";
 $browndog_password="";
 
+# rabbitmq connection
+$rabbitmq_host="rabbitmq";
+$rabbitmq_port="5672";
+$rabbitmq_vhost="/";
+$rabbitmq_queue="pecan";
+$rabbitmq_username="guest";
+$rabbitmq_password="guest";
+
 # R binary
 $Rbinary="/usr/bin/R";
 
@@ -63,7 +55,7 @@
 $anonymous_page = 99;
 
 # name of current machine
-$fqdn=exec('hostname -f');
+$fqdn="docker";
 
 # List of all host and options. The list should be the server pointing
 # to an array. The second array contains a key value pair used to
@@ -86,27 +78,25 @@
 #                additional parameters for the job.sh.
 # - scratchdir : folder to be used for scratchspace when running certain
 #                models (such as ED)
-$hostlist=array($fqdn => array(),
+$hostlist=array($fqdn => 
+                    array("rabbitmq" => "amqp://guest:guest@rabbitmq/%2F"),
                 "geo.bu.edu" =>
-                    array("qsub"    => "qsub -V -N @NAME@ -o @STDOUT@ -e @STDERR@ -S /bin/bash",
-                          "jobid"   => "Your job ([0-9]+) .*",
-                          "qstat"   => "qstat -j @JOBID@ || echo DONE",
-                          "prerun"  => "module load udunits R/R-3.0.0_gnu-4.4.6",
-                          "postrun" => "sleep 60",
-                          "models"  => array("ED2" =>
+                    array("qsub"     => "qsub -V -N @NAME@ -o @STDOUT@ -e @STDERR@ -S /bin/bash",
+                          "jobid"    => "Your job ([0-9]+) .*",
+                          "qstat"    => "qstat -j @JOBID@ || echo DONE",
+                          "prerun"   => "module load udunits R/R-3.0.0_gnu-4.4.6",
+                          "postrun"  => "sleep 60",
+                          "models"   => array("ED2" =>
                               array("prerun"  => "module load hdf5"))));
 
 # Folder where PEcAn is installed
 $R_library_path="/home/carya/R/library";
 
-# Location where PEcAn is installed, not really needed anymore
-$pecan_home="/home/carya/pecan/";
-
 # Folder where the runs are stored
-$output_folder="/home/carya/output/";
+$output_folder="/data/workflows";
 
 # Folder where the generated files are stored
-$dbfiles_folder=$output_folder . "/dbfiles";
+$dbfiles_folder="/data/dbfiles";
 
 # location of BETY DB set to empty to not create links, can be both
 # relative or absolute paths or full URL's. Should point to the base
@@ -125,5 +115,10 @@
 # uncomment the following variable to enable the simple interface
 #$simpleBETY = TRUE;
 
+# syncing details
+
+$server_url="192.168.0.5";    // local test server
+$client_sceret="";
+$server_auth_token="";
 
 ?>
diff --git a/docker/config/cron_log_config b/docker/config/cron_log_config
deleted file mode 100644
index 786ed9b34ce..00000000000
--- a/docker/config/cron_log_config
+++ /dev/null
@@ -1,5 +0,0 @@
-s100000
-n5
-N3
-t86400
-!logwatcher
diff --git a/docker/install_R.sh b/docker/install_R.sh
deleted file mode 100644
index 1abf6c760c3..00000000000
--- a/docker/install_R.sh
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/bin/bash
-
-. /build/install_pecan_preprocessor.sh
-
-echo "######################################################################"
-echo "R"
-echo "######################################################################"
-if [ -z "${R_LIBS_USER}" ]; then
-  echo 'export R_LIBS_USER=${HOME}/R/library' >> ${HOME}/.bashrc
-  echo 'R_LIBS_USER=${HOME}/R/library' >> ${HOME}/.Renviron
-  export export R_LIBS_USER=${HOME}/R/library
-  mkdir -p ${R_LIBS_USER}
-
-  case "$OS_VERSION" in
-    RH_*)
-      echo 'export PATH=${PATH}:/usr/pgsql-9.5/bin' >> ${HOME}/.bashrc
-      export PATH=${PATH}:/usr/pgsql-9.5/bin
-      ;;
-  esac
-fi
-echo 'if(!"devtools" %in% installed.packages()) install.packages("devtools", repos="http://cran.rstudio.com/")' | R --vanilla
-echo 'if(!"udunits2" %in% installed.packages()) install.packages("udunits2", configure.args=c(udunits2="--with-udunits2-include=/usr/include/udunits2"), repo="http://cran.rstudio.com")'  | R --vanilla
-
-# packages for BrownDog shiny app
-echo 'if(!"leaflet" %in% installed.packages()) install.packages("leaflet", repos="http://cran.rstudio.com/")' | R --vanilla
-echo 'if(!"RJSONIO" %in% installed.packages()) install.packages("RJSONIO", repos="http://cran.rstudio.com/")' | R --vanilla
-
-#echo 'update.packages(repos="http://cran.rstudio.com/", ask=FALSE)' |  R --vanilla
-echo 'x <- rownames(old.packages(repos="http://cran.rstudio.com/")); update.packages(repos="http://cran.rstudio.com/", ask=FALSE, oldPkgs=x[!x %in% "rgl"])' |  R --vanilla
-
-#echo 'update.packages(repos="http://cran.rstudio.com/", ask=FALSE)' | R --vanilla
-echo 'x <- rownames(old.packages(repos="http://cran.rstudio.com/")); update.packages(repos="http://cran.rstudio.com/", ask=FALSE, oldPkgs=x[!x %in% "rgl"])' | R --vanilla
diff --git a/docker/install_packages.sh b/docker/install_packages.sh
deleted file mode 100644
index 6ece1b32631..00000000000
--- a/docker/install_packages.sh
+++ /dev/null
@@ -1,87 +0,0 @@
-#!/bin/bash
-
-. /build/install_pecan_preprocessor.sh
-
-echo "######################################################################"
-echo "SETTING UP REPOS"
-echo "######################################################################"
-case "$OS_VERSION" in
-  RH_5)
-     yum install -y wget
-     wget -O /etc/yum.repos.d/cornell.repo http://download.opensuse.org/repositories/home:cornell_vrdc/CentOS_CentOS-6/home:cornell_vrdc.repo
-     rpm -Uvh http://download.fedoraproject.org/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm
-    ;;
-  RH_6)
-     yum install -y wget
-     wget -O /etc/yum.repos.d/cornell.repo http://download.opensuse.org/repositories/home:cornell_vrdc/CentOS_CentOS-6/home:cornell_vrdc.repo
-     yum -y localinstall https://download.postgresql.org/pub/repos/yum/9.5/redhat/rhel-6-x86_64/pgdg-centos95-9.5-2.noarch.rpm
-     rpm -Uvh http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
-    ;;
-  RH_7)
-     yum install -y wget
-     wget -O /etc/yum.repos.d/cornell.repo wget http://download.opensuse.org/repositories/home:cornell_vrdc/CentOS_7/home:cornell_vrdc.repo
-     yum -y localinstall https://download.postgresql.org/pub/repos/yum/9.5/redhat/rhel-7-x86_64/pgdg-centos95-9.5-2.noarch.rpm
-     rpm -Uvh http://download.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-6.noarch.rpm
-    setsebool -P httpd_can_network_connect 1
-    ;;
-  Ubuntu)
-    # if [ ! -e /etc/apt/sources.list.d/R.list ]; then
-    #    sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -s -c`/" > /etc/apt/sources.list.d/R.list'
-    #    apt-key adv --keyserver keyserver.ubuntu.com --recv E084DAB9
-    # fi
-    if [ ! -e /etc/apt/sources.list.d/ruby.list ]; then
-       sh -c 'echo "deb http://ppa.launchpad.net/brightbox/ruby-ng/ubuntu xenial main" > /etc/apt/sources.list.d/ruby.list'
-       apt-key adv --keyserver keyserver.ubuntu.com --recv C3173AA6
-    fi
-    # if [ ! -e /etc/apt/sources.list.d/pgdg.list ]; then
-    #    sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt `lsb_release -s -c`-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
-    #   wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc |  apt-key add -
-    # fi
-     apt-get -qq -y update
-    ;;
-esac
-
-echo "######################################################################"
-echo "INSTALLING PACKAGES"
-echo "######################################################################"
-case "$OS_VERSION" in
-  RH_*)
-     yum install -y git R gfortran openssl-devel
-     yum install -y openmpi openmpi-devel netcdf netcdf-openmpi netcdf-devel netcdf-openmpi-devel netcdf-fortran-devel netcdf-fortran-openmpi
-     ln -s /usr/lib64/openmpi/bin/mpicc /usr/bin/mpicc
-     ln -s /usr/lib64/openmpi/bin/mpif90 /usr/bin/mpif90
-    # for ED
-     yum install -y hdf5-openmpi-devel
-    # for LPJ-GUESS
-     yum install -y cmake
-    # for DALEC
-     yum install -y gsl-devel liblas-devel lapack-devel
-    # for PEcAn
-     yum install -y ed libpng-devel libpng12-devel libjpeg-turbo-devel jags4 jags4-devel python-devel udunits2-devel gdal-devel proj-devel proj-devel proj-nad proj-epsg libxml2-devel udunits2-devel gmp-devel
-    # for PostgreSQL
-     yum install -y postgresql95-server postgresql95-devel postgis2_95
-    # web gui
-     yum install -y httpd php php-pgsql php-xml
-    ;;
-  Ubuntu)
-     apt-get -y install build-essential gfortran git r-base-core r-base r-base-dev jags liblapack-dev libnetcdf-dev netcdf-bin bc libcurl4-gnutls-dev curl udunits-bin libudunits2-dev libgmp-dev python-dev libgdal1-dev libproj-dev expect
-     apt-get -y install openmpi-bin libopenmpi-dev
-     apt-get -y install libgsl0-dev libssl-dev
-    #
-     apt-get -y install r-cran-ggplot2
-    # for maeswrap
-     apt-get -y install r-cran-rgl
-    # for R doc
-     apt-get -y install texinfo texlive-latex-base texlive-latex-extra texlive-fonts-recommended
-    # ruby
-     apt-get -y install ruby2.1 ruby2.1-dev
-    # for LPJ-GUESS
-     apt-get -y install cmake
-    # for PostgreSQL
-    # apt-get -y install libdbd-pgsql postgresql-9.5 postgresql-client-9.5 libpq-dev postgresql-9.5-postgis-2.2 postgresql-9.5-postgis-scripts
-     apt-get -y install postgresql-client-9.5
-    # for web gui
-    # apt-get -y install apache2 libapache2-mod-php7.0 php7.0 libapache2-mod-passenger php7.0-xml php-ssh2 php7.0-pgsql
-    # Ubuntu 14.04 php5-pgsql libapache2-mod-php5 php5 and no php-xml
-    ;;
-esac
diff --git a/docker/install_pecan.sh b/docker/install_pecan.sh
deleted file mode 100644
index e848c17ff93..00000000000
--- a/docker/install_pecan.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-. /build/install_pecan_preprocessor.sh
-
-echo "######################################################################"
-echo "PECAN"
-echo "######################################################################"
-if [ ! -e ${HOME}/pecan ]; then
-  cd
-  git clone https://github.com/PecanProject/pecan.git
-fi
-cd ${HOME}/pecan
-git pull
-mkdir .install
-make
diff --git a/docker/install_pecan_preprocessor.sh b/docker/install_pecan_preprocessor.sh
deleted file mode 100644
index 0f715370898..00000000000
--- a/docker/install_pecan_preprocessor.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/bin/bash
-
-set -e
-
-#if [ "`whoami`" == "root" ]; then
-#  echo "Don't run this script as root"
-#  exit -1
-#fi
-
-# overiding environment variables
-
-export HOME='/home/carya'
-
-# configuration
-# BROWNDOG_URL="http://dap.ncsa.illinois.edu:8184/convert/";
-# BROWNDOG_USERNAME="";
-# BROWNDOG_PASSWORD="";
-#
-# GOOGLE_MAP_KEY=""
-
-#SETUP_VM=""
-#SETUP_PALEON=""
-#REBUILD=""
-
-# commented out might need it later for communication purpose
-#RSTUDIO_SERVER="1.0.136"
-#SHINY_SERVER="1.5.3.838"
-
-if [ -e $(dirname $0)/install_pecan.config ]; then
-  . $(dirname $0)/install_pecan.config
-fi
-
-if [ -e /etc/redhat-release ]; then
-  OS_VERSION="RH_$( sed -r 's/.* ([0-9]+)\..*/\1/' /etc/redhat-release )"
-  HTTP_CONF="/etc/httpd/conf.d/"
-  chmod o+x ${HOME}
-else
-  OS_VERSION="Ubuntu"
-  HTTP_CONF="/etc/apache2/conf-available/"
-fi
diff --git a/docker/install_pecan_web.sh b/docker/install_pecan_web.sh
deleted file mode 100644
index 6f749e8bb53..00000000000
--- a/docker/install_pecan_web.sh
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/bin/bash
-
-. /build/install_pecan_preprocessor.sh
-
-echo "######################################################################"
-echo "PECAN-WEB"
-echo "######################################################################"
-
-#configuration
-
-BROWNDOG_URL="http://dap.ncsa.illinois.edu:8184/convert/";
-BROWNDOG_USERNAME="";
-BROWNDOG_PASSWORD="";
-
-GOOGLE_MAP_KEY=""
-
-echo "Intalling php and apache2"
-
-# for web gui
-apt-get -y install apache2 libapache2-mod-php7.0 php7.0 libapache2-mod-passenger php7.0-xml php-ssh2 php7.0-pgsql
-
-echo "Setting up web gui"
-curl -o /var/www/html/pecan.pdf https://www.gitbook.com/download/pdf/book/pecan/pecan-documentation
-rm /var/www/html/index.html
-ln -s  ${HOME}/pecan/documentation/index_vm.html /var/www/html/index.html
-
-if [ ! -e ${HOME}/pecan/web/config.php ]; then
-  sed -e "s#browndog_url=.*#browndog_url=\"${BROWNDOG_URL}\";#" \
-      -e "s#browndog_username=.*#browndog_username=\"${BROWNDOG_USERNAME}\";#" \
-      -e "s#browndog_password=.*#browndog_password=\"${BROWNDOG_PASSWORD}\";#" \
-      -e "s#googleMapKey=.*#googleMapKey=\"${GOOGLE_MAP_KEY}\";#" \
-      -e "s/carya/$USER/g" ${HOME}/pecan/web/config.example.php > ${HOME}/pecan/web/config.php
-fi
-
-if [ ! -e ${HTTP_CONF}/pecan.conf ]; then
-  cat > /tmp/pecan.conf << EOF
-Alias /pecan ${HOME}/pecan/web
-<Directory ${HOME}/pecan/web>
-  DirectoryIndex index.php
-  Options +ExecCGI
-  Require all granted
-</Directory>
-EOF
-  cp /tmp/pecan.conf ${HTTP_CONF}/pecan.conf
-  rm /tmp/pecan.conf
-fi
-
-a2enconf pecan.conf
-
-/etc/init.d/apache2 restart
diff --git a/docker/install_sipnet.sh b/docker/install_sipnet.sh
deleted file mode 100644
index cd251803cd7..00000000000
--- a/docker/install_sipnet.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-
-
-. /build/install_pecan_preprocessor.sh
-
-echo "######################################################################"
-echo "SIPNET"
-echo "######################################################################"
-if [ ! -e ${HOME}/sipnet_unk ]; then
-  cd
-  curl -o sipnet_unk.tar.gz http://isda.ncsa.illinois.edu/~kooper/PEcAn/models/sipnet_unk.tar.gz
-  tar zxf sipnet_unk.tar.gz
-  rm sipnet_unk.tar.gz
-fi
-cd ${HOME}/sipnet_unk/
-make clean
-make
-cp sipnet /usr/local/bin/sipnet.runk
-make clean
-
-if [ ! -e ${HOME}/sipnet_r136 ]; then
-  cd
-  curl -o sipnet_r136.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/sipnet_r136.tar.gz
-  tar zxf sipnet_r136.tar.gz
-  rm sipnet_r136.tar.gz
-  sed -i 's#$(LD) $(LIBLINKS) \(.*\)#$(LD) \1 $(LIBLINKS)#' ${HOME}/sipnet_r136/Makefile
-fi
-cd ${HOME}/sipnet_r136/
-make clean
-make
-cp sipnet /usr/local/bin/sipnet.r136
-make clean
diff --git a/docker/models/Dockerfile.ed2 b/docker/models/Dockerfile.ed2
new file mode 100644
index 00000000000..54a7090042c
--- /dev/null
+++ b/docker/models/Dockerfile.ed2
@@ -0,0 +1,63 @@
+# ----------------------------------------------------------------------
+# BUILD MODEL BINARY
+# ----------------------------------------------------------------------
+FROM debian:testing as model-binary
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+
+# install dependencies
+RUN apt-get update \
+    && apt-get install -y \
+       build-essential \
+       curl \
+       gfortran \
+       git \
+       libhdf5-dev \
+       libopenmpi-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# download, unzip and build ed2
+WORKDIR /src
+RUN git clone https://github.com/EDmodel/ED2.git \
+    && cd ED2/ED/build \
+    && curl -o make/include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s` \
+    && if [ "${MODEL_VERSION}" != "git" ]; then git checkout ${MODEL_VERSION}; fi \
+    && ./install.sh -g -p VM
+
+########################################################################
+
+# ----------------------------------------------------------------------
+# BUILD PECAN FOR MODEL
+# ----------------------------------------------------------------------
+FROM pecan/executor:latest
+
+# ----------------------------------------------------------------------
+# INSTALL MODEL SPECIFIC PIECES
+# ----------------------------------------------------------------------
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+       libgfortran5 \
+       libopenmpi3 \
+    && rm -rf /var/lib/apt/lists/*
+
+# INSTALL PEcAn.ED2
+#COPY models/ed2 /src/ed/
+#RUN Rscript --vanilla -e  "devtools::install_local('/src/ed'); q(status=as.integer(!'PEcAn.ED2' %in% installed.packages()))" 
+
+# ----------------------------------------------------------------------
+# SETUP FOR SPECIFIC MODEL
+# ----------------------------------------------------------------------
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+
+# variables to store in docker image
+ENV APPLICATION="./job.sh" \
+    MODEL_TYPE="ED2" \
+    MODEL_VERSION="${MODEL_VERSION}" \
+    RABBITMQ_QUEUE="${MODEL_TYPE}_${MODEL_VERSION}"
+
+# COPY model binary
+COPY --from=model-binary /src/ED2/ED/build/ed_2.1-opt /usr/local/bin/ed2.${MODEL_VERSION}
diff --git a/docker/models/Dockerfile.sipnet b/docker/models/Dockerfile.sipnet
new file mode 100644
index 00000000000..a96cb529f61
--- /dev/null
+++ b/docker/models/Dockerfile.sipnet
@@ -0,0 +1,59 @@
+# ----------------------------------------------------------------------
+# BUILD SIPNET BINARY
+# ----------------------------------------------------------------------
+FROM debian as sipnet-binary
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=136
+
+# install dependencies
+RUN apt-get update \
+    && apt-get install -y \
+       curl \
+       gcc \
+       make \
+    && rm -rf /var/lib/apt/lists/*
+
+# download, unzip and build sipnet
+WORKDIR /src
+RUN curl -o sipnet_r${MODEL_VERSION}.tar.gz http://isda.ncsa.illinois.edu/~kooper/PEcAn/sipnet/sipnet_r${MODEL_VERSION}.tar.gz \
+    && tar zxf sipnet_r${MODEL_VERSION}.tar.gz \
+    && cd sipnet_r${MODEL_VERSION} \
+    && make \
+    && mv sipnet /src
+
+########################################################################
+
+# ----------------------------------------------------------------------
+# BUILD PECAN FOR SIPNET
+# ----------------------------------------------------------------------
+FROM pecan/executor:latest
+
+# ----------------------------------------------------------------------
+# INSTALL SIPNET SPECIFIC PIECES
+# ----------------------------------------------------------------------
+
+# INSTALL PEcAn.data.atmosphere
+#COPY modules/data.atmosphere /src/data.atmosphere/
+#RUN Rscript --vanilla -e  "devtools::install_local('/src/data.atmosphere'); q(status=as.integer(!'PEcAn.data.atmosphere' %in% installed.packages()))" 
+
+# INSTALL PEcAn.SIPNET
+#COPY models/sipnet /src/sipnet/
+#RUN Rscript --vanilla -e  "devtools::install_local('/src/sipnet'); q(status=as.integer(!'PEcAn.SIPNET' %in% installed.packages()))" 
+
+# ----------------------------------------------------------------------
+# SETUP FOR SPECIFIC SIPNET VERSION
+# ----------------------------------------------------------------------
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=136
+
+# variables to store in docker image
+ENV APPLICATION="./job.sh" \
+    MODEL_TYPE="SIPNET_" \
+    MODEL_VERSION="${MODEL_VERSION}" \
+    RABBITMQ_QUEUE="${MODEL_TYPE}_${MODEL_VERSION}"
+
+# COPY sipnet binary
+COPY --from=sipnet-binary /src/sipnet /usr/local/bin/sipnet.${SIPNET_VERSION}
+
diff --git a/docker/receiver.py b/docker/receiver.py
new file mode 100644
index 00000000000..c067847e29b
--- /dev/null
+++ b/docker/receiver.py
@@ -0,0 +1,69 @@
+import json
+import logging
+import os
+import subprocess
+import traceback
+
+import pika
+
+
+rabbitmq_uri   = os.getenv('RABBITMQ_URI',   'amqp://guest:guest@rabbitmq/%2F')
+rabbitmq_queue = os.getenv('RABBITMQ_QUEUE', 'pecan')
+application    = os.getenv('APPLICATION',    'job.sh')
+
+# called for every message, this will start the program and ack message if all is ok.
+def callback(ch, method, properties, body):
+    logging.info(body)
+    jbody = json.loads(body)
+
+    logging.info("Starting job in %s." % jbody['folder'])
+    try:
+        output = subprocess.check_output(application, stderr=subprocess.STDOUT, shell=True, cwd=jbody['folder'])
+        status = 'OK'
+        logging.info("Finished running job.")
+    except subprocess.CalledProcessError as e:
+        logging.exception("Error running job.", e)
+        output = e.output
+        status = 'ERROR'
+    except Exception as e:
+        logging.exception("Error running job.", e)
+        output = str(e)
+        status = 'ERROR'
+    finally:
+        ch.basic_ack(delivery_tag=method.delivery_tag)
+
+    try:
+        with open(os.path.join(jbody['folder'], 'rabbitmq.out'), 'w') as out:
+            out.write(str(output) + "\n")
+            out.write(status + "\n")
+    except Exception as e:
+        logging.exception("Error writing status.", e)
+
+
+def start_rabbitmq():
+    # create connection to rabbitmq
+    connection = pika.BlockingConnection(pika.URLParameters(rabbitmq_uri))
+    channel = connection.channel()
+
+    # make sure queue exists
+    channel.queue_declare(queue=rabbitmq_queue, durable=True)
+
+    # receive 1 message at a time, call callback function
+    channel.basic_qos(prefetch_count=1)
+    channel.basic_consume(callback, queue=rabbitmq_queue)
+
+    # receive messages
+    try:
+        logging.info(' [*] Waiting for messages. To exit press CTRL+C')
+        channel.start_consuming()
+    except KeyboardInterrupt:
+        pass
+    finally:
+        connection.close()
+
+
+if __name__ == "__main__":
+    logging.basicConfig(format='%(asctime)-15s [%(threadName)-15s] %(levelname)-7s : %(name)s - %(message)s',
+                        level=logging.INFO)
+    logging.getLogger('requests.packages.urllib3.connectionpool').setLevel(logging.WARN)
+    start_rabbitmq()
diff --git a/docker/runcmd.R b/docker/runcmd.R
deleted file mode 100755
index c339264f974..00000000000
--- a/docker/runcmd.R
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/usr/bin/env Rscript
-
-require(PEcAn.logger)
-
-run_model <- function(model, revision, binary, outdir, lat, lon, start_date, end_date, delete_raw, overwrite=FALSE) {
-  # check if model already ran successfullly
-  if (file.exists("DONE")) {
-    if (overwrite) {
-      file.remove("DONE")
-    } else {
-      PEcAn.logger::logger.info("Model already ran successfullly")
-      return(TRUE)
-    }
-  }
-
-    # check if model already ran unsuccessfully
-  if (file.exists("ERROR")) {
-    if (overwrite) {
-      file.remove("ERROR")
-    } else {
-      PEcAn.logger::logger.info("Model already ran unsuccessfully")
-      return(FALSE)
-    }
-  }
-
-  # run model
-  result_binary <- system2(binary, stdout="stdout.log", stderr="stderr.log")
-  if (result_binary != 0) {
-    file.create("ERROR")
-    PEcAn.logger::logger.error("Program exited with exit code of", result_binary, "See logfiles for more details.")
-    return(FALSE)
-  }
-
-  # some model specific checks to see if there was a failure
-  # TODO this check should become part of the model package
-  if (model == "ED2") {
-    # TODO check the log file to see if everything was OK.
-  }
-
-  # convert model output to netcdf
-  args <- list(outdir, lat, lon, start_date, end_date, delete_raw, revision, overwrite)
-  func <- get(paste0("model2netcdf.", model), asNamespace(paste0("PEcAn.", model)))
-  do.call(func, args)
-
-  # success
-  file.create("DONE")
-  return(TRUE)
-}
-
-model      <- toupper(Sys.getenv("MODEL"))
-revision   <- Sys.getenv("REVISION")
-binary     <- Sys.getenv("BINARY")
-outdir     <- Sys.getenv("OUTDIR")
-lat        <- Sys.getenv("SITE_LAT")
-lon        <- Sys.getenv("SITE_LON")
-start_date <- Sys.getenv("START_DATE")
-end_date   <- Sys.getenv("END_DATE")
-delete_raw <- Sys.getenv("DELETE_RAW")
-overwrite  <- Sys.getenv("OVERWRITE")
-
-run_model(model, revision, binary, outdir, lat, lon, start_date, end_date, delete_raw, overwrite)
diff --git a/docker/runit/cron b/docker/runit/cron
deleted file mode 100644
index e36fbfd51ec..00000000000
--- a/docker/runit/cron
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-
-exec /usr/sbin/cron -f
diff --git a/docker/runit/cron_log b/docker/runit/cron_log
deleted file mode 100644
index c0c15e1ca78..00000000000
--- a/docker/runit/cron_log
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-
-exec chpst -u nobody svlogd -tt /var/log/cron/
diff --git a/docker/sender.py b/docker/sender.py
new file mode 100644
index 00000000000..fb5b834c3db
--- /dev/null
+++ b/docker/sender.py
@@ -0,0 +1,31 @@
+import json
+import sys
+
+import pika
+
+
+# parse command line arguments
+# send.py <rabbitmq_uri> <queue> <message>
+rabbitmq_uri     = sys.argv[1]
+rabbitmq_queue   = sys.argv[2]
+rabbitmq_message = {
+    'folder': sys.argv[3]
+}
+
+# create connection to rabbitmq
+connection = pika.BlockingConnection(pika.URLParameters(rabbitmq_uri))
+channel = connection.channel()
+
+# make sure queue exists
+channel.queue_declare(queue=rabbitmq_queue, durable=True)
+
+# publish message on queue
+channel.basic_publish(exchange='',
+                      routing_key=rabbitmq_queue,
+                      body=json.dumps(rabbitmq_message),
+                      properties=pika.BasicProperties(
+                         delivery_mode = 2, # make message persistent
+                      ))
+
+# close connection
+connection.close()
diff --git a/docker/setup_postgresql.sh b/docker/setup_postgresql.sh
deleted file mode 100644
index 3e0250a3263..00000000000
--- a/docker/setup_postgresql.sh
+++ /dev/null
@@ -1,43 +0,0 @@
-echo "######################################################################"
-echo "POSTGRES"
-echo "######################################################################"
-#    ADD export PATH=${PATH}:/usr/pgsql-9.5/bin
-#    ADD exclude=postgresql* to /etc/yum.repos.d/CentOS-Base.repo or /etc/yum/pluginconf.d/rhnplugin.conf
-#    SEE https://wiki.postgresql.org/wiki/YUM_Installation#Configure_your_YUM_repository
-case "$OS_VERSION" in
-  RH_5)
-    echo "No PostgreSQL configuration (yet) for RedHat 5"
-    exit 1
-    ;;
-  RH_6)
-    sudo service postgresql-9.5 initdb
-    sudo sh -c 'if ! grep -Fq "bety" /var/lib/pgsql/9.5/data/pg_hba.conf ; then
-      sed -i "/# TYPE/ a\
-local   all             bety                                    trust\n\
-host    all             bety            127.0.0.1/32            trust\n\
-host    all             bety            ::1/128                 trust" /var/lib/pgsql/9.5/data/pg_hba.conf
-    fi'
-    chkconfig postgresql-9.5 on
-    sudo service postgresql-9.5 start
-    ;;
-  RH_7)
-    sudo /usr/pgsql-9.5/bin/postgresql95-setup initdb
-    sudo sh -c 'if ! grep -Fq "bety" /var/lib/pgsql/9.5/data/pg_hba.conf ; then
-      sed -i "/# TYPE/ a\
-local   all             bety                                    trust\n\
-host    all             bety            127.0.0.1/32            trust\n\
-host    all             bety            ::1/128                 trust" /var/lib/pgsql/9.5/data/pg_hba.conf
-    fi'
-    sudo systemctl enable postgresql-9.5.service
-    sudo systemctl start postgresql-9.5.service
-    ;;
-  Ubuntu)
-    sudo sh -c 'if ! grep -Fq "bety" /etc/postgresql/9.5/main/pg_hba.conf ; then
-      sed -i "/# TYPE/ a\
-local   all             bety                                    trust\n\
-host    all             bety            127.0.0.1/32            trust\n\
-host    all             bety            ::1/128                 trust" /etc/postgresql/9.5/main/pg_hba.conf
-fi'
-    sudo service postgresql restart
-    ;;
-esac
diff --git a/docker/system_services.sh b/docker/system_services.sh
deleted file mode 100644
index 9e991c011b0..00000000000
--- a/docker/system_services.sh
+++ /dev/null
@@ -1,90 +0,0 @@
-#!/bin/bash
-export LC_ALL=C
-export DEBIAN_FRONTEND=noninteractive
-minimal_apt_get_install='apt-get install -y --no-install-recommends'
-
-## temporarily disable dpkg fsync to make building faster.
-if [[ ! -e /etc/dpkg/dpkg.cfg.d/docker-apt-speedup ]]; then
-	echo force-unsafe-io > /etc/dpkg/dpkg.cfg.d/docker-apt-speedup
-fi
-
-## prevent initramfs updates from trying to run grub and lilo.
-export INITRD=no
-mkdir -p /etc/container_environment
-echo -n no > /etc/container_environment/INITRD
-
-## enable Ubuntu Universe and Multiverse.
-sed -i 's/^#\s*\(deb.*universe\)$/\1/g' /etc/apt/sources.list
-sed -i 's/^#\s*\(deb.*multiverse\)$/\1/g' /etc/apt/sources.list
-apt-get update
-
-## fix some issues with APT packages.
-dpkg-divert --local --rename --add /sbin/initctl
-ln -sf /bin/true /sbin/initctl
-
-## replace the 'ischroot' tool to make it always return true.
-dpkg-divert --local --rename --add /usr/bin/ischroot
-ln -sf /bin/true /usr/bin/ischroot
-
-## upgrade all packages.
-apt-get dist-upgrade -y --no-install-recommends
-
-## install HTTPS support for APT.
-$minimal_apt_get_install apt-utils apt-transport-https ca-certificates language-pack-en
-
-## fix locale.
-locale-gen en_US.UTF-8
-update-locale LANG=en_US.UTF-8 LC_CTYPE=en_US.UTF-8 LANGUAGE=en_US:en LC_ALL=en_US.UTF-8
-echo -n en_US.UTF-8 > /etc/container_environment/LANG
-echo -n en_US.UTF-8 > /etc/container_environment/LC_CTYPE
-echo -n en_US:en > /etc/container_environment/LANGUAGE
-echo -n en_US.UTF-8 > /etc/container_environment/LC_ALL
-
-## install init process.
-cp /build/bin/my_init /sbin/
-chmod 750 /sbin/my_init
-mkdir -p /etc/my_init.d
-mkdir -p /etc/container_environment
-touch /etc/container_environment.sh
-touch /etc/container_environment.json
-chmod 700 /etc/container_environment
-
-groupadd -g 8377 docker_env
-chown :docker_env /etc/container_environment.sh /etc/container_environment.json
-chmod 640 /etc/container_environment.sh /etc/container_environment.json
-ln -s /etc/container_environment.sh /etc/profile.d/
-echo ". /etc/container_environment.sh" >> /root/.bashrc
-
-## install runit.
-$minimal_apt_get_install runit cron
-
-## install cron daemon.
-mkdir -p /etc/service/cron
-mkdir -p /var/log/cron
-chmod 600 /etc/crontabs
-cp /build/runit/cron /etc/service/cron/run
-cp /build/config/cron_log_config /var/log/cron/config
-chown -R nobody  /var/log/cron
-chmod +x /etc/service/cron/run
-
-## remove useless cron entries.
-rm -f /etc/cron.daily/standard
-rm -f /etc/cron.daily/upstart
-rm -f /etc/cron.daily/dpkg
-rm -f /etc/cron.daily/password
-rm -f /etc/cron.weekly/fstrim
-
-## often used tools.
-$minimal_apt_get_install curl less nano psmisc wget
-
-## fix other small problem.
-rm /bin/sh
-ln -s /bin/bash /bin/sh
-echo `. /etc/lsb-release; echo ${DISTRIB_CODENAME/*, /}` >> /etc/container_environment/DISTRIB_CODENAME
-
-## cleanup
-# apt-get clean
-# rm -rf /build
-# rm -rf /tmp/* /var/tmp/*
-# rm -rf /var/lib/apt/lists/*
-# rm -f /etc/dpkg/dpkg.cfg.d/02apt-speedup
diff --git a/docker/update_machine.sh b/docker/update_machine.sh
deleted file mode 100644
index ebbde9bba6b..00000000000
--- a/docker/update_machine.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/bash
-
-. /build/install_pecan_preprocessor.sh
-
-# actual install/update
-echo "######################################################################"
-echo "UPDATING MACHINE"
-echo "######################################################################"
-if [ ! -e /home/carya/ ]; then
-  mkdir /home/carya/
-  chmod 755 /home/carya/
-fi
-
-case "$OS_VERSION" in
-  RH_*)
-     yum update -y
-    if [ "$SETUP_VM" != "" ]; then
-       sed -i -e "s/^127.0.0.1 .*\$/127.0.0.1 ${HOSTNAME}.pecan ${HOSTNAME} localhost localhost.localdomain localhost4 localhost4.localdomain4/" /etc/hosts
-    fi
-    ;;
-  Ubuntu)
-     apt-get -qq -y update
-     apt-get -y dist-upgrade
-     apt-get -y purge --auto-remove
-    if [ "$SETUP_VM" != "" ]; then
-       sed -i -e "s/^127.0.0.1 .*\$/127.0.0.1 ${HOSTNAME}.pecan ${HOSTNAME} localhost/" /etc/hosts
-    fi
-    ;;
-  *)
-    echo "Unknown OS"
-    exit 1
-    ;;
-esac
diff --git a/documentation/index_vm.html b/documentation/index_vm.html
index 3def0882920..df3bfb18b94 100644
--- a/documentation/index_vm.html
+++ b/documentation/index_vm.html
@@ -11,7 +11,7 @@ <h1>PEcAn</h1>
 <li><a href="/rstudio/">RStudio</a></li>
 <li><a href="/pecan/setups/">Basic Setups</a></li>
 <li><a href="https://github.com/PecanProject">Code Repository</a></li>
-<li><a href="https://gitter.im/PecanProject/pecan">Chat Room</a></li>
+<li><a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE">Chat Room</a></li>
 <li><a href="https://github.com/PecanProject/pecan/issues/new">Submit an Issue / Bug Report</a></li>
 <li><a href="http://pecanproject.org">Project Homepage</a></li>
 </ul>
diff --git a/documentation/tutorials/01_Demo_Basic_Run/Demo01.Rmd b/documentation/tutorials/01_Demo_Basic_Run/Demo01.Rmd
index ae2254a5e09..91733254a58 100644
--- a/documentation/tutorials/01_Demo_Basic_Run/Demo01.Rmd
+++ b/documentation/tutorials/01_Demo_Basic_Run/Demo01.Rmd
@@ -110,7 +110,7 @@ You will see a data policy statement if you selected a data source with a policy
 
 #### If you get an error in your run 
 
-If you get an error in your run as part of a live demo or class activity, it is probably simplest to start over and try changing options and re-running (e.g. with a different site or PFT), as time does not permit detailed debugging. If the source of the error is not immediately obvious, you may want to take a look at the workflow.Rout to see the log of the PEcAn workflow or the logfile.txt to see the model execution output log and then refer to the [Documentation](http://pecanproject.github.io/documentation.html) or the [Chat Room](https://gitter.im/PecanProject/pecan) for help.
+If you get an error in your run as part of a live demo or class activity, it is probably simplest to start over and try changing options and re-running (e.g. with a different site or PFT), as time does not permit detailed debugging. If the source of the error is not immediately obvious, you may want to take a look at the workflow.Rout to see the log of the PEcAn workflow or the logfile.txt to see the model execution output log and then refer to the [Documentation](http://pecanproject.github.io/documentation.html) or the [Chat Room](https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE) for help.
 
 ### Model Run Workflow
 
diff --git a/documentation/tutorials/02_Demo_Uncertainty_Analysis/Demo02.Rmd b/documentation/tutorials/02_Demo_Uncertainty_Analysis/Demo02.Rmd
index 749a2a506df..81b2bd4bed0 100644
--- a/documentation/tutorials/02_Demo_Uncertainty_Analysis/Demo02.Rmd
+++ b/documentation/tutorials/02_Demo_Uncertainty_Analysis/Demo02.Rmd
@@ -109,5 +109,5 @@ The next set of tutorials will focus on the process of data assimilation and par
 
 Additional information about specific tasks (adding sites, models, data; software updates; etc.) and analyses (e.g. data assimilation) can be found in the PEcAn [documentation](https://pecanproject.github.io/pecan-documentation/)
 
-If you encounter a problem with PEcAn that’s not covered in the documentation, or if PEcAn is missing functionality you need, please search [known bugs and issues](https://github.com/PecanProject/pecan/issues?q=), submit a [bug report](https://github.com/PecanProject/pecan/issues/new), or ask a question in our [chat room](https://gitter.im/PecanProject/pecan). Additional questions can be directed to the [project manager](mailto:tonygard@bu.edu?subject=PEcAn Demo::)
+If you encounter a problem with PEcAn that’s not covered in the documentation, or if PEcAn is missing functionality you need, please search [known bugs and issues](https://github.com/PecanProject/pecan/issues?q=), submit a [bug report](https://github.com/PecanProject/pecan/issues/new), or ask a question in our [chat room](https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE). Additional questions can be directed to the [project manager](mailto:tonygard@bu.edu?subject=PEcAn Demo::)
 
diff --git a/models/biocro/DESCRIPTION b/models/biocro/DESCRIPTION
index ae067553d38..f4d8202298d 100644
--- a/models/biocro/DESCRIPTION
+++ b/models/biocro/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.BIOCRO
 Type: Package
 Title: PEcAn package for integration of the BioCro model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Deepak Jaiswal, Christopher Black
 Maintainer: David LeBauer <dlebauer@illinois.edu>
 Description: This module provides functions to link BioCro to PEcAn.
@@ -31,4 +31,5 @@ License: FreeBSD + file LICENSE
 Copyright: Energy Biosciences Institute, Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/biocro/R/write.configs.BIOCRO.R b/models/biocro/R/write.configs.BIOCRO.R
index 2bc90c6a8b3..d4c5d999976 100644
--- a/models/biocro/R/write.configs.BIOCRO.R
+++ b/models/biocro/R/write.configs.BIOCRO.R
@@ -17,14 +17,12 @@ PREFIX_XML <- "<?xml version=\"1.0\"?>\n<!DOCTYPE config SYSTEM \"biocro.dtd\">\
 ##' @title Convert samples for biocro
 ##' @param trait.samples a matrix or dataframe of samples from the trait distribution
 ##' @param biocro_version numeric, but currently only checks whether version is less than 1.0
-##' @return matrix or dataframe with values transformed
+##' @return dataframe with values transformed
 ##' @export
 ##' @author David LeBauer
 convert.samples.BIOCRO <- function(trait.samples, biocro_version=1.0) {
 
-  if (is.list(trait.samples)) {
-    trait.samples <- as.data.frame(trait.samples)
-  }
+  trait.samples <- as.data.frame(trait.samples)
   trait.names <- colnames(trait.samples)
 
   ## transform values with different units cuticular conductance - BETY default is
diff --git a/models/biocro/inst/extdata/pecan.biocro.xml b/models/biocro/inst/extdata/pecan.biocro.xml
index 10ecd4752a6..1afbc5a9d49 100644
--- a/models/biocro/inst/extdata/pecan.biocro.xml
+++ b/models/biocro/inst/extdata/pecan.biocro.xml
@@ -12,8 +12,8 @@
       <password>bety</password>
       <dbname>bety</dbname>
       <host>localhost</host>
-      <dbfiles>$HOME/.pecan/dbfiles</dbfiles>
     </bety>
+    <dbfiles>$HOME/.pecan/dbfiles</dbfiles>
   </database>
   <meta.analysis>
     <iter>3000</iter>
diff --git a/models/biocro/man/convert.samples.BIOCRO.Rd b/models/biocro/man/convert.samples.BIOCRO.Rd
index bd3a8896c32..8964f3284de 100644
--- a/models/biocro/man/convert.samples.BIOCRO.Rd
+++ b/models/biocro/man/convert.samples.BIOCRO.Rd
@@ -12,7 +12,7 @@ convert.samples.BIOCRO(trait.samples, biocro_version = 1)
 \item{biocro_version}{numeric, but currently only checks whether version is less than 1.0}
 }
 \value{
-matrix or dataframe with values transformed
+dataframe with values transformed
 }
 \description{
 convert parameters from PEcAn database default units to biocro defaults
diff --git a/models/biocro/man/met2model.BIOCRO.Rd b/models/biocro/man/met2model.BIOCRO.Rd
index 49e18797939..d88c1021439 100644
--- a/models/biocro/man/met2model.BIOCRO.Rd
+++ b/models/biocro/man/met2model.BIOCRO.Rd
@@ -4,8 +4,8 @@
 \alias{met2model.BIOCRO}
 \title{Write BioCro met files}
 \usage{
-met2model.BIOCRO(in.path, in.prefix, outfolder, overwrite = FALSE, lat, lon,
-  start_date, end_date, ...)
+met2model.BIOCRO(in.path, in.prefix, outfolder, overwrite = FALSE, lat,
+  lon, start_date, end_date, ...)
 }
 \arguments{
 \item{in.path}{path on disk where CF file lives}
diff --git a/models/biocro/tests/testthat/data/pecan.biocro.xml b/models/biocro/tests/testthat/data/pecan.biocro.xml
index 59d2f7b5eb3..8ad2fab701d 100644
--- a/models/biocro/tests/testthat/data/pecan.biocro.xml
+++ b/models/biocro/tests/testthat/data/pecan.biocro.xml
@@ -12,9 +12,9 @@
       <password>bety</password>
       <dbname>bety</dbname>
       <host>localhost</host>
-      <dbfiles>$HOME/.pecan/dbfiles</dbfiles>
       <driver>PostgreSQL</driver>
     </bety>
+    <dbfiles>$HOME/.pecan/dbfiles</dbfiles>
   </database>
   <meta.analysis>
     <iter>3000</iter>
diff --git a/models/biocro/tests/testthat/test.write.configs.BIOCRO.R b/models/biocro/tests/testthat/test.write.configs.BIOCRO.R
index 1825f3d7759..ec050668d7b 100644
--- a/models/biocro/tests/testthat/test.write.configs.BIOCRO.R
+++ b/models/biocro/tests/testthat/test.write.configs.BIOCRO.R
@@ -21,10 +21,6 @@ test_that("convert.samples.BIOCRO works for BioCro 0.9", {
   expect_equal(biocro.parms$SLA, samples$biocro.saof$SLA)
   expect_equal(biocro.parms$Rd, samples$biocro.saof$leaf_respiration_rate_m2)
   expect_equal(biocro.parms$b1, samples$biocro.saof$stomatal_slope.BB)
-
-  ## re-create bug #1491
-  test.list <- list(vmax = 1, b0 = 2)
-  convert.samples.BIOCRO(test.list, 0.9)  ## this should work
 })
 
 test_that("convert.samples.BIOCRO works for BioCro 1.0", {
@@ -38,6 +34,20 @@ test_that("convert.samples.BIOCRO works for BioCro 1.0", {
   expect_equal(biocro.parms$b1, samples$biocro.saof$stomatal_slope.BB)
 })
 
+test_that("convert.samples.BIOCRO accepts list, matrix, data frame", {
+  in_df <- data.frame(Vcmax = 1, b0 = 2, SLA=3)
+  in_lst <- list(Vcmax = 1, b0 = 2, SLA = 3)
+  in_mtrx <- matrix(1:3, ncol = 3, dimnames = list(NULL, c("Vcmax", "b0", "SLA")))
+  
+  out <- in_df
+  out$SLA <- out$SLA/10 # bety sends kg/m2, biocro takes g/cm2
+  colnames(out) <- c("vmax1", "b0", "iSp")
+    
+  expect_equal(convert.samples.BIOCRO(in_df, 1.0), out)  # Redmine #1491
+  expect_equal(convert.samples.BIOCRO(in_lst, 1.0), out)
+  expect_equal(convert.samples.BIOCRO(in_mtrx, 1.0), out)
+})
+
 test_that("write.config.BIOCRO produces expected output", {
   for (q in rownames(samples$biocro.saof)) {
     outdir <- file.path(settings$modeloutdir, q)
diff --git a/models/cable/DESCRIPTION b/models/cable/DESCRIPTION
index 95875ab4e80..480e63fb5ff 100644
--- a/models/cable/DESCRIPTION
+++ b/models/cable/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.CABLE
 Type: Package
 Title: PEcAn package for integration of the CABLE model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Kaitlin Ragosta
 Maintainer: Anthony Gardella <tonygard@bu.edu>
 Description: This module provides functions to link the (CABLE) to PEcAn.
@@ -17,4 +17,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/cable/man/write.config.CABLE.Rd b/models/cable/man/write.config.CABLE.Rd
index e9d649106f6..6c6259fd459 100644
--- a/models/cable/man/write.config.CABLE.Rd
+++ b/models/cable/man/write.config.CABLE.Rd
@@ -26,5 +26,5 @@ Requires a pft xml object, a list of trait values for a single model run,
 and the name of the file to create
 }
 \author{
-Rob Kooper
+Rob Kooper, Kaitlin Ragosta
 }
diff --git a/models/clm45/DESCRIPTION b/models/clm45/DESCRIPTION
index c94708a90bb..5846abab8e4 100644
--- a/models/clm45/DESCRIPTION
+++ b/models/clm45/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.CLM45
 Type: Package
 Title: PEcAn package for integration of CLM4.5 model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
@@ -23,4 +23,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/clm45/man/met2model.CLM45.Rd b/models/clm45/man/met2model.CLM45.Rd
index 07b549864e5..afe68376cbb 100644
--- a/models/clm45/man/met2model.CLM45.Rd
+++ b/models/clm45/man/met2model.CLM45.Rd
@@ -4,8 +4,8 @@
 \alias{met2model.CLM45}
 \title{met2model for CLM45}
 \usage{
-met2model.CLM45(in.path, in.prefix, outfolder, start_date, end_date, lst = 0,
-  lat, lon, ..., overwrite = FALSE, verbose = FALSE)
+met2model.CLM45(in.path, in.prefix, outfolder, start_date, end_date,
+  lst = 0, lat, lon, ..., overwrite = FALSE, verbose = FALSE)
 }
 \arguments{
 \item{in.path}{location on disk where inputs are stored}
diff --git a/models/clm45/man/model2netcdf.CLM45.Rd b/models/clm45/man/model2netcdf.CLM45.Rd
index 1994ec87342..3896d6aae55 100644
--- a/models/clm45/man/model2netcdf.CLM45.Rd
+++ b/models/clm45/man/model2netcdf.CLM45.Rd
@@ -17,6 +17,9 @@ model2netcdf.CLM45(outdir, sitelat, sitelon, start_date, end_date)
 
 \item{end_date}{End time of the simulation}
 }
+\description{
+Code to convert CLM45 netcdf output into into CF standard
+}
 \author{
 Michael Dietze
 }
diff --git a/models/dalec/DESCRIPTION b/models/dalec/DESCRIPTION
index 800a9e7376c..4e3d6211d83 100644
--- a/models/dalec/DESCRIPTION
+++ b/models/dalec/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.DALEC
 Type: Package
 Title: PEcAn package for integration of the DALEC model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze, Tristain Quaife
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: This module provides functions to link DALEC to PEcAn.
@@ -21,4 +21,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/dvmdostem/DESCRIPTION b/models/dvmdostem/DESCRIPTION
index 011dcd34728..ab8d2db50f4 100644
--- a/models/dvmdostem/DESCRIPTION
+++ b/models/dvmdostem/DESCRIPTION
@@ -1,13 +1,14 @@
 Package: PEcAn.dvmdostem
 Type: Package
 Title: PEcAn package for integration of the dvmdostem model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Tobey Carman, Shawn Serbin
 Maintainer: Tobey Carman <tcarman2@alaska.edu>, Shawn Serbin <sserbin@bnl.gov>
 Description: This module provides functions to link the dvmdostem model to
     PEcAn.
 Imports:
+	ncdf4,
     PEcAn.utils (>= 1.4.8),
     rjson
 Suggests:
@@ -18,4 +19,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/dvmdostem/inst/workflow_small.R b/models/dvmdostem/inst/workflow_small.R
index 9957b6a8f3b..4094ee9438c 100644
--- a/models/dvmdostem/inst/workflow_small.R
+++ b/models/dvmdostem/inst/workflow_small.R
@@ -75,7 +75,7 @@ settings <- PEcAn.utils::do_conversions(settings)
 # Query the trait database for data and priors
 if (PEcAn.utils::status.check("TRAIT") == 0){
   PEcAn.utils::status.start("TRAIT")
-  settings <- PEcAn.DB::runModule.get.trait.data(settings)
+  settings <- PEcAn.workflow::runModule.get.trait.data(settings)
   PEcAn.settings::write.settings(settings, outputfile='pecan.TRAIT.xml')
   PEcAn.utils::status.end()
 } else if (file.exists(file.path(settings$outdir, 'pecan.TRAIT.xml'))) {
@@ -95,7 +95,7 @@ if(!is.null(settings$meta.analysis)) {
 # Write model specific configs
 if (PEcAn.utils::status.check("CONFIG") == 0){
   PEcAn.utils::status.start("CONFIG")
-  settings <- PEcAn.utils::runModule.run.write.configs(settings)
+  settings <- PEcAn.workflow::runModule.run.write.configs(settings)
   PEcAn.settings::write.settings(settings, outputfile='pecan.CONFIGS.xml')
   PEcAn.utils::status.end()
 } else if (file.exists(file.path(settings$outdir, 'pecan.CONFIGS.xml'))) {
diff --git a/models/dvmdostem/man/model2netcdf.dvmdostem.Rd b/models/dvmdostem/man/model2netcdf.dvmdostem.Rd
index e0e3d68de50..75710ef9925 100644
--- a/models/dvmdostem/man/model2netcdf.dvmdostem.Rd
+++ b/models/dvmdostem/man/model2netcdf.dvmdostem.Rd
@@ -9,6 +9,9 @@ model2netcdf.dvmdostem(outdir, runstart, runend)
 \arguments{
 \item{outdir}{Location of dvmdostem model output}
 }
+\description{
+Code to convert dvmdostem netcdf output into into CF standard
+}
 \examples{
  
 \dontrun{
diff --git a/models/dvmdostem/tests/testthat/test-model2netcdf.dvmdostem.R b/models/dvmdostem/tests/testthat/test-model2netcdf.dvmdostem.R
new file mode 100644
index 00000000000..b2b9eca1503
--- /dev/null
+++ b/models/dvmdostem/tests/testthat/test-model2netcdf.dvmdostem.R
@@ -0,0 +1,8 @@
+
+context("test model2netcdf.dvmdostem")
+
+test_that("PLACEHOLDER", {
+	# Package checking fails if there are no tests at all,
+	# so this is an empty placeholder to let checks finish.
+	# Please replace it with real tests.
+})
\ No newline at end of file
diff --git a/models/ed/.gitignore b/models/ed/.gitignore
new file mode 100644
index 00000000000..30dba85ade2
--- /dev/null
+++ b/models/ed/.gitignore
@@ -0,0 +1 @@
+vignettes/ed_run_data
diff --git a/models/ed/DESCRIPTION b/models/ed/DESCRIPTION
index 2793623bdba..593ee6b3822 100644
--- a/models/ed/DESCRIPTION
+++ b/models/ed/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.ED2
 Type: Package
 Title: PEcAn package for integration of ED2 model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze, Carl
     Davidson, Rob Kooper, Shawn Serbin, Alexey Shiklomanov
 Maintainer: Mike Dietze <dietze@bu.edu>
@@ -24,11 +24,19 @@ Imports:
     stringr(>= 1.1.0),
     udunits2 (>= 0.11),
     XML (>= 3.98-1.4),
-    hdf5r
+    hdf5r,
+    tidyr,
+    dplyr,
+    tibble,
+    lubridate,
+    magrittr,
+    purrr
 Suggests:
     testthat (>= 1.0.2)
 License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
+Roxygen: list(markdown = TRUE)
diff --git a/models/ed/NAMESPACE b/models/ed/NAMESPACE
index a7d004310e7..39e6fc9855b 100644
--- a/models/ed/NAMESPACE
+++ b/models/ed/NAMESPACE
@@ -1,26 +1,62 @@
 # Generated by roxygen2: do not edit by hand
 
-export(ed2in_set_value)
-export(ed2in_set_value_list)
+S3method(print,ed2in)
+S3method(write_ed2in,default)
+S3method(write_ed2in,ed2in)
+export(check_css)
+export(check_ed2in)
+export(check_ed_metheader)
+export(check_ed_metheader_format)
+export(check_pss)
+export(check_site)
+export(create_css)
+export(create_ed_veg)
+export(create_pss)
+export(create_site)
+export(download_edi)
+export(ed.var)
+export(example_css)
+export(example_pss)
+export(example_site)
 export(get.model.output.ED2)
+export(get_ed2in_dates)
+export(get_met_dates)
+export(get_restartfile.ED2)
+export(is.ed2in)
+export(list.files.nodir)
 export(met2model.ED2)
+export(met_flag_description)
+export(met_variable_description)
 export(model2netcdf.ED2)
+export(modify_ed2in)
 export(parse.history)
 export(put_E_values)
 export(put_T_values)
 export(read.output.ED2)
 export(read.output.file.ed)
 export(read_E_files)
+export(read_S_files)
 export(read_T_files)
+export(read_css)
+export(read_ed2in)
+export(read_ed_metheader)
+export(read_ed_veg)
+export(read_pss)
 export(read_restart.ED2)
+export(read_site)
 export(remove.config.ED2)
+export(run_ed_singularity)
+export(translate_vars_ed)
 export(veg2model.ED2)
 export(write.config.ED2)
 export(write.config.jobsh.ED2)
 export(write.config.xml.ED2)
+export(write_css)
+export(write_ed2in)
+export(write_ed_metheader)
+export(write_ed_veg)
+export(write_pss)
 export(write_restart.ED2)
+export(write_site)
 import(PEcAn.utils)
-importFrom(ncdf4,ncatt_get)
-importFrom(ncdf4,ncdim_def)
-importFrom(ncdf4,ncvar_add)
-importFrom(ncdf4,ncvar_get)
+importFrom(magrittr,"%>%")
diff --git a/models/ed/R/SDA.helpers.ED2.R b/models/ed/R/SDA.helpers.ED2.R
index f80f632489b..1a054f76ee5 100644
--- a/models/ed/R/SDA.helpers.ED2.R
+++ b/models/ed/R/SDA.helpers.ED2.R
@@ -5,13 +5,48 @@
 #' \code{<workflowID>/out}
 #' @param runid PEcAn run ID
 #' @param file.time Start or end time from SDA analysis
+#' @export
 get_restartfile.ED2 <- function(mod_outdir, runid, file.time) {
     runid <- as.character(runid)
     histfile_path <- file.path(mod_outdir, runid)
+    
+    # the frequency of history files might change depending on assimilation timestep
+    # we can identify this from the timestamps
+    history_files <- dir(histfile_path, "-S-")
+    # extract time stamps info from the file names
+    htimestamps <- sapply(seq_along(history_files), function(f){
+      index  <- gregexpr("-S-", history_files[1])[[1]]
+      tstamp <- substr(history_files[f], index[1] + 3, index[1] + 12)
+    })
+    
+    # NOTE: ED2 writes annual history files on the same month e.g. in ed_model.F90:
+    #
+    #           history_time   = new_month .and. isoutput /= 0 .and.                              &
+    #                            current_time%month == imontha .and.                              &
+    #                            mod(real(current_time%year-iyeara),frqstate) == 0.
+    #
+    # So the annual history file after starting a run at 1961/01/01 will be "history-S-1962-01-01-000000-g01.h5"
+    # this version of code checks for annual -S- files, but putting these flags here to remind that there can be monthly or daily history files 
+    annual_check <- monthly_check <- daily_check <- FALSE # this will result in reading the first file as YYYY-01-01 regardless of assimilation time step
+    
+    # if(length(htimestamps) > 1){
+    #   diff_check     <- difftime(htimestamps[2], htimestamps[1], units = c("hours"))
+    #   monthly_check  <- ifelse(diff_check > 744, FALSE, TRUE)
+    #   daily_check    <- ifelse(diff_check > 24,  FALSE, TRUE)
+    #   # if you want to extend this to checks for sub-daily assimilations, also modify timestamp extraction above
+    # }
+    
+    # file.time comes from upstream in the format of "yyyy-12-31 23:59:59 UTC"
+    # to match ED2 naming for annual history files, round to next day  "YYYY-01-01 UTC"
+    ed.hist.annual <- lubridate::ceiling_date(file.time, "1 day")
+     
+    file_year     <-  ifelse(annual_check,  lubridate::year(file.time),  lubridate::year(ed.hist.annual))
+    file_month    <-  ifelse(monthly_check, lubridate::month(file.time), lubridate::month(ed.hist.annual))
+    file_day      <-  ifelse(daily_check,   lubridate::day(file.time),   lubridate::day(ed.hist.annual))
+    
+    # check how ED2 writes other -S- files
+    
 
-    file_year <- lubridate::year(file.time)
-    file_month <- lubridate::month(file.time)
-    file_day <- lubridate::day(file.time)
     datetime_string <- sprintf("%04d-%02d-%02d-000000", 
                                file_year, 
                                file_month,
diff --git a/models/ed/R/check_ed2in.R b/models/ed/R/check_ed2in.R
new file mode 100644
index 00000000000..1082a867916
--- /dev/null
+++ b/models/ed/R/check_ed2in.R
@@ -0,0 +1,101 @@
+#' Check ED2IN
+#'
+#' Check the basic structure of `ed2in` object, as well as consistency among 
+#' arguments (e.g. run dates and coordinates are within the range of vegetation 
+#' and meteorology data).
+#'
+#' @inheritParams write_ed2in
+#' @export
+check_ed2in <- function(ed2in) {
+  # Check that required variables are set (not blank or have unfilled @@ tags)
+  can_be_unset <- c(
+    "LU_DATABASE",
+    "SOIL_DATABASE",
+    "IPHENYS1",
+    "IPHENYSF",
+    "IPHENYF1",
+    "IPHENYFF"
+  )
+  unset <- !names(ed2in) %in% can_be_unset &
+    (purrr::map_lgl(ed2in, ~all(is.na(.))) | grepl("@.*?@", ed2in))
+  if (sum(unset) > 0) {
+    PEcAn.logger::logger.severe(
+      "The following required ED2IN tags are unset: ",
+      paste(names(which(unset)), collapse = ", ")
+    )
+  }
+
+  # Run dates fall within met dates
+  met_object <- read_ed_metheader(ed2in[["ED_MET_DRIVER_DB"]])
+  met_dates <- get_met_dates(met_object)
+  ed2in_dates <- get_ed2in_dates(ed2in)
+
+  outside_dates <- (!ed2in_dates %in% met_dates)
+  if (sum(outside_dates) > 0) {
+    PEcAn.logger::logger.severe(
+      "The following run dates in ED2IN are not in met driver data: ",
+      paste(ed2in_dates[outside_dates], collapse = ", ")
+    )
+  }
+
+  ed2in_lat <- ed2in[["POI_LAT"]]
+  ed2in_lon <- ed2in[["POI_LON"]]
+
+  if (ed2in[["RUNTYPE"]] != "HISTORY") {
+    # Run coordinates match vegetation prefix
+    veg_input <- read_ed_veg(ed2in[["SFILIN"]])
+    if (veg_input$latitude != ed2in_lat) {
+      PEcAn.logger::logger.severe(
+        "ED2IN latitude ", ed2in_lat,
+        " does not match vegetation input latitude ", veg_input$latitude
+      )
+    }
+    if (veg_input$longitude != ed2in_lon) {
+      PEcAn.logger::logger.severe(
+        "ED2IN latitude ", ed2in_lon,
+        " does not match vegetation input latitude ", veg_input$longitude
+      )
+    }
+  } else {
+    # Check that at least one history file exists
+    history_files <- match_file(ed2in[["SFILIN"]])
+    if (!length(history_files) > 0) {
+      PEcAn.logger::logger.severe(
+        "No history files matched for prefix ", ed2in[["SFILIN"]]
+      )
+    }
+  }
+
+  # Run coordinates match meteorology drivers
+  met_lat <- purrr::map_dbl(met_object, "ymin")
+  met_dlat <- purrr::map_dbl(met_object, "dy") / 2
+  met_lon <- purrr::map_dbl(met_object, "xmin")
+  met_dlon <- purrr::map_dbl(met_object, "dx") / 2
+  if (!any(between(ed2in_lat, met_lat - met_dlat, met_lat + met_dlat))) {
+    PEcAn.logger::logger.severe(
+      "ED2IN latitude ",
+      ed2in_lat,
+      " does not match meteorology latitudes ",
+      paste(met_lat - met_dlat, met_lat + met_dlat, sep = " to ", collapse = ", ")
+    )
+  }
+  if (!any(between(ed2in_lon, met_lon - met_dlon, met_lon + met_dlon))) {
+    PEcAn.logger::logger.severe(
+      "ED2IN latitude ",
+      ed2in_lon,
+      " does not match meteorology longitudes ",
+      paste(met_lon - met_dlon, met_lon + met_dlon, sep = " to ", collapse = ", ")
+    )
+  }
+
+  invisible(TRUE)
+}
+
+#' Check if value is between (inclusive) a range
+#'
+#' @param x Value to check
+#' @param lower Lower limit
+#' @param upper Upper limit
+between <- function(x, lower, upper) {
+  x >= lower & x <= upper
+}
diff --git a/models/ed/R/check_ed_metheader.R b/models/ed/R/check_ed_metheader.R
new file mode 100644
index 00000000000..e68a76a3788
--- /dev/null
+++ b/models/ed/R/check_ed_metheader.R
@@ -0,0 +1,80 @@
+#' Check ED met header object
+#'
+#' Check that the object has all components, and throw an error if anything is 
+#' wrong. Optionally, do some basic checks of actualy meteorology files as 
+#' well.
+#'
+#' `check_ed_metheader_format` checks an individual format (one item in the 
+#' `ed_metheader` list). `check_ed_metheader` applies these checks to each item 
+#' in the format list.
+#'
+#' @param ed_metheader ED meteorology header object (see [read_ed_metheader])
+#' @param ed_metheader_format A single format inside the met header object
+#' @inheritParams read_ed_metheader
+#' @export
+check_ed_metheader <- function(ed_metheader, check_files = TRUE) {
+  testthat::test_that(
+    "ED met header object is a nested list",
+    {
+      testthat::expect_true(!is.null(names(ed_metheader[[1]])))
+    }
+  )
+  .z <- lapply(ed_metheader, check_ed_metheader_format, check_files = check_files)
+  invisible(TRUE)
+}
+
+#' @rdname check_ed_metheader
+#' @export
+check_ed_metheader_format <- function(ed_metheader_format, check_files = TRUE) {
+  testthat::test_that(
+    "Format has the correct names",
+    {
+      correct_names <- c("path_prefix", "nlon", "nlat", "dx", "dy", "xmin", "ymin", "variables")
+      all(names(ed_metheader_format) %in% correct_names)
+    }
+  )
+  testthat::test_that(
+    "ED met header files exist and are not empty",
+    {
+      met_files <- PEcAn.utils::match_file(ed_metheader_format$path_prefix)
+      testthat::expect_gte(length(met_files), 1)
+      testthat::expect_true(all(file.exists(met_files)))
+      testthat::expect_true(all(file.size(met_files) > 0))
+    }
+  )
+
+  testthat::test_that(
+    "Met header metadata fields are valid",
+    {
+      testthat::expect_true(is.numeric(ed_metheader_format$nlon))
+      testthat::expect_true(is.numeric(ed_metheader_format$nlat))
+      testthat::expect_true(is.numeric(ed_metheader_format$dx))
+      testthat::expect_true(is.numeric(ed_metheader_format$dy))
+      testthat::expect_true(is.numeric(ed_metheader_format$xmin))
+      testthat::expect_true(is.numeric(ed_metheader_format$ymin))
+      testthat::expect_is(ed_metheader_format$variables, "data.frame")
+    }
+  )
+
+  if (check_files) {
+    met_files <- PEcAn.utils::match_file(ed_metheader_format$path_prefix, suffix = "h5")
+    .z <- lapply(met_files, check_ed_metfile, variables = ed_metheader_format$variables)
+  }
+}
+
+#' Check individual ED metfile
+#'
+#' @param metfile Path to meteorology file
+#' @param variables Variables table from [ed_metheader][read_ed_metheader] object
+#' @return `NULL`, invisibly, if successful or throw an error
+check_ed_metfile <- function(metfile, variables) {
+  hfile <- hdf5r::H5File$new(metfile, mode = "r")
+  # Remove variables that are not constants
+  variables <- variables[variables$flag != 4, ]
+  testthat::test_that(
+    "All variables present in metfile",
+    {
+      testthat::expect_true(all(variables$variable %in% hfile$ls()$name))
+    }
+  )
+}
diff --git a/models/ed/R/check_veg.R b/models/ed/R/check_veg.R
new file mode 100644
index 00000000000..1b756213dc5
--- /dev/null
+++ b/models/ed/R/check_veg.R
@@ -0,0 +1,67 @@
+#' Check individual ED input files
+#'
+#' Check internal file formatting, and optionally check for compatibility 
+#' against related files.
+#'
+#' @param css css data object (see [read_css])
+#' @param pss pss data object (see [read_pss])
+#' @param site site data object (see [read_site])
+#' @return `NULL` (invisibly)
+#' @export
+check_css <- function(css, pss = NULL) {
+  testthat::test_that(
+    "css file is formatted correctly",
+    {
+      testthat::expect_is(css, "data.frame")
+      testthat::expect_gte(nrow(css), 1)
+      testthat::expect_equal(
+        colnames(css),
+        c("time", "patch", "cohort", "dbh", "hite", "pft",
+          "n", "bdead", "balive", "lai")
+      )
+    }
+  )
+  if (!is.null(pss)) {
+    testthat::test_that(
+      "css file and pss file are compatible",
+      {
+        # All cohort patches are defined in patch file
+        testthat::expect_true(all(unique(css$patch) %in% unique(pss$patch)))
+      }
+    )
+  }
+}
+
+#' @rdname check_css
+#' @export
+check_pss <- function(pss, site = NULL) {
+  testthat::test_that(
+    "pss file is formatted correctly",
+    {
+      testthat::expect_is(pss, "data.frame")
+      testthat::expect_gte(nrow(pss), 1)
+    }
+  )
+  if (!is.null(site)) {
+    testthat::test_that(
+      "pss and site files are compatible",
+      {
+        testthat::expect_true(all(unique(pss$site) %in% unique(site$sitenum)))
+      }
+    )
+  }
+}
+
+#' @rdname check_css
+#' @export
+check_site <- function(site) {
+  testthat::test_that(
+    "site file is formatted correctly",
+    {
+      testthat::expect_gte(nrow(site), 1)
+      testthat::expect_true(!is.null(attributes(site)))
+      testthat::expect_is(attr(site, "nsite"), "numeric")
+      testthat::expect_true(attr(site, "file_format") %in% c(1, 2, 3))
+    }
+  )
+}
diff --git a/models/ed/R/create_veg.R b/models/ed/R/create_veg.R
new file mode 100644
index 00000000000..fc62d09434d
--- /dev/null
+++ b/models/ed/R/create_veg.R
@@ -0,0 +1,75 @@
+#' Create full ED vegetation input object
+#'
+#' @param css [css][read_css] object (`data.frame`)
+#' @param pss [pss][read_pss] object (`data.frame`)
+#' @param site [site][read_site] object (`data.frame`)
+#' @param latitude Latitude coordinate
+#' @param longitude Longitude coordinate
+#' @param ... Additional objects to store in list
+#' @inheritParams create_css
+#' @export
+create_ed_veg <- function(css, pss, site, latitude, longitude, check = TRUE, ...) {
+  if (check) {
+    check_css(css, pss)
+    check_pss(pss, site)
+    check_site(site)
+  }
+  list(
+    css = css,
+    pss = pss,
+    site = site,
+    latitude = latitude,
+    longitude = longitude,
+    ...
+  )
+}
+
+#' Create css, pss, and site files from examples
+#'
+#' @param input Named `list` or `data.frame` containing columns to replace in examples
+#' @param check Logical. If `TRUE` (default), also check files for validity.
+#' @return css, pss, or site object (`data.frame`, possibly with attributes)
+#' @export
+create_css <- function(input, check = TRUE) {
+  new_css <- modify_df(input, example_css)
+  if (check) {
+    check_css(new_css)
+  }
+  new_css
+}
+
+#' @rdname create_css
+#' @export
+create_pss <- function(input, check = TRUE) {
+  new_pss <- modify_df(input, example_pss)
+  if (check) {
+    check_pss(new_pss)
+  }
+  new_pss
+}
+
+#' @rdname create_css
+#' @export
+create_site <- function(input, check = TRUE) {
+  new_site <- modify_df(input, example_site)
+  attr(new_site, "nsite") <- nrow(new_site)
+  attr(new_site, "file_format") <- 1
+  if (check) {
+    check_site(new_site)
+  }
+  new_site
+}
+
+#' Modify a reference `data.frame`
+#' 
+#' Wrapper around `modifyList` to allow expanding a `data.frame` by modifying 
+#' only a single column.
+#'
+#' @param input Named `list` or `data.frame` containing columns to replace in `base`
+#' @param base Reference object to modify
+#' @return Modified `data.frame`
+modify_df <- function(input, base) {
+  col_names <- colnames(base)
+  out_list <- modifyList(as.list(base), as.list(input))
+  as.data.frame(out_list)[col_names]
+}
diff --git a/models/ed/R/download_edi.R b/models/ed/R/download_edi.R
new file mode 100644
index 00000000000..6351ea7f81f
--- /dev/null
+++ b/models/ed/R/download_edi.R
@@ -0,0 +1,19 @@
+#' Download ED inputs
+#'
+#' Download and unzip common ED inputs from a public Open Science Framework 
+#' (OSF) repository (https://osf.io/b6umf). Inputs include the Olson Global 
+#' Ecosystems (OGE) database (`oge2OLD`) and the `chd` and `dgd` databases.
+#'
+#' The total download size around 28 MB.
+#'
+#' @param directory Target directory for unzipping files. Will be created if it 
+#' doesn't exist.
+#' @return `TRUE`, invisibly
+#' @export
+download_edi <- function(directory) {
+  download_link <- "https://files.osf.io/v1/resources/b6umf/providers/osfstorage/5a948ea691b689000fa2a588/?zip="
+  target_file <- paste0(directory, ".zip")
+  download.file(download_link, target_file)
+  unzip(target_file, exdir = directory)
+  invisible(TRUE)
+}
diff --git a/models/ed/R/ed2in_set_value.R b/models/ed/R/ed2in_set_value.R
deleted file mode 100644
index 8b6233139c6..00000000000
--- a/models/ed/R/ed2in_set_value.R
+++ /dev/null
@@ -1,57 +0,0 @@
-#' @title Substitute single value into ED2IN
-#' 
-#' @author Alexey Shiklomanov
-#' @description Given a tag, find that tag in the provided ED2IN character 
-#' vector and change its value. If the tag is not found, do nothing.
-#' 
-#' @param tag ED2IN tag, e.g. "SFILIN"
-#' @param value Value for setting the tag
-#' @param ed2in Character vector containing ED2IN file, usually generated by 
-#' \code{readLines}.
-#' 
-#' @export
-ed2in_set_value <- function(tag, value, ed2in, 
-                            modstring = "Modified by PEcAn") {
-    if (grepl("NL%", tag)) {
-      PEcAn.logger::logger.warn("NL% is automatically prepended ",
-                               "to tags. Removing it from provided tag.")
-      tag <- gsub('NL%', '', tag)
-    }
-    tag <- toupper(tag)
-    regex <- sprintf("(^[[:blank:]]*NL%%%s)[[:blank:]]+=.*", tag)
-    in_ed2in <- any(grepl(regex, ed2in))
-    if (!in_ed2in) {
-      PEcAn.logger::logger.warn("Tag ", shQuote(tag), " not found in ED2IN. ")
-      return(ed2in)
-    }
-
-    # If value is a string, escape it with quotes
-    numval <- suppressWarnings(as.numeric(value))
-    if (is.na(numval)) {
-        value <- shQuote(value)
-    }
-
-    ed2in_out <- gsub(regex, paste0("\\1 = ", value, "    !! ", modstring),
-                      ed2in)
-    return(ed2in_out)
-}
-
-#' @title Substitute list of tag-value pairs into ED2IN
-#' 
-#' @author Alexey Shiklomanov
-#' @param tag_val_list Named list of tag-value pairs. List names should match 
-#' ed2in tags.
-#' @param ... Other parameters to \code{ed2in_set_value}
-#' @inheritParams ed2in_set_value
-#' @export
-ed2in_set_value_list <- function(tag_val_list, ed2in, ...) {
-  ed2in_out <- ed2in
-  for (tag in names(tag_val_list)) {
-    ed2in_out <- ed2in_set_value(tag = tag,
-                                 value = tag_val_list[[tag]],
-                                 ed2in = ed2in_out,
-                                 ...)
-  }
-  return(ed2in_out)
-}
-
diff --git a/models/ed/R/ed_varlookup.R b/models/ed/R/ed_varlookup.R
new file mode 100644
index 00000000000..811d0b3d648
--- /dev/null
+++ b/models/ed/R/ed_varlookup.R
@@ -0,0 +1,70 @@
+#' Lookup function for translating commonly used ED variables
+#' returns out list, readvar variables to read from file, expr if any derivation is needed
+#' @export
+ed.var <- function(varname) {
+  if(varname == "AGB") {
+    out = list(readvar = "AGB_CO", 
+               type = 'co', units = "kgC/plant", 
+               drelated = NULL,                    # other deterministically related vars?
+               expr    = "AGB_CO")                                                 
+  } else if(varname == "TotLivBiom") {
+    out = list(readvar = c("BALIVE"),
+               type = 'co', units = "kgC/plant", 
+               drelated = NULL,
+               expr    = "BALIVE")                                                 
+  } else if(varname == "BA") {
+    out = list(readvar = "BA_CO",
+               type = 'co', units = "cm2/plant", 
+               drelated = NULL,
+               expr    = "BA_CO")                                                  
+  } else if(varname == "DBH") {
+    out = list(readvar = "DBH",
+               type = 'co', units = "cm/plant",
+               drelated = NULL,
+               expr    = "DBH")                                                    
+  } else if(varname == "AbvGrndWood") {
+    out = list(readvar =  c("AGB_CO"), #until I change BLEAF keeper to be annual work with total AGB
+               type = 'co', units = "kgC/plant", 
+               drelated = NULL, 
+               expr    = "AGB_CO")                                           
+  } else if(varname == "leaf_carbon_content") {
+    out = list(readvar = "BLEAF", 
+               type = 'co', units = "kgC/plant", 
+               drelated = NULL, 
+               expr    = "BLEAF")                                                  
+  } else if(varname == "root_carbon_content") {
+    out = list(readvar = "BROOT", 
+               type = 'co', units = "kgC/plant", 
+               drelated = NULL, 
+               expr    = "BROOT")   
+  } else if(varname == "reproductive_litter_carbon_content") {
+    out = list(readvar = "BSEEDS_CO", 
+               type = 'co', units = "kgC/plant", 
+               drelated = NULL, 
+               expr    = "BSEEDS_CO") 
+  } else if(varname == "storage_carbon_content") {
+    out = list(readvar = "BSTORAGE", 
+               type = 'co', units = "kgC/plant", 
+               drelated = NULL, 
+               expr    = "BSTORAGE")
+  } else if(varname == "GWBI") {
+    out = list(readvar = "DDBH_DT", # this is actually rate of change in DBH, we'll calculate GWBI from it 
+               type = 'co', units = "cm/yr", 
+               drelated = NULL,
+               expr    = "DDBH_DT") 
+  } else if(varname == "fast_soil_pool_carbon_content") {
+    out = list(readvar = "FAST_SOIL_C", 
+               type = 'pa', units = "kg/m2", 
+               drelated = NULL,
+               expr    = "FAST_SOIL_C")    
+  } else if(varname == "structural_soil_pool_carbon_content") {
+    out = list(readvar = "STRUCTURAL_SOIL_C", 
+               type = 'pa', units = "kg/m2", 
+               drelated = NULL,
+               expr    = "STRUCTURAL_SOIL_C")    
+  } else { # No Match!
+    warning(paste0("Couldn't find varname ", varname, "!"))
+    out = NULL
+  }
+  return(out)
+}
diff --git a/models/ed/R/example_veg.R b/models/ed/R/example_veg.R
new file mode 100644
index 00000000000..79614e9e473
--- /dev/null
+++ b/models/ed/R/example_veg.R
@@ -0,0 +1,23 @@
+#' Example css, pss, and site objects
+#'
+#' @export
+example_css <- tibble::tribble(
+  ~time, ~patch, ~cohort, ~dbh, ~hite, ~pft, ~n, ~bdead, ~balive, ~lai,
+  2008,   1,      1,      12.50, 0,     9,   0.001, 0,    0,      0
+)
+
+#' @rdname example_css
+#' @export
+example_pss <- tibble::tribble(
+  ~site, ~time, ~patch, ~trk, ~age, ~area, ~water, ~fsc, ~stsc, ~stsl, ~ssc, ~psc, ~msn, ~fsn,
+  1,      2008, 1,      1,    70,   1,      0,      1,    5,    5,      0.01, 0,    1,    1
+)
+
+#' @rdname example_css
+#' @export
+example_site <- tibble::tribble(
+  ~sitenum, ~area, ~TCI, ~elev, ~slope, ~aspect, ~soil,
+  1,        1,    -7,    100,   0,      0,        3
+)
+attr(example_site, "nsite") <- 1
+attr(example_site, "file_format") <- 1
diff --git a/models/ed/R/get_ed2in_dates.R b/models/ed/R/get_ed2in_dates.R
new file mode 100644
index 00000000000..b87416671dc
--- /dev/null
+++ b/models/ed/R/get_ed2in_dates.R
@@ -0,0 +1,37 @@
+#' Extract sequence of dates from ED2IN file
+#'
+#' @inheritParams write_ed2in
+#' @return Vector of dates from start date to end date by 1 day
+#' @export
+get_ed2in_dates <- function(ed2in) {
+  ed2in_start_time <- ed2in2time(ed2in[["ITIMEA"]])
+  start_date <- lubridate::make_datetime(
+    ed2in[["IYEARA"]],
+    ed2in[["IMONTHA"]],
+    ed2in[["IDATEA"]],
+    ed2in_start_time$hour,
+    ed2in_start_time$minute
+  )
+
+  ed2in_end_time <- ed2in2time(ed2in[["ITIMEZ"]])
+  end_date <- lubridate::make_datetime(
+    ed2in[["IYEARZ"]],
+    ed2in[["IMONTHZ"]],
+    ed2in[["IDATEZ"]],
+    ed2in_end_time$hour,
+    ed2in_end_time$minute
+  )
+  lubridate::as_date(seq(start_date, end_date, by = "1 day"))
+}
+
+#' Convert ED2IN `ITIMEA/Z` string to hour and minute
+#'
+#' @param itimea ED2IN time string, e.g. "1200"
+#' @return List containing numeric values of hour and minute
+ed2in2time <- function(itimea) {
+  timechar <- sprintf("%04d", itimea)
+  list(
+    hour = as.numeric(substr(timechar, 1, 2)),
+    minute = as.numeric(substr(timechar, 3, 4))
+  )
+}
diff --git a/models/ed/R/get_met_dates.R b/models/ed/R/get_met_dates.R
new file mode 100644
index 00000000000..197aeb4b447
--- /dev/null
+++ b/models/ed/R/get_met_dates.R
@@ -0,0 +1,34 @@
+#' Get meteorology dates
+#'
+#' Figure out the dates for which a given meteorology is available by parsing 
+#' the matching file names.
+#' @inheritParams write_ed_metheader
+#' @return Vector of dates for a run
+#' @export
+get_met_dates <- function(ed_metheader) {
+  met_paths <- purrr::map(ed_metheader, "path_prefix")
+  met_file_list <- purrr::map(met_paths, PEcAn.utils::match_file, suffix = "h5")
+  month_list <- purrr::map2(
+    met_paths,
+    met_file_list,
+    ~gsub(normalizePath(.x, mustWork = FALSE), "", normalizePath(.y, mustWork = FALSE))
+  )
+  month_vec_raw <- tolower(gsub(".h5", "", Reduce(c, month_list)))
+  month_vec <- lubridate::parse_date_time(month_vec_raw, "ym")
+  date_list <- purrr::map(month_vec, dates_in_month)
+  sort(Reduce(c, date_list))
+}
+
+#' Get all the dates in a month
+#'
+#' For a given date, figure out its month and return all of the dates for that 
+#' month.
+#' @param date Date as string or date object
+#' @return Sequence of dates from the first to the last day of the month.
+dates_in_month <- function(date) {
+  stopifnot(lubridate::mday(date) == 1)
+  end_date <- date +
+    lubridate::days(lubridate::days_in_month(date)) -
+    lubridate::days(1)
+  lubridate::as_date(seq(date, end_date, by = "1 day"))
+}
diff --git a/models/ed/R/met2model.ED2.R b/models/ed/R/met2model.ED2.R
index 616106daf9a..ed36691fc42 100644
--- a/models/ed/R/met2model.ED2.R
+++ b/models/ed/R/met2model.ED2.R
@@ -7,59 +7,63 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 
-## R Code to convert from NACP intercomparison NETCDF met files into ED2 ascii met files
-
-## If files already exist in 'Outfolder', the default function is NOT to overwrite them and only
-## gives user the notice that file already exists. If user wants to overwrite the existing files,
-## just change overwrite statement below to TRUE.
-
-
-##' met2model wrapper for ED2
-##'
-##' @title met2model for ED2
-##' @export
-##' @param in.path location on disk where inputs are stored
-##' @param in.prefix prefix of input and output files
-##' @param outfolder location on disk where outputs will be stored
-##' @param start_date the start date of the data to be downloaded (will only use the year part of the date)
-##' @param end_date the end date of the data to be downloaded (will only use the year part of the date)
-##' @param lst timezone offset to GMT in hours
-##' @param overwrite should existing files be overwritten
-##' @param verbose should the function be very verbose
-##' @importFrom ncdf4 ncvar_get ncdim_def ncatt_get ncvar_add
+#' met2model wrapper for ED2
+#'
+#' If files already exist in 'Outfolder', the default function is NOT to 
+#' overwrite them and only gives user the notice that file already exists. If 
+#' user wants to overwrite the existing files, just change overwrite statement 
+#' below to TRUE.
+#'
+#' @export
+#' @param in.path location on disk where inputs are stored
+#' @param in.prefix prefix of input and output files
+#' @param outfolder location on disk where outputs will be stored
+#' @param start_date the start date of the data to be downloaded (will only use the year part of the date)
+#' @param end_date the end date of the data to be downloaded (will only use the year part of the date)
+#' @param lst timezone offset to GMT in hours
+#' @param overwrite should existing files be overwritten
+#' @param verbose should the function be very verbose
+#' @param leap_year Enforce Leap-years? If set to TRUE, will require leap years to have 366 days. If set to false, will require all years to have 365 days. Default = TRUE.
 met2model.ED2 <- function(in.path, in.prefix, outfolder, start_date, end_date, lst = 0, lat = NA,
-                          lon = NA, overwrite = FALSE, verbose = FALSE, ...) {
+                          lon = NA, overwrite = FALSE, verbose = FALSE, leap_year = TRUE, ...) {
+  
   overwrite <- as.logical(overwrite)
 
   # results are stored in folder prefix.start.end
   start_date <- as.POSIXlt(start_date, tz = "UTC")
   end_date   <- as.POSIXlt(end_date, tz = "UTC")
   met_folder <- outfolder
-  met_header <- file.path(met_folder, "ED_MET_DRIVER_HEADER")
-
-  results <- data.frame(file = c(met_header),
-                        host = c(PEcAn.remote::fqdn()),
-                        mimetype = c("text/plain"),
-                        formatname = c("ed.met_driver_header files format"),
-                        startdate = c(start_date),
-                        enddate = c(end_date),
-                        dbfile.name = "ED_MET_DRIVER_HEADER",
-                        stringsAsFactors = FALSE)
+  met_header_file <- file.path(met_folder, "ED_MET_DRIVER_HEADER")
+
+  results <- data.frame(
+    file = met_header_file,
+    host = PEcAn.remote::fqdn(),
+    mimetype = "text/plain",
+    formatname = "ed.met_driver_header files format",
+    startdate = start_date,
+    enddate = end_date,
+    dbfile.name = "ED_MET_DRIVER_HEADER",
+    stringsAsFactors = FALSE
+  )
 
   ## check to see if the outfolder is defined, if not create directory for output
   dir.create(met_folder, recursive = TRUE, showWarnings = FALSE)
 
-  ### FUNCTIONS
   dm <- c(0, 32, 60, 91, 121, 152, 182, 213, 244, 274, 305, 335, 366)
   dl <- c(0, 32, 61, 92, 122, 153, 183, 214, 245, 275, 306, 336, 367)
   month <- c("JAN", "FEB", "MAR", "APR", "MAY", "JUN", "JUL", "AUG", "SEP", "OCT", "NOV", "DEC")
   mon_num <- c("01", "02", "03", "04", "05", "06", "07", "08", "09", "10", "11", "12")
-  day2mo <- function(year, day) {
-    leap      <- lubridate::leap_year(year)
+  day2mo <- function(year, day, leap_year) {
     mo        <- rep(NA, length(day))
-    mo[leap]  <- findInterval(day[leap], dl)
-    mo[!leap] <- findInterval(day[!leap], dm)
-    return(mo)
+    if ( !leap_year) {
+      mo <- findInterval(day, dm)
+      return(mo)
+    } else {
+      leap      <- lubridate::leap_year(year)
+      mo[leap]  <- findInterval(day[leap], dl)
+      mo[!leap] <- findInterval(day[!leap], dm)
+      return(mo)
+    }
   }
 
   # get start/end year since inputs are specified on year basis
@@ -70,6 +74,11 @@ met2model.ED2 <- function(in.path, in.prefix, outfolder, start_date, end_date, l
   ## loop over files
   for (year in start_year:end_year) {
     ncfile <- file.path(in.path, paste(in.prefix, year, "nc", sep = "."))
+    if (!file.exists(ncfile)) {
+      PEcAn.logger::logger.severe(
+        "Input file ", ncfile, "(year ", year, ") ", "not found."
+      )
+    }
 
     ## extract file root name froot <- substr(files[i],1,28) print(c(i,froot))
 
@@ -105,14 +114,25 @@ met2model.ED2 <- function(in.path, in.prefix, outfolder, start_date, end_date, l
     sec  <- nc$dim$time$vals
     Tair <- ncdf4::ncvar_get(nc, "air_temperature")
     Qair <- ncdf4::ncvar_get(nc, "specific_humidity")  #humidity (kg/kg)
-    U    <- ncdf4::ncvar_get(nc, "eastward_wind")
-    V    <- ncdf4::ncvar_get(nc, "northward_wind")
+    U    <- try(ncdf4::ncvar_get(nc, "eastward_wind"),  silent = TRUE)
+    V    <- try(ncdf4::ncvar_get(nc, "northward_wind"), silent = TRUE)
     Rain <- ncdf4::ncvar_get(nc, "precipitation_flux")
     pres <- ncdf4::ncvar_get(nc, "air_pressure")
     SW   <- ncdf4::ncvar_get(nc, "surface_downwelling_shortwave_flux_in_air")
     LW   <- ncdf4::ncvar_get(nc, "surface_downwelling_longwave_flux_in_air")
     CO2  <- try(ncdf4::ncvar_get(nc, "mole_fraction_of_carbon_dioxide_in_air"), silent = TRUE)
 
+    use_UV <- is.numeric(U) & is.numeric(V)
+
+    if(!use_UV){
+      U <- try(ncdf4::ncvar_get(nc, "wind_speed"), silent = TRUE)
+      if(is.numeric(U)){
+        PEcAn.logger::logger.info("eastward_wind and northward_wind are absent, using wind_speed to approximate eastward_wind")
+        V <- rep(0, length(U))
+      }else{
+        PEcAn.logger::logger.severe("No eastward_wind and northward_wind or wind_speed in the met data")
+      }
+    }
     useCO2 <- is.numeric(CO2)
 
     ## convert time to seconds
@@ -120,33 +140,33 @@ met2model.ED2 <- function(in.path, in.prefix, outfolder, start_date, end_date, l
 
     ncdf4::nc_close(nc)
 
-    dt <- PEcAn.utils::seconds_in_year(year) / length(sec)
+    dt <- PEcAn.utils::seconds_in_year(year, leap_year) / length(sec)
 
     toff <- -as.numeric(lst) * 3600 / dt
 
     ## buffer to get to GMT
-    slen <- length(SW)
-    Tair <- c(rep(Tair[1], toff), Tair)[1:slen]
-    Qair <- c(rep(Qair[1], toff), Qair)[1:slen]
-    U    <- c(rep(U[1], toff), U)[1:slen]
-    V    <- c(rep(V[1], toff), V)[1:slen]
-    Rain <- c(rep(Rain[1], toff), Rain)[1:slen]
-    pres <- c(rep(pres[1], toff), pres)[1:slen]
-    SW   <- c(rep(SW[1], toff), SW)[1:slen]
-    LW   <- c(rep(LW[1], toff), LW)[1:slen]
+    slen <- seq_along(SW)
+    Tair <- c(rep(Tair[1], toff), Tair)[slen]
+    Qair <- c(rep(Qair[1], toff), Qair)[slen]
+    U  <- c(rep(U[1], toff), U)[slen]
+    V  <- c(rep(V[1], toff), V)[slen]
+    Rain <- c(rep(Rain[1], toff), Rain)[slen]
+    pres <- c(rep(pres[1], toff), pres)[slen]
+    SW   <- c(rep(SW[1], toff), SW)[slen]
+    LW   <- c(rep(LW[1], toff), LW)[slen]
     if (useCO2) {
-      CO2 <- c(rep(CO2[1], toff), CO2)[1:slen]
+      CO2 <- c(rep(CO2[1], toff), CO2)[slen]
     }
 
     ## build time variables (year, month, day of year)
     skip <- FALSE
-    nyr <- floor(udunits2::ud.convert(length(sec) * dt, "seconds", "years"))
+    nyr <- floor(length(sec) * dt / 86400 / 365)
     yr   <- NULL
     doy  <- NULL
     hr   <- NULL
     asec <- sec
     for (y in seq(year, year + nyr - 1)) {
-      diy <- PEcAn.utils::days_in_year(y)
+      diy <- PEcAn.utils::days_in_year(y, leap_year)
       ytmp <- rep(y, udunits2::ud.convert(diy / dt, "days", "seconds"))
       dtmp <- rep(seq_len(diy), each = day_secs / dt)
       if (is.null(yr)) {
@@ -161,13 +181,13 @@ met2model.ED2 <- function(in.path, in.prefix, outfolder, start_date, end_date, l
       rng <- length(doy) - length(ytmp):1 + 1
       if (!all(rng >= 0)) {
         skip <- TRUE
-        PEcAn.logger::logger.warn(paste(year, "is not a complete year and will not be included"))
+        PEcAn.logger::logger.warn(year, " is not a complete year and will not be included")
         break
       }
       asec[rng] <- asec[rng] - asec[rng[1]]
       hr[rng]   <- (asec[rng] - (dtmp - 1) * day_secs) / day_secs * 24
     }
-    mo <- day2mo(yr, doy)
+    mo <- day2mo(yr, doy, leap_year)
     if (length(yr) < length(sec)) {
       rng <- (length(yr) + 1):length(sec)
       if (!all(rng >= 0)) {
@@ -210,8 +230,8 @@ met2model.ED2 <- function(in.path, in.prefix, outfolder, start_date, end_date, l
     dlwrfA <- LW  # downward long wave radiation [W/m2]
     presA  <- pres  # pressure [Pa]
     hgtA   <- rep(50, n)  # geopotential height [m]
-    ugrdA  <- U  # zonal wind [m/s]
-    vgrdA  <- V  # meridional wind [m/s]
+    ugrdA <- U  # zonal wind [m/s]
+    vgrdA <- V  # meridional wind [m/s]
     shA    <- Qair  # specific humidity [kg_H2O/kg_air]
     tmpA   <- Tair  # temperature [K]
     if (useCO2) {
@@ -274,31 +294,34 @@ met2model.ED2 <- function(in.path, in.prefix, outfolder, start_date, end_date, l
     }
 
     ## write DRIVER file
-    sites <- 1
-    metgrid <- c(1, 1, 1, 1, lon, lat)
     metvar <- c("nbdsf", "nddsf", "vbdsf", "vddsf", "prate", "dlwrf",
                 "pres", "hgt", "ugrd", "vgrd", "sh", "tmp", "co2")
-    nmet <- length(metvar)
-    metfrq <- rep(dt, nmet)
-    metflag <- rep(1, nmet)
+    metvar_table <- data.frame(
+      variable = metvar,
+      update_frequency = dt,
+      flag = 1
+    )
     if (!useCO2) {
-      metflag[metvar == "co2"] <- 4
-      metfrq[metvar == "co2"] <- 380
+      metvar_table[metvar_table$variable == "co2",
+                   c("update_frequency", "flag")] <- list(380, 4)
     }
-    write.table("header", met_header, row.names = FALSE, col.names = FALSE)
-    write.table(sites, met_header, row.names = FALSE, col.names = FALSE, append = TRUE)
-    write.table(met_folder, met_header, row.names = FALSE, col.names = FALSE, append = TRUE,
-                quote = FALSE)
-    write.table(matrix(metgrid, nrow = 1), met_header, row.names = FALSE, col.names = FALSE,
-                append = TRUE, quote = FALSE)
-    write.table(nmet, met_header, row.names = FALSE, col.names = FALSE, append = TRUE, quote = FALSE)
-    write.table(matrix(metvar, nrow = 1), met_header, row.names = FALSE, col.names = FALSE, append = TRUE)
-    write.table(matrix(metfrq, nrow = 1), met_header, row.names = FALSE, col.names = FALSE, append = TRUE,
-                quote = FALSE)
-    write.table(matrix(metflag, nrow = 1), met_header, row.names = FALSE, col.names = FALSE,
-                append = TRUE, quote = FALSE)
+
+    ed_metheader <- list(list(
+      path_prefix = met_folder,
+      nlon = 1,
+      nlat = 1,
+      dx = 1,
+      dy = 1,
+      xmin = lon,
+      ymin = lat,
+      variables = metvar_table
+    ))
+
+    check_ed_metheader(ed_metheader)
+    write_ed_metheader(ed_metheader, met_header_file,
+                       header_line = shQuote("Made_by_PEcAn_met2model.ED2"))
   }  ### end loop over met files
 
-  print("Done with met2model.ED2")
+  PEcAn.logger::logger.info("Done with met2model.ED2")
   return(invisible(results))
 } # met2model.ED2
diff --git a/models/ed/R/model2netcdf.ED2.R b/models/ed/R/model2netcdf.ED2.R
index 98adf31ab30..bf3e92fbb80 100644
--- a/models/ed/R/model2netcdf.ED2.R
+++ b/models/ed/R/model2netcdf.ED2.R
@@ -164,12 +164,13 @@ model2netcdf.ED2 <- function(outdir, sitelat, sitelon, start_date, end_date, pft
 
 ##' Function for reading -T- files
 ##'
-##' yr     : the year being processed
-##' yfiles : the years on the filenames, will be used to matched tfiles for that year
-##'
+##' @details
 ##'  e.g.    yr = 1999
 ##'      yfiles = 1999 2000
 ##'      tfiles = "analysis-T-1999-00-00-000000-g01.h5" "analysis-T-2000-00-00-000000-g01.h5"
+##'
+##' @param yr the year being processed
+##' @param yfiles the years on the filenames, will be used to matched tfiles for that year
 ##' @export
 read_T_files <- function(yr, yfiles, tfiles, outdir, start_date, end_date, ...){
   
@@ -769,9 +770,7 @@ put_T_values <- function(yr, nc_var, out, lat, lon, begins, ends, ...){
 
 ##' Function for reading -E- files
 ##'
-##' yr      : the year being processed
-##' yfiles  : the years on the filenames, will be used to matched efiles for that year
-##'
+##' @details
 ##'  e.g.     yr = 1999
 ##'      yfiles = 1999 1999 1999 1999 1999 1999 1999 2000 2000 2000 2000
 ##'      efiles = "analysis-E-1999-06-00-000000-g01.h5" "analysis-E-1999-07-00-000000-g01.h5"
@@ -783,6 +782,10 @@ put_T_values <- function(yr, nc_var, out, lat, lon, begins, ends, ...){
 ##'
 ##' pft_names  : character vector with names of PFTs
 ##' pft_names <- c("temperate.Early_Hardwood", "temperate.Late_Hardwood")
+##'
+##' @param yr the year being processed
+##' @param yfiles the years on the filenames, will be used to matched efiles for that year
+##'
 ##' @export
 read_E_files <- function(yr, yfiles, efiles, outdir, start_date, end_date, pft_names, ...){
   
@@ -966,3 +969,152 @@ put_E_values <- function(yr, nc_var, out, lat, lon, begins, ends, pft_names, ...
   
 } # put_E_values
 
+
+
+
+#' S-file contents are not written to standard netcdfs but are used by read_restart
+#' from SDA's perspective it doesn't make sense to write and read to ncdfs because ED restarts from history files
+#' 
+#' @param sfile history file name e.g. "history-S-1961-01-01-000000-g01.h5"
+#' @param outdir path to run outdir, where the -S- file is
+#' @param pft_names string vector, names of ED2 pfts in the run, e.g. c("temperate.Early_Hardwood", "temperate.Late_Conifer")
+#' @param pecan_names string vector, pecan names of requested variables, e.g. c("AGB", "AbvGrndWood")
+#' 
+#' @export
+read_S_files <- function(sfile, outdir, pft_names, pecan_names = NULL){
+  
+  PEcAn.logger::logger.info(paste0("*** Reading -S- file ***"))
+  
+  # commonly used vars
+  if(is.null(pecan_names)) pecan_names <- c("AGB", "AbvGrndWood", "GWBI", "DBH")
+  
+  ed_varnames <- pecan_names
+  
+  # TODO: ed.var lookup function can also return deterministically related variables
+  
+  # translate pecan vars to ED vars
+  trans_out    <- translate_vars_ed(ed_varnames)
+  ed_varnames  <- trans_out$vars  # variables to read from history files
+  ed_derivs    <- trans_out$expr  # derivations to obtain pecan standard variables
+  add_vars     <- trans_out$addvars # these are the vars -if there are any- that won't be updated by analysis, but will be used in write_restart
+  ed_units     <- trans_out$units # might use
+  
+  # List of vars to extract includes the requested one, plus others needed below 
+  add_vars <- c(add_vars, "PFT", "AREA", "PACO_N", "NPLANT","DAGB_DT", "BDEAD", "DBH", 
+                "BSTORAGE", "BALIVE", "BLEAF", "BROOT", "BSEEDS_CO", "BSAPWOODA", "BSAPWOODB")
+  vars <- c(ed_varnames, add_vars) 
+  
+  # list to collect outputs
+  ed.dat <- list()
+  
+  nc <- ncdf4::nc_open(file.path(outdir, sfile))
+  allvars <- names(nc$var)
+  if(!is.null(vars)) allvars <- allvars[ allvars %in% vars ]
+  
+  for(j in seq_along(allvars)){
+    ed.dat[[j]] <- list()
+    ed.dat[[j]] <- ncdf4::ncvar_get(nc, allvars[j])
+  }
+  names(ed.dat) <- allvars
+  
+  ncdf4::nc_close(nc)
+  
+  
+  # for now this function does not read any ED variable that has soil as a dimension
+  soil.check <- grepl("soil", pft_names)
+  if(any(soil.check)){
+    # for now keep soil out
+    pft_names <- pft_names[!(soil.check)]
+  }
+  
+  npft <- length(pft_names)
+  data(pftmapping, package = "PEcAn.ED2")
+  pft_nums <- sapply(pft_names, function(x) pftmapping$ED[pftmapping$PEcAn == x]) 
+  
+  out <- list()
+  for(varname in pecan_names) {
+    out[[varname]] <- array(NA, npft)
+  }
+  
+  
+  # Get cohort-level variables 
+  pft        <- ed.dat$PFT
+  plant_dens <- ed.dat$NPLANT  # Cohort stem density -- plant/m2
+  dbh        <- ed.dat$DBH # used in allometric eqns -- dbh
+  
+  # Get patch areas. In general patches aren't the same area, so this is needed to area-weight when averaging up to site level. Requires minor finnagling to convert patch-level AREA to a cohort-length variable. 
+  patch_area  <- ed.dat$AREA    # unitless, a proportion of total site area  -- one entry per patch (always add up to 1)
+  paco_n      <- ed.dat$PACO_N  # number of cohorts per patch
+  
+  patch_index <- rep(1:length(paco_n), times = paco_n)
+  
+  # read xml to extract allometric coeffs later
+  configfile <- paste0(gsub("/out/", "/run/", outdir), "/config.xml")
+  pars <- XML::xmlToList(XML::xmlParse(configfile))
+  # remove non-pft sublists
+  pars[names(pars)!="pft"] <- NULL
+  # pass pft numbers as sublist names
+  names(pars) <- pft_nums
+  
+  # Aggregate
+  for(l in seq_along(pecan_names)) {
+    
+    variable <- convert.expr(ed_derivs[l])  # convert
+    expr <- variable$variable.eqn$expression
+    
+    sapply(variable$variable.eqn$variables, function(x) assign(x, ed.dat[[x]], envir = .GlobalEnv))
+    tmp.var <- eval(parse(text = expr)) # parse
+    
+    if(ed_units[l] %in% c("kg/m2")){ # does this always mean this is a patch-level variable w/o per-pft values?
+      out[[pecan_names[l]]] <- NA
+      out[[pecan_names[l]]] <- sum(tmp.var*patch_area, na.rm = TRUE)
+      
+    }else{# per-pft vars
+      for(k in seq_len(npft)) {
+        ind <- (pft == pft_nums[k])
+        
+        if(any(ind)) {
+          # check for different variables/units?
+          if(pecan_names[l] == "GWBI"){
+            # use allometric equations to calculate GWBI from DDBH_DT
+            ddbh_dt <- tmp.var
+            ddbh_dt[!ind] <- 0
+            dagb_dt <- ed.dat$DAGB_DT
+            dagb_dt[!ind] <- 0
+            
+            # get b1Bl/b2Bl/dbh_adult from xml
+            # these are in order so you can use k, but you can also extract by pft
+            small   <- dbh <= as.numeric(pars[[k]]$dbh_adult)
+            ddbh_dt[small]  <- as.numeric(pars[[k]]$b1Bl_small) / 2 * ddbh_dt[small]  ^ as.numeric(pars[[k]]$b2Bl_small)
+            ddbh_dt[!small] <- as.numeric(pars[[k]]$b1Bl_large) / 2 * ddbh_dt[!small] ^ as.numeric(pars[[k]]$b2Bl_large)
+            gwbi_ch <- dagb_dt - ddbh_dt
+            #     kgC/m2/yr = kgC/plant/yr  *   plant/m2  
+            plant2cohort <- gwbi_ch * plant_dens
+            cohort2patch <- tapply(plant2cohort, list("patch" = patch_index), sum, na.rm = TRUE)
+            out[[pecan_names[l]]][k] <- sum(cohort2patch*patch_area, na.rm = TRUE)
+            
+          }else if(ed_units[l] %in% c("kgC/plant")){
+            pft.var <- tmp.var
+            pft.var[!ind] <- 0
+            #     kgC/m2 = kgC/plant  *   plant/m2  
+            plant2cohort <- pft.var * plant_dens
+            # sum cohorts to aggrete to patches
+            cohort2patch <- tapply(plant2cohort, list("patch" = patch_index), sum, na.rm = TRUE)
+            # scale up to site-level 
+            out[[pecan_names[l]]][k] <- sum(cohort2patch*patch_area, na.rm = TRUE)
+            
+          }
+        }  #any(ind)-if SHOULD THERE BE AN ELSE? DOES ED2 EVER DRIVES SOME PFTs TO EXTINCTION? 
+      } #k-loop
+      
+    }# per-pft or not
+  } #l-loop
+  
+  
+  # pass everything, unaggregated
+  out$restart <- ed.dat
+  
+  
+  return(out)
+  
+} # read_S_files
\ No newline at end of file
diff --git a/models/ed/R/modify_ed2in.R b/models/ed/R/modify_ed2in.R
new file mode 100644
index 00000000000..089e5f6b0bc
--- /dev/null
+++ b/models/ed/R/modify_ed2in.R
@@ -0,0 +1,237 @@
+#' Modify an ED2IN object
+#'
+#' This is a convenience function for modifying an `ed2in` list object.  
+#' Arguments passed in all caps are assumed to be ED2IN namelist parameters and 
+#' are inserted directly into the `ed2in` list objects. Lowercase arguments are 
+#' defined explicitly (see "Parameters"), and those that do not match explicit 
+#' arguments will be ignored with a warning. Because the lowercase arguments 
+#' come with additional validity checks, they are recommended over modifying 
+#' the ED2IN file directly via uppercase arguments.
+#'
+#' Namelist arguments are applied last, and will silently overwrite any 
+#' arguments set by special case arguments.
+#'
+#' Namelist arguments can be stored in a list and passed in via the `.dots` 
+#' argument (e.g. `.dots = list(SFILIN = "/path/prefix_", ...)`), or using the 
+#' `rlang::!!!` splicing operator. If both are provided, they will be spliced 
+#' together, with the `...` taking precedence.
+#'
+#' For `output_types`, select one or more of the following:
+#'  - "fast" -- Fast analysis; mostly polygon-level averages (`IFOUTPUT`)
+#'  - "daily -- Daily means (one file per day) (`IDOUTPUT`)
+#'  - "monthly" -- Monthly means (one file per month) (`IMOUTPUT`)
+#'  - "monthly_diurnal" -- Monthly means of the diurnal cycle (one file per 
+#'  month) (`IQOUTPUT`)
+#'  - "annual" -- Annual (one file per year) (`IYOUTPUT`)
+#'  - "instant" -- Instantaneous fluxes, mostly polygon-level variables, one 
+#'  file per year (`ITOUTPUT`)
+#'  - "restart" -- Restart file for HISTORY runs. (`ISOUTPUT`)
+#'  - "all" -- All output types
+#'
+#' @inheritParams read_ed2in
+#' @param ... Namelist arguments (see Description and Details)
+#' @param veg_prefix Vegetation file prefix (`SFILIN`). If `lat` and `lon` are part of the prefix, 
+#' @param latitude Run latitude coordinate. If `veg_prefix` is also provided, 
+#' pass to [read_ed_veg], otherwise set in ED2IN directly. Should be omitted if 
+#' `lat` and `lon` are already part of `veg_prefix`.
+#' @param longitude Run longitude coordinate. If `veg_prefix` is also provided, 
+#' pass to [read_ed_veg], otherwise set in ED2IN directly. Should be omitted if 
+#' `lat` and `lon` are already part of `veg_prefix`.
+#' @param met_driver Path and filename of met driver header 
+#' (`ED_MET_DRIVER_DB`)
+#' @param start_date Run start date (`IMONTHA`, `IDATEA`, `IYEARA`, `ITIMEA`)
+#' @param end_date Run end date (`IMONTHZ`, `IDATEZ`, `IYEARZ` `ITIMEZ`)
+#' @param EDI_path Path to `EDI` directory, which often has the `VEG_DATABASE` 
+#' and `THSUMS_DATABASE` files.
+#' @param output_types Character vector of output types (see Details)
+#' @param output_dir Output directory, for `FFILOUT` (analysis) and `SFILOUT` 
+#'(history) files
+#' @param run_dir Directory in which to store run-related config files (e.g. `config.xml`).
+#' @param runtype ED initialization mode; either "INITIAL" or "HISTORY"
+#' @param pecan_defaults Logical. If `TRUE`, set common `ED2IN` defaults.
+#' @param add_if_missing Logical. If `TRUE`, all-caps arguments not found in 
+#'existing `ed2in` list will be added to the end.  Default = `FALSE`.
+#' @param check_paths Logical. If `TRUE` (default), for any parameters that 
+#' expect files, check that files exist and throw an error if they don't.
+#' @param .dots A list of `...` arguments.
+#' @return Modified `ed2in` list object. See [read_ed2in].
+#' @export
+modify_ed2in <- function(ed2in, ...,
+                         veg_prefix = NULL,
+                         latitude = NULL,
+                         longitude = NULL,
+                         met_driver = NULL,
+                         start_date = NULL,
+                         end_date = NULL,
+                         EDI_path = NULL,
+                         output_types = NULL,
+                         output_dir = NULL,
+                         run_dir = NULL,
+                         runtype = NULL,
+                         run_name = NULL,
+                         pecan_defaults = FALSE,
+                         add_if_missing = FALSE,
+                         check_paths = TRUE,
+                         .dots = list()) {
+
+  if (is.null(.dots)) {
+    .dots <- list()
+  }
+  dots <- modifyList(.dots, list(...))
+  is_upper <- names(dots) == toupper(names(dots))
+  lower_args <- names(dots)[!is_upper]
+  if (length(lower_args) > 0) {
+    PEcAn.logger::logger.warn(
+      "The following lowercase arguments are not supported, and will be dropped: ",
+      paste(lower_args, collapse = ", ")
+    )
+  }
+
+  if (pecan_defaults) {
+    ed2in[["IMETAVG"]] <- -1
+    ed2in[["IPHEN_SCHEME"]] <- 0
+    ed2in[["IPHENYS1"]] <- NA
+    ed2in[["IPHENYSF"]] <- NA
+    ed2in[["PHENPATH"]] <- ""
+    ed2in[["IED_INIT_MODE"]] <- 0
+    ed2in[["SOIL_DATABASE"]] <- ""
+    ed2in[["LU_DATABASE"]] <- ""
+  }
+
+  if (!is.null(runtype)) {
+    if (!toupper(runtype) %in% c("INITIAL", "HISTORY")) {
+      PEcAn.logger::logger.severe(
+        "Invalid runtype ", runtype,
+        ". Must be either 'INITIAL' or 'HISTORY'."
+      )
+    }
+    ed2in[["RUNTYPE"]] <- runtype
+  }
+
+  if (!is.null(run_name)) {
+    ed2in[["EXPNME"]] <- run_name
+  }
+
+  if (!is.null(veg_prefix)) {
+    if (check_paths) {
+      .z <- PEcAn.utils::match_file(veg_prefix, suffix = "css", expect = 1)
+      .z <- PEcAn.utils::match_file(veg_prefix, suffix = "pss", expect = 1)
+      .z <- PEcAn.utils::match_file(veg_prefix, suffix = "site", expect = 1)
+    }
+    ed2in[["SFILIN"]] <- normalizePath(veg_prefix, mustWork = FALSE)
+    ed2in[["IED_INIT_MODE"]] <- 3
+    ed_veg <- read_ed_veg(veg_prefix, latitude = latitude, longitude = longitude)
+    ed2in[["POI_LAT"]] <- ed_veg$latitude
+    ed2in[["POI_LON"]] <- ed_veg$longitude
+  }
+
+  if (is.null(veg_prefix) && !is.null(latitude)) {
+    ed2in[["POI_LAT"]] <- latitude
+  }
+
+  if (is.null(veg_prefix) && !is.null(longitude)) {
+    ed2in[["POI_LON"]] <- longitude
+  }
+
+  if (!is.null(EDI_path)) {
+    ed2in[["VEG_DATABASE"]] <- normalizePath(file.path(EDI_path, "oge2OLD", "OGE2_"), mustWork = FALSE)
+    ed2in[["THSUMS_DATABASE"]] <- paste0(normalizePath(file.path(EDI_path, "ed_inputs")), "/")
+  }
+
+  if (!is.null(met_driver)) {
+    if (check_paths) {
+      if (!file.exists(met_driver)) {
+        PEcAn.logger::logger.severe(
+          "Met driver file ", met_driver, " not found."
+        )
+      }
+      if (!file.size(met_driver) > 0) {
+        PEcAn.logger::logger.severe(
+          "Met driver file ", met_driver, " found but is empty."
+        )
+      }
+    }
+    ed2in[["ED_MET_DRIVER_DB"]] <- normalizePath(met_driver)
+  }
+
+  if (!is.null(start_date)) {
+    # Change dates for both initial and history
+    # This should be OK because initial (I...A) are ignored if runtype = HISTORY,
+    # and history (I...H) are ignored if runtype = INITIAL
+    ed2in[["IYEARA"]] <- ed2in[["IYEARH"]] <- lubridate::year(start_date)
+    ed2in[["IMONTHA"]] <- ed2in[["IMONTHH"]] <- lubridate::month(start_date)
+    ed2in[["IDATEA"]] <- ed2in[["IDATEH"]] <- lubridate::day(start_date)
+    ed2in[["ITIMEA"]] <- ed2in[["ITIMEH"]] <-
+      as.numeric(strftime(start_date, "%H%M", tz = "UTC"))
+    ed2in[["METCYC1"]] <- ed2in[["IYEARA"]]
+  }
+  
+
+  if (!is.null(end_date)) {
+    ed2in[["IYEARZ"]] <- lubridate::year(end_date)
+    ed2in[["IMONTHZ"]] <- lubridate::month(end_date)
+    ed2in[["IDATEZ"]] <- lubridate::day(end_date)
+    ed2in[["ITIMEZ"]] <- as.numeric(strftime(end_date, "%H%M", tz = "UTC"))
+    ed2in[["METCYCF"]] <- ed2in[["IYEARZ"]]
+  }
+
+  if (!is.null(output_types)) {
+    valid_types <- c(
+      IFOUTPUT = "fast",
+      IDOUTPUT = "daily",
+      IMOUTPUT = "monthly",
+      IQOUTPUT = "monthly_diurnal",
+      IYOUTPUT = "annual",
+      ITOUTPUT = "instant",
+      ISOUTPUT = "restart"
+    )
+    if (output_types == "all") {
+      output_types <- valid_types
+    }
+    invalid_types <- output_types[!output_types %in% valid_types]
+    if (length(invalid_types) > 0) {
+      PEcAn.logger::logger.severe(
+        "Invalid output types provided: ", paste(invalid_types, collapse = ", "),
+        ". Only the following output types are supported: ",
+        paste(valid_types, collapse = ", ")
+      )
+    }
+    # 3 for HDF5 output, 0 for no output
+    on_types <- (valid_types %in% output_types) * 3
+    names(on_types) <- names(valid_types)
+    ed2in <- modifyList(ed2in, as.list(on_types))
+  }
+
+  if (!is.null(output_dir)) {
+    dir.create(output_dir, showWarnings = FALSE)
+    ed2in[["FFILOUT"]] <- file.path(normalizePath(output_dir), "analysis")
+    ed2in[["SFILOUT"]] <- file.path(normalizePath(output_dir), "history")
+  }
+
+  if (!is.null(run_dir)) {
+    dir.create(run_dir, showWarnings = FALSE)
+    ed2in[["IEDCNFGF"]] <- file.path(normalizePath(run_dir), "config.xml")
+    ed2in[["EVENT_FILE"]] <- file.path(normalizePath(run_dir), "myevents.xml")
+  }
+
+  namelist_args <- dots[is_upper]
+  in_ed2in <- names(namelist_args) %in% names(ed2in)
+  if (sum(!in_ed2in) > 0) {
+    new_args <- namelist_args[!in_ed2in]
+    if (!add_if_missing) {
+      PEcAn.logger::logger.warn(
+        "The following namelist arguments were missing from ED2IN ",
+        "and will be ignored because `add_if_missing = FALSE`: ",
+        paste(names(new_args), collapse = ", ")
+      )
+      namelist_args <- namelist_args[in_ed2in]
+    } else {
+      PEcAn.logger::logger.debug(
+        "Adding the following new arguments to ED2IN: ",
+        paste(names(new_args), collapse = ", ")
+      )
+    }
+  }
+  ed2in <- modifyList(ed2in, namelist_args)
+  ed2in
+}
diff --git a/models/ed/R/other.helpers.ED2.R b/models/ed/R/other.helpers.ED2.R
index ba602bfc8ae..bb454c427e7 100644
--- a/models/ed/R/other.helpers.ED2.R
+++ b/models/ed/R/other.helpers.ED2.R
@@ -2,9 +2,33 @@
 #' 
 #' @author Alexey Shiklomanov
 #' @inheritParams base::list.files
+#' @export
 list.files.nodir <- function(path, ...) {
     allfiles <- list.files(path, ...)
-    dirs <- list.dirs(path, ...)
+    dirs <- list.dirs(path, full.names = FALSE)
     outfiles <- setdiff(allfiles, dirs)
     return(outfiles)
 }
+
+
+#' Function translating pecan vars to ED vars
+#' var.names <- c("DBH", "AGB", "AbvGrndWood")
+#' @export 
+translate_vars_ed <- function(varnames) {
+  
+  var.list <- add.list <- list()
+  ed_vars <- ed_derivations <- ed_units <- rep(NA, length(varnames))
+ 
+  for(n in seq_along(varnames)){
+    edvarout          <- ed.var(varnames[n])
+    var.list[[n]]     <- edvarout$readvar
+    ed_derivations[n] <- edvarout$expr
+    add.list[[n]]     <- edvarout$drelated
+    ed_units[n]       <- edvarout$units
+  }
+  
+  varnames    <- unique(unlist(var.list))
+  addvarnames <- unique(unlist(add.list))
+  return(list(vars = varnames, addvars = addvarnames, expr = ed_derivations, units = ed_units))
+}
+
diff --git a/models/ed/R/read_ed2in.R b/models/ed/R/read_ed2in.R
new file mode 100644
index 00000000000..6a7b6707fa1
--- /dev/null
+++ b/models/ed/R/read_ed2in.R
@@ -0,0 +1,100 @@
+#' Read ED2IN file to named list
+#'
+#' Parse an ED2IN file to a named list.
+#'
+#' @param filename Full path to ED2IN file
+#' @return Named list of `tag = value`
+#' @export
+read_ed2in <- function(filename) {
+  raw_file <- readLines(filename)
+
+  # Extract tag-value pairs
+  ed2in_tag_rxp <- paste0(
+    "^[[:blank:]]*",              # Initial whitespace (does not start with a `!` comment)
+    "NL%([[:graph:]]+)",          # Capture namelist tag (1)
+    "[[:blank:]]+=[[:blank:]]*",  # Equals, with optional surrounding whitespace
+    "(",                          # Begin value capture (2)
+    "[[:digit:].-]+(,[[:blank:]]*[[:digit:].-]+)*",   # Number, or number list
+    "|",                          # ...or...
+    "@.*?@",                      # Old substitution tag (e.g. @MYVALUE@)
+    "|",                          # ...or...
+    "'[[:graph:][:blank:]]*'",    # Quoted string, or list of strings
+    ")",                          # End value capture
+    "[[:blank:]]*!?.*$"           # Trailing whitespace and possible comments
+  )
+
+  tag_lines <- grep(ed2in_tag_rxp, raw_file, perl = TRUE)
+  sub_file <- raw_file[tag_lines]
+  tags <- gsub(ed2in_tag_rxp, "\\1", sub_file, perl = TRUE)
+  values <- gsub(ed2in_tag_rxp, "\\2", sub_file, perl = TRUE)
+
+  # Extract comments. They will be stored in the object attributes.
+  all_lines <- seq_along(raw_file)
+  comment_linenos <- all_lines[!all_lines %in% tag_lines]
+  comment_values <- raw_file[comment_linenos]
+
+  # Convert to a list to allow storing of multiple data types
+  values_list <- as.list(values)
+
+  numeric_values <- !is.na(suppressWarnings(as.numeric(values))) |
+    grepl("^@.*?@$", values)    # Unquoted old substitutions are numeric
+  values_list[numeric_values] <- lapply(values_list[numeric_values], as.numeric)
+  # NOTE: This should throw a warning if any old substitution tags are present
+
+  # Convert values that are a list of numbers to a numeric vector
+  numlist_values <- grep(
+    "[[:digit:].-]+(,[[:blank:]]*[[:digit:].-]+)+",
+    values
+  )
+  values_list[numlist_values] <- lapply(
+    values_list[numlist_values],
+    function(x) as.numeric(strsplit(x, split = ",")[[1]])
+  )
+
+  # Convert values that are a list of strings to a character vector
+  charlist_values <- grep("'.*?'(,'.*?')+", values)
+  values_list[charlist_values] <- lapply(
+    values_list[charlist_values],
+    function(x) strsplit(x, split = ",")[[1]]
+  )
+
+  # Remove extra quoting of strings
+  quoted_values <- grep("'.*?'", values)
+  values_list[quoted_values] <- lapply(
+    values_list[quoted_values],
+    gsub,
+    pattern = "'",
+    replacement = ""
+  )
+
+  structure(
+    values_list,
+    names = tags,
+    class = c("ed2in", "list"),
+    comment_linenos = comment_linenos,
+    comment_values = comment_values,
+    value_linenos = tag_lines
+  )
+}
+
+#' Print method for `ed2in`
+#'
+#' Sets attributes to `NULL` before printing, so the output isn't as messy.
+#'
+#' @inheritParams base::print
+#' 
+#' @export
+print.ed2in <- function(x, ...) {
+  attributes(x) <- attributes(x)["names"]
+  print.default(x, ...)
+}
+
+#' Check if object is `ed2in`
+#'
+#' Simple test if object inheirts from class `"ed2in"`.
+#'
+#' @param x Object to be tested
+#' @export
+is.ed2in <- function(x) {
+  inherits(x, "ed2in")
+}
diff --git a/models/ed/R/read_ed_metheader.R b/models/ed/R/read_ed_metheader.R
new file mode 100644
index 00000000000..3f79556d2f7
--- /dev/null
+++ b/models/ed/R/read_ed_metheader.R
@@ -0,0 +1,155 @@
+#' Read ED meteorology header file
+#'
+#' Read a ED_MET_DRIVER_HEADER file into a list-like object that can be 
+#' manipulated within R. Returns a list of file formats.
+#'
+#' The output is an unnamed list with each element corresponding to a single 
+#' file format. Each file format contains the following elements:
+#'
+#' - `path_prefix` -- Path and prefix of files
+#' - `nlon` -- Number of longitude grid cells
+#' - `nlat` -- Number of latitude grid cells
+#' - `dx` -- Size of longitude grid cell
+#' - `dy` -- Size of latitude grid cell
+#' - `xmin` -- Minimum longitude
+#' - `ymin` -- Minimum latitude
+#' - `variables` -- Data frame of variables, with the columns described below.  
+#' Starred columns are required for writing. This table is left joined with 
+#' [met_variable_description] and [met_flag_description].
+#'    - `variable` -- Variable name
+#'    - `description` -- Variable description
+#'    - `unit` -- Variable unit
+#'    - `update_frequency` -- Update frequency (seconds) or scalar values if 
+#'    `flag=4`
+#'    - `flag` -- Variable flags.
+#'    - `flag_description` -- Description of variable flag
+#'
+#' The formatting of a meteorlogy header file is as follows (from the [ED 
+#' GitHub Wiki][https://github.com/EDmodel/ED2/wiki/Drivers]):
+#'
+#'```
+#'<number of file formats>    # Repeat lines below this number of times
+#'<path and prefix of files>
+#'<nlon>, <nlat>, <dx>, <dy>, <xmin>, <ymin>
+#'<number of variables>
+#'<list of variable names>
+#'<list of update frequencies (seconds) or scalar values if flag=4>
+#'<list of variable flags>
+#'```
+#'
+#' The variables in the third row are defined as follows:
+#' @param filename File name (including path) of met driver header file, as 
+#' character
+#' @param check Logical, whether or not to check file for correctness (default 
+#' = `TRUE`)
+#' @param check_files Logical. If `TRUE`, perform basic diagnostics on met 
+#' files as well.
+#' @return List of ED met input parameters. See Details.
+#' @export
+read_ed_metheader <- function(filename, check = TRUE, check_files = TRUE) {
+  if (!file.exists(filename)) {
+    PEcAn.logger::logger.severe("File", filename, "not found")
+  }
+  full_file <- readLines(filename)
+  comment_line <- character()
+  nvar_rxp <- "^[[:space:]]*[[:digit:]]+[[:space:]]*$"
+  for (check_line in full_file) {
+    is_nvars <- grepl(nvar_rxp, check_line)
+    if (is_nvars) {
+      nvars <- as.numeric(check_line)
+      break
+    } else {
+      comment_line <- c(comment_line, check_line)
+    }
+  }
+  if (!exists("nvars")) {
+    PEcAn.logger::logger.severe(
+      "Unable to parse ED met driver header file: ", filename
+    )
+  }
+  ed_metheader <- vector("list", nvars)
+  var_lines <- 6
+  for (i in seq_len(nvars)) {
+    block <- seq(2 + length(comment_line) + (i-1) * var_lines, length.out = var_lines)
+    sub_file <- full_file[block]
+    path_prefix <- sub_file[1]
+    met_files <- PEcAn.utils::match_file(path_prefix)
+    if (!length(met_files) >= 0) {
+      msg <- paste("No files matched for prefix", path_prefix)
+      if (check) {
+        PEcAn.logger::logger.severe(msg)
+      } else {
+        PEcAn.logger::logger.warn(msg)
+      }
+    }
+    metadata <- unlist(read.table(text = sub_file[2]))
+    names(metadata) <- c("nlon", "nlat", "dx", "dy", "xmin", "ymin")
+    nvars <- as.numeric(sub_file[3])
+    variables_raw <- read.table(text = sub_file[4:6], header = TRUE)
+    variables_raw$value_type <- c("update_frequency", "flag")
+    variables_table <- variables_raw %>%
+      tidyr::gather("variable", "value", -value_type) %>%
+      tidyr::spread("value_type", "value") %>%
+      dplyr::left_join(met_variable_description, by = "variable") %>%
+      dplyr::left_join(met_flag_description, by = "flag")
+    ed_metheader[[i]] <- list(
+      path_prefix = path_prefix,
+      nlon = metadata["nlon"],
+      nlat = metadata["nlat"],
+      dx = metadata["dx"],
+      dy = metadata["dy"],
+      xmin = metadata["xmin"],
+      ymin = metadata["ymin"],
+      variables = variables_table
+    )
+  }
+  if (check) {
+    check_ed_metheader(ed_metheader)
+  }
+  ed_metheader
+}
+
+#' Description of meteorology variables
+#'
+#' Helpful information about ED_MET_DRIVER files.
+#'
+#' `data.frame` with the following columns:
+#' - `variable` -- Variable name
+#' - `description` -- Variable description
+#' - `unit` -- Variable unit (character, parse-able by `udunints2`)
+#' @export
+met_variable_description <- tibble::tribble(
+  ~variable, ~description, ~unit,
+  "nbdsf", "near IR beam downward solar radiation", "W m-2",
+  "nddsf", "near IR diffuse downward solar radiation", "W m-2",
+  "vbdsf", "visible beam downward solar radiation", "W m-2",
+  "vddsf", "visible diffuse downward solar radiation", "W m-2",
+  "prate", "precipitation rate (kg H2O)", "kg m-2 s-1",
+  "dlwrf", "downward long wave radiation", "W m-2",
+  "pres", "pressure", "Pa",
+  "hgt", "geopotential height", "m",
+  "ugrd", "zonal wind", "m s-1",
+  "vgrd", "meridional wind", "m s-1",
+  "sh", "specific humidity (kg water / kg air)", "kg kg-1",
+  "tmp", "temperature", "K",
+  "co2", "surface co2 concentration", "ppm",
+  "lat", "grid of latitude coordinates, if this variable is present line 3 is ignored", NA,
+  "lon", "grid of longitude coordinates, if this variable is present line 3 is ignored", NA
+)
+
+#' Description of meteorology flags
+#'
+#' Descriptions of ED met header variable flags.
+#' 
+#' `data.frame` with the following columns:
+#'  - `flag` -- Numeric flag (in header file)
+#'  - `flag_description` -- Description of flag
+#' @export
+met_flag_description <- tibble::tribble(
+  ~flag, ~flag_description,
+  0, "read gridded data - no time interpolation",
+  1, "read gridded data - with time interpolation",
+  2, "read gridded data - constant in time, not changing (if this is lat/lon, will overwrite line 3 information)",
+  3, "read one value representing the whole grid - no time interpolation",
+  4, "specify a constant for all polygons, constant in time (most likely reference height)"
+)
diff --git a/models/ed/R/read_ed_veg.R b/models/ed/R/read_ed_veg.R
new file mode 100644
index 00000000000..e55ce0ca0b9
--- /dev/null
+++ b/models/ed/R/read_ed_veg.R
@@ -0,0 +1,127 @@
+#' Read ED2 vegetation inputs
+#'
+#' Read ED2 css, pss, and site files into a single ED input object.
+#'
+#' @param path_prefix Full path and prefix to initial condition files.
+#' @param latitude Run latitude (default = `NULL`). If `NULL`, deduced from file name.
+#' @param longitude Run longitude (default = `NULL`). If `NULL`, deduced from file name.
+#' @param check Whether or not to check css, pss, and site files for validity.  
+#' Default = `TRUE`.
+#' @return List containing `css`, `pss`, and `site` objects, `latitude` and 
+#' `longitude`, and `orig_paths`, a list of paths to the original `css`, `pss`, 
+#' and `site` files.
+#' @export
+read_ed_veg <- function(path_prefix, latitude = NULL, longitude = NULL,
+                        check = TRUE) {
+  latlon_rxp <- "-?[[:digit:]]{1,3}(\\.[[:digit:]]*)?"
+  if (!is.null(latitude)) {
+    lat_prefix <- paste0("lat", as.character(latitude))
+  } else {
+    lat_prefix <- paste0("lat", latlon_rxp)
+  }
+  if (!is.null(longitude)) {
+    lon_prefix <- paste0("lon", as.character(longitude))
+  } else {
+    lon_prefix <- paste0("lon", latlon_rxp)
+  }
+  if (grepl("\\.$", path_prefix)) {
+    dot <- ""
+  } else {
+    dot <- "."
+  }
+  path_prefix_full <- paste0(path_prefix, dot, lat_prefix, lon_prefix)
+
+  file_matches <- PEcAn.utils::match_file(path_prefix_full, expect = 3)
+  css_file <- PEcAn.utils::match_file(path_prefix_full, suffix = "css", expect = 1)
+  pss_file <- PEcAn.utils::match_file(path_prefix_full, suffix = "pss", expect = 1)
+  site_file <- PEcAn.utils::match_file(path_prefix_full, suffix = "site", expect = 1)
+
+  if (is.null(latitude)) {
+    latitude <- get_latlon(css_file, "lat")
+  }
+
+  if (is.null(longitude)) {
+    longitude <- get_latlon(css_file, "lon")
+  }
+
+  css <- read_css(css_file, check = FALSE)
+  pss <- read_pss(pss_file, check = FALSE)
+  site <- read_site(site_file, check = FALSE)
+
+  create_ed_veg(
+    css = css,
+    pss = pss,
+    site = site,
+    latitude = latitude,
+    longitude = longitude,
+    check = TRUE,
+    orig_paths = list(
+      css = css_file,
+      pss = pss_file,
+      site = site_file
+    )
+  )
+}
+
+#' Parse latitude or longitude
+#'
+#' Automatically determine latitude or longitude from an ED input filepath. If 
+#' the latitude/longitude regular expression isn't matched, this will throw an 
+#' error.
+#'
+#' @param filepath Path to a css, pss, or site file
+#' @param latlon Which value to retrieve, either "lat" for latitude or "lon" 
+#' for longitude
+#' @return Numeric value of latitude or longitude
+get_latlon <- function(filepath, latlon) {
+  stopifnot(latlon %in% c("lat", "lon"))
+  fname <- basename(filepath)
+  latlon_rxp <- "-?[[:digit:]]{1,3}(\\.[[:digit:]]*)?"
+  rxp <- paste0(".*", latlon, "(", latlon_rxp, ").*")
+  stopifnot(grepl(rxp, fname))
+  out <- as.numeric(gsub(rxp, "\\1", fname))
+  stopifnot(!is.na(out), length(out) == 1)
+  out
+}
+
+#' Read individual css, pss, and site files
+#'
+#' Read files into objects usable by other PEcAn.ED2 utilities, and optionally check for errors.
+#' @param filepath Full path to css, pss, or site file
+#' @param check Logical. If `TRUE` (default), [check][check_css] that file is valid.
+#' @param ... Additional arguments to [check functions][check_css].
+#' @return `data.frame` containing
+#' @export
+read_css <- function(filepath, check = TRUE, ...) {
+  css <- read.table(filepath, header = TRUE)
+  if (check) {
+    check_css(css, ...)
+  }
+  css
+}
+
+#' @rdname read_css
+#' @export
+read_pss <- function(filepath, check = TRUE) {
+  pss <- read.table(filepath, header = TRUE)
+  if (check) {
+    check_pss(pss, ...)
+  }
+  pss
+}
+
+#' @rdname read_css
+#' @export
+read_site <- function(filepath, check = TRUE, ...) {
+  top_line <- readLines(filepath, n = 1)
+  nsite <- as.numeric(gsub(".*nsite +([[:digit:]]+).*", "\\1", top_line))
+  file_format <- as.numeric(gsub(".*file_format +([[:digit:]]+).*", "\\1", top_line))
+  site <- read.table(filepath, header = TRUE, skip = 1)
+  attr(site, "nsite") <- nsite
+  attr(site, "file_format") <- file_format
+  if (check) {
+    check_site(site, ...)
+  }
+  site
+}
+
diff --git a/models/ed/R/read_restart.ED2.R b/models/ed/R/read_restart.ED2.R
index 6523356ec91..66cc7878467 100644
--- a/models/ed/R/read_restart.ED2.R
+++ b/models/ed/R/read_restart.ED2.R
@@ -1,6 +1,6 @@
 #' @title State data assimilation read-restart for ED2
 #'
-#' @author Alexey Shiklomanov
+#' @author Alexey Shiklomanov, Istem Fer
 #' @inheritParams PEcAn.ModelName::read_restart.ModelName
 #' @examples
 #' \dontrun{
@@ -18,81 +18,115 @@ read_restart.ED2 <- function(outdir,
                              settings, 
                              var.names, 
                              params) {
-
-    name_separator <- "."
-
-    rundir <- settings$host$rundir
-    mod_outdir <- settings$host$outdir
-
-    confxml <- get_configxml.ED2(rundir, runid)
-
-    histfile <- get_restartfile.ED2(mod_outdir, runid, stop.time)
-    if (is.null(histfile)) {
-      PEcAn.logger::logger.severe("Failed to find ED2 history restart file.")
+  
+  # depends on code run on local or remote, currently runs locally
+  rundir <- settings$rundir
+  mod_outdir <- settings$modeloutdir # is there a case this is different than outdir?
+  
+  
+  histfile <- get_restartfile.ED2(mod_outdir, runid, stop.time)
+  if (is.null(histfile)) {
+    PEcAn.logger::logger.severe("Failed to find ED2 history restart file.")
+  }
+  
+  
+  pft_names <- sapply(settings$pfts, '[[', 'name')
+  
+  
+  # var.names <- c("AbvGrndWood", "GWBI", "TotLivBiom", "leaf_carbon_content") 
+  histout <- read_S_files(sfile       = basename(histfile), 
+                          outdir      = dirname(histfile), 
+                          pft_names   = pft_names, 
+                          pecan_names = var.names)
+  
+  # unit conversions and other aggregations
+  forecast <- list()
+  
+  for (var_name in var.names) {
+    
+    # should there be a tag passed via settings to check for per pft assimilation vs totals?
+    perpft <- FALSE # for now just working with totals for HF tree-ring DA
+    
+    if (var_name == "AGB") {
+      
+      forecast_tmp                        <- switch(perpft+1, sum(histout$AGB, na.rm = TRUE), histout$AGB) # kgC/m2
+      forecast[[length(forecast)+1]]      <- udunits2::ud.convert(forecast_tmp, "kg/m^2", "Mg/ha") # conv to MgC/ha 
+      names(forecast)[length(forecast)]   <- switch(perpft+1, "AGB", paste0("AGB.", pft_names))
+      
     }
-
-    nc <- ncdf4::nc_open(histfile)
-    on.exit(ncdf4::nc_close(nc))
-
-    # Identify PFTs
-    # This assumes that PFT order is the same between pecan.xml and ED's 
-    # config.xml.
-    # A better solution would set the PFT numbers in the pecan.xml, or names in 
-    # config.xml.
-    pftnums <- sapply(confxml, '[[', 'num')
-    pftnames <- sapply(settings$pfts, '[[', 'name')
-    names(pftnames) <- pftnums
-
-    #### Common variables ####
-
-    # PFT by cohort
-    pft_co <- ncdf4::ncvar_get(nc, "PFT")
-
-    # Patch area
-    patch_area <- ncdf4::ncvar_get(nc, "AREA")
-
-    # Create a patch index indicator vector
-    patch_index <- patch_cohort_index(nc)
-
-    forecast <- list()
-
-    for (var_name in var.names) {
-
-        pft_full_names <- paste("pft", pftnames,
-                                sep = name_separator)
-        names(pft_full_names) <- pftnums
-
-        ## TODO: Convert to PEcAn standard names
-        if (var_name == "AGB") {
-
-            # Cohort AGB -- kgC plant-1
-            agb_co_plant <- ncdf4::ncvar_get(nc, "AGB_CO")
-
-            # Cohort stem density -- Plant m-2
-            co_plant <- ncdf4::ncvar_get(nc, "NPLANT")
-
-            # Cohort AGB -- kgC m-2
-            agb_co <- agb_co_plant * co_plant
-
-            # Aggregate AGB by patch and PFT
-            agb_patch_pft <- tapply(agb_co, 
-                                    list("PFT" = pft_co, "patch" = patch_index), 
-                                    sum)
-
-            # AGB by PFT and area
-            agb_pft_x_area <- apply(agb_patch_pft, 1, "*", patch_area)
-            agb_pft <- colSums(agb_pft_x_area, na.rm = TRUE)
-            
-            names(agb_pft) <- pft_full_names[names(agb_pft)]
-            forecast[[var_name]] <- agb_pft
-        } else {
-            PEcAn.logger::logger.error("Variable ", var_name,
-                                      " not currently supported",
-                                      " by read.restart.ED2")
-        }
+    
+    if (var_name == "TotLivBiom") {
+      
+      forecast_tmp                        <- switch(perpft+1, sum(histout$TotLivBiom, na.rm = TRUE), histout$TotLivBiom) # kgC/m2
+      forecast[[length(forecast)+1]]      <- udunits2::ud.convert(forecast_tmp, "kg/m^2", "Mg/ha") # conv to MgC/ha 
+      names(forecast)[length(forecast)]   <- switch(perpft+1, "TotLivBiom", paste0("TotLivBiom.", pft_names))
+      
     }
-
-    return(unlist(forecast))
+    
+    if (var_name == "AbvGrndWood") {
+      
+      forecast_tmp                        <- switch(perpft+1, sum(histout$AbvGrndWood, na.rm = TRUE), histout$AbvGrndWood) # kgC/m2
+      forecast[[length(forecast)+1]]      <- udunits2::ud.convert(forecast_tmp, "kg/m^2", "Mg/ha") # conv to MgC/ha 
+      names(forecast)[length(forecast)]   <- switch(perpft+1, "AbvGrndWood", paste0("AbvGrndWood.", pft_names))
+      
+    }
+    
+    if (var_name == "leaf_carbon_content") {
+      
+      forecast_tmp                        <- switch(perpft+1, sum(histout$leaf_carbon_content, na.rm = TRUE), histout$leaf_carbon_content) # kgC/m2
+      forecast[[length(forecast)+1]]      <- udunits2::ud.convert(forecast_tmp, "kg/m^2", "Mg/ha") # conv to MgC/ha 
+      names(forecast)[length(forecast)]   <- switch(perpft+1, "leaf_carbon_content", paste0("leaf_carbon_content.", pft_names))
+      
+    }
+    
+    if (var_name == "storage_carbon_content") {
+      
+      forecast[[length(forecast)+1]]      <- switch(perpft+1, sum(histout$storage_carbon_content, na.rm = TRUE), histout$storage_carbon_content) # kgC/m2
+      names(forecast)[length(forecast)]   <- switch(perpft+1, "storage_carbon_content", paste0("storage_carbon_content.", pft_names))
+      
+    }
+    
+    
+    if (var_name == "GWBI") {
+      
+      forecast_tmp                        <- switch(perpft+1, sum(histout$GWBI, na.rm = TRUE), histout$GWBI) # kgC/m2/yr
+      forecast[[length(forecast)+1]]      <- udunits2::ud.convert(forecast_tmp, "kg/m^2/yr", "Mg/ha/yr") # conv to MgC/ha/yr 
+      names(forecast)[length(forecast)]   <- switch(perpft+1, "GWBI", paste0("GWBI.", pft_names))
+      
+    }
+    
+    if (var_name == "fast_soil_pool_carbon_content") {
+      
+      forecast[[length(forecast)+1]]      <- histout$fast_soil_pool_carbon_content # kgC/m2
+      names(forecast)[length(forecast)]   <- "fast_soil_pool_carbon_content"
+      
+    }
+    
+    if (var_name == "structural_soil_pool_carbon_content") {
+      
+      forecast[[length(forecast)+1]]      <- histout$structural_soil_pool_carbon_content # kgC/m2
+      names(forecast)[length(forecast)]   <- "structural_soil_pool_carbon_content"
+      
+    }
+    
+    
+  } # var.names loop
+  
+  restart <- list()
+  # pass certain things for write_restart to use (so that there we don't have to re-read and re-calculate stuff)
+  # IMPORTANT NOTE: in the future, these "certain things" need to be confined to old states that will be used
+  # to carry out deternimistic relationships, no other read/write restart should copy this logic
+  restart$restart  <- histout$restart
+  restart$histfile <- histfile
+  
+  params$restart <- restart
+  
+  PEcAn.logger::logger.info("Finished --", runid)
+  
+  X_tmp <- list(X = unlist(forecast), params = params)
+  
+  return(X_tmp)
+  
 } # read_restart.ED2
 
 
diff --git a/models/ed/R/run_ed_singularity.R b/models/ed/R/run_ed_singularity.R
new file mode 100644
index 00000000000..56c33fe643a
--- /dev/null
+++ b/models/ed/R/run_ed_singularity.R
@@ -0,0 +1,45 @@
+#' Run ED singularity container
+#'
+#' Uses [base::system2] to run ED or EDR via a Singularity container.
+#'
+#' On some systems, to run Singularity properly, you will need to bind 
+#' additional paths. To do this, pass the arguments as a character vector to 
+#' `singularity_args`. For instance:
+#'
+#' ```
+#' bindpaths <- c("/scratch", "/data")
+#' run_ed_singularity(..., singularity_args = paste("--bind", bindpaths))
+#' ```
+#'
+#' By default, [base::system2] prints the output to the console. To store 
+#' standard ED output in a variable as a character vector, set `stdout = TRUE`. 
+#' To redirect all output to the variable, including GCC exceptions, use 
+#' `stderr = TRUE` (this will automatically set `stdout = TRUE` as well). 
+#' Output can also be redirected to a file via `stderr = "/path/to/file.log"`.
+#'
+#' @param img_path Path to Singularity container (usually a `.simg` file)
+#' @param ed2in_path Path to ED2IN file.
+#' @param app Singularity "app" to run. Either "ED" or "EDR".
+#' @param singularity_args Additional arguments to be passed to `singularity run` (before)
+#' @param Additional arguments to [base::system2]
+#' @export
+run_ed_singularity <- function(img_path, ed2in_path,
+                               app = "ED",
+                               singularity_args = NULL,
+                               ...) {
+  if (!file.exists(img_path)) {
+    PEcAn.logger::logger.severe("Image file ", img_path, " not found.")
+  }
+  if (!file.exists(ed2in_path)) {
+    PEcAn.logger::logger.severe("ED2IN file ", ed2in_path, " not found.")
+  }
+  sys_args <- c(
+    "run",
+    "--app", app,
+    singularity_args,
+    normalizePath(img_path, mustWork = TRUE),
+    "-f",
+    normalizePath(ed2in_path, mustWork = TRUE)
+  )
+  system2("singularity", sys_args, ...)
+}
diff --git a/models/ed/R/veg2model.ED2.R b/models/ed/R/veg2model.ED2.R
index 3dedfefc315..6284b4c7488 100644
--- a/models/ed/R/veg2model.ED2.R
+++ b/models/ed/R/veg2model.ED2.R
@@ -39,12 +39,37 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source){
   
   # for FIA these steps are unnecessary, it already has the pss info
   if(source != "FIA"){
-    time    <- ifelse(!is.null(pss$time), pss$time, start_year)
-    n.patch <- ifelse(!is.null(pss$n.patch), pss$n.patch, 1)
-    trk     <- ifelse(!is.null(pss$trk), pss$trk, 1)
-    age     <- ifelse(!is.null(pss$age), pss$age, 100)
+    if(!is.null(pss$time)){
+      time <- as.numeric(pss$time)
+    }else{
+      PEcAn.logger::logger.info("No year info passed via metadata, using start year: ", start_year)
+      time <- start_year
+    }
+    if(!is.null(pss$n.patch)){
+      n.patch <- as.numeric(pss$n.patch)
+    }else{
+      PEcAn.logger::logger.info("No patch number info passed via metadata, assuming 1 patch.")
+      n.patch <- 1
+    }
+    if(!is.null(pss$trk)){
+      trk <- as.numeric(pss$trk)
+    }else{
+      PEcAn.logger::logger.info("No trk info passed via metadata, assuming 1.")
+      trk <- 1
+    }
+    if(!is.null(pss$age)){
+      age <- as.numeric(pss$age)
+    }else{
+      PEcAn.logger::logger.info("No stand age info passed via metadata, assuming 100.")
+      age <- 100
+    }
+    if(!is.null(pss$area)){
+      area <- as.numeric(pss$area)
+    }else{
+      PEcAn.logger::logger.severe("No area info passed via metadata, please provide area of your plot in m2 under 'settings$run$inputs$css$metadata$area'.")
+    }
     
-    pss <- data.frame(time = time, patch = n.patch, trk = trk, age = age)
+    pss <- data.frame(time = rep(time, n.patch), patch = seq_len(n.patch), trk = rep(trk, n.patch), age = rep(age, n.patch))
     
     PEcAn.logger::logger.info(paste0("Values used in the patch file - time:", 
                                     pss$time, ", patch:", pss$patch, ", trk:", 
@@ -53,8 +78,6 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source){
     # TODO : soils can also be here, passed from settings
   }
   
-  n.patch   <- nrow(pss)
-  
   ## fill missing data w/ defaults
   pss$site  <- 1
   pss$area  <- 1 / n.patch
@@ -63,7 +86,7 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source){
   # Reorder columns
   pss <- pss[, c("site", "time", "patch", "trk", "age", "area", "water")]
   
-  # Add soil data
+  # Add soil data: Currently uses default values, will soil_process overwrite it afterwards?
   soil            <- c(1, 5, 5, 0.01, 0, 1, 1)  #soil C & N pools (biogeochem) defaults (fsc,stsc,stsl,ssc,psc,msn,fsn)
   soil.dat        <- as.data.frame(matrix(soil, n.patch, 7, byrow = TRUE))
   names(soil.dat) <- c("fsc", "stsc", "stsl", "ssc", "psc", "msn", "fsn")
@@ -80,7 +103,9 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source){
   # might further need removing dead trees by mortality status
   # css <- remove_dead_trees()
 
-  if(is.null(css$patch)){
+  if(!is.null(css$Subplot)){
+    css$patch  <- css$Subplot
+  }else{
     css$patch  <- 1
   }
 
@@ -94,13 +119,12 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source){
 
     
   if(is.null(css$n)){ 
-    # will get back to giving sensical values
-    css$n <- 0.001
+    css$n <- 1/area
   }
   
   if(is.null(css$cohort)){ 
-    # will get back to giving sensical values
-    css$cohort <- 1:nrow(css)
+    # every tree is its own cohort, ED2 will fuse them or simulate them individually depending on max.cohort
+    css$cohort <-  do.call("c", lapply(seq_len(n.patch), function(x) 1:sum(css$patch==x))) 
   }
   
   inv.years <- as.numeric(unique(css$year))
@@ -110,6 +134,7 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source){
     PEcAn.logger::logger.severe("No available years found in the data.")
   }
   css$time <- max(av.years)
+  
   # filter out other years
   css <- css[css$year == css$time, ]
   
@@ -128,10 +153,8 @@ veg2model.ED2 <- function(outfolder, veg_info, start_date, new_site, source){
     }
   }
   
-    
   # --- Continue work formatting css 
-  n.cohort                      <- nrow(css)
-  css$time[is.na(css$time)]     <- 1
+  css$time[is.na(css$time)]     <- start_year
   css$cohort[is.na(css$cohort)] <- 1:sum(is.na(css$cohort))
   css$dbh[is.na(css$dbh)]       <- 1  # assign nominal small dbh to missing
   density.median                <- median(css$n[which(css$n > 0)])
diff --git a/models/ed/R/write.configs.ed.R b/models/ed/R/write.configs.ed.R
index 89faec2f3bf..2fdd8d3d6e2 100644
--- a/models/ed/R/write.configs.ed.R
+++ b/models/ed/R/write.configs.ed.R
@@ -22,8 +22,6 @@ PREFIX_XML <- "<?xml version=\"1.0\"?>\n<!DOCTYPE config SYSTEM \"ed.dtd\">\n"
 ##' 
 ##' Performs model specific unit conversions on a a list of trait values,
 ##' such as those provided to write.config
-##' @name convert.samples.ED
-##' @title Convert samples for ed
 ##' @param trait.samples a matrix or dataframe of samples from the trait distribution
 ##' @return matrix or dataframe with values transformed
 ##' @author Shawn Serbin, David LeBauer, Carl Davidson, Ryan Kelly
@@ -92,21 +90,24 @@ convert.samples.ED <- function(trait.samples) {
 
 
 ##-------------------------------------------------------------------------------------------------#
-##' Writes an xml and ED2IN config files for use with the Ecological Demography model.
+##' Write ED configuration files
 ##'
-##' Requires a pft xml object, a list of trait values for a single model run,
-##' and the name of the file to create
-##' @name write.config.ED2
-##' @title Write ED configuration files
+##' Writes an xml and ED2IN config files for use with the Ecological Demography 
+##' model. Requires a pft xml object, a list of trait values for a single model 
+##' run, and the name of the file to create
+#'
 ##' @param trait.values Named list of trait values, with names corresponding to PFT
 ##' @param settings list of settings from pecan settings file
 ##' @param run.id id of run
 ##' @param defaults list of defaults to process. Default=settings$constants
+##' @param check Logical. If `TRUE`, check ED2IN validity before running and 
+##' throw an error if anything is wrong (default = `FALSE`)
+##' 
 ##' @return configuration file and ED2IN namelist for given run
 ##' @export
-##' @author David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov
+##' @author David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov, Istem Fer
 ##-------------------------------------------------------------------------------------------------#
-write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings$constants) {
+write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings$constants, check = FALSE, ...) {
   
   
   jobsh <- write.config.jobsh.ED2(settings = settings, run.id = run.id)
@@ -124,36 +125,55 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
   
   ##----------------------------------------------------------------------
   ## Edit ED2IN file for runs
+  revision <- settings$model$revision
+  if (is.null(revision)) {
+    model <- db.query(paste("SELECT * FROM models WHERE id =", settings$model$id), params = settings$database$bety)
+    revision <- model$revision
+  }
+  revision <- gsub("^r", "", revision)
+
   if (!is.null(settings$model$edin) && file.exists(settings$model$edin)) {
-    ed2in.text <- readLines(con = settings$model$edin, n = -1)
+    ed2in.text <- read_ed2in(settings$model$edin)
   } else {
     filename <- system.file(settings$model$edin, package = "PEcAn.ED2")
     if (filename == "") {
-      if (!is.null(settings$model$revision)) {
-        rev <- gsub("^r", "", settings$model$revision)
-      } else {
-        model <- db.query(paste("SELECT * FROM models WHERE id =", settings$model$id), params = settings$database$bety)
-        rev <- gsub("^r", "", model$revision)
-      }
-      filename <- system.file(paste0("ED2IN.r", rev), package = "PEcAn.ED2")
+      filename <- system.file(paste0("ED2IN.r", revision), package = "PEcAn.ED2")
     }
     if (filename == "") {
       PEcAn.logger::logger.severe("Could not find ED template")
     }
     PEcAn.logger::logger.info("Using", filename, "as template")
-    ed2in.text <- readLines(con = filename, n = -1)
+    ed2in.text <- read_ed2in(filename)
   }
-  
+
   metstart <- tryCatch(format(as.Date(settings$run$site$met.start), "%Y"), 
                        error = function(e) settings$run$site$met.start)
   metend <- tryCatch(format(as.Date(settings$run$site$met.end), "%Y"), 
                      error = function(e) settings$run$site$met.end)
   
-  ed2in.text <- gsub("@SITE_LAT@", settings$run$site$lat, ed2in.text)
-  ed2in.text <- gsub("@SITE_LON@", settings$run$site$lon, ed2in.text)
-  ed2in.text <- gsub("@SITE_MET@", settings$run$inputs$met$path, ed2in.text)
-  ed2in.text <- gsub("@MET_START@", metstart, ed2in.text)
-  ed2in.text <- gsub("@MET_END@", metend, ed2in.text)
+
+  ed2in.text <- modify_ed2in(
+    ed2in.text,
+    latitude = as.numeric(settings$run$site$lat),
+    longitude = as.numeric(settings$run$site$lon),
+    met_driver = settings$run$inputs$met$path,
+    start_date = startdate,
+    end_date = enddate,
+    MET_START = metstart,
+    MET_END = metend,
+    IMETAVG = -1,   # See below,
+    add_if_missing = TRUE,
+    check_paths = check
+  )
+
+  # The flag for IMETAVG tells ED what to do given how input radiation was 
+  # originally averaged
+  # -1 = I don't know, use linear interpolation
+  # 0 = No average, the values are instantaneous
+  # 1 = Averages ending at the reference time
+  # 2 = Averages beginning at the reference time
+  # 3 = Averages centered at the reference time Deafult is -1
+  
   
   if (is.null(settings$model$phenol.scheme)) {
     PEcAn.logger::logger.error(paste0("no phenology scheme set; \n",
@@ -161,21 +181,30 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
                                      "tag under <model> tag in settings file"))
   } else if (settings$model$phenol.scheme == 1) {
     ## Set prescribed phenology switch in ED2IN
-    ed2in.text <- gsub("@PHENOL_SCHEME@", settings$model$phenol.scheme, ed2in.text)
-    ## Phenology filename
-    ed2in.text <- gsub("@PHENOL@", settings$model$phenol, ed2in.text)
-    ## Set start year of phenology
-    ed2in.text <- gsub("@PHENOL_START@", settings$model$phenol.start, ed2in.text)
-    ## Set end year of phenology
-    ed2in.text <- gsub("@PHENOL_END@", settings$model$phenol.end, ed2in.text)
-    
-    ## If not prescribed set alternative phenology scheme.
+    ed2in.text <- modify_ed2in(
+      ed2in.text,
+      IPHEN_SCHEME   = as.numeric(settings$model$phenol.scheme),
+      PHENPATH       = settings$model$phenol,
+      IPHENYS1       = settings$model$phenol.start,
+      PIPHENYSF      = settings$model$phenol.end,
+      IPHENYF1       = settings$model$phenol.start,
+      IPHENYFF       = settings$model$phenol.end,
+      add_if_missing = TRUE,
+      check_paths    = check
+    )
   } else {
-    ed2in.text <- gsub(" @PHENOL_SCHEME@", settings$model$phenol.scheme, ed2in.text)
-    # Insert blanks into ED2IN file so ED2 runs without error
-    ed2in.text <- gsub("@PHENOL@", "", ed2in.text)
-    ed2in.text <- gsub("@PHENOL_START@", "", ed2in.text)
-    ed2in.text <- gsub("@PHENOL_END@", "", ed2in.text)
+    ## If not prescribed set alternative phenology scheme.
+    ed2in.text <- modify_ed2in(
+      ed2in.text,
+      IPHEN_SCHEME   = as.numeric(settings$model$phenol.scheme),
+      PHENPATH       = "",
+      IPHENYS1       = settings$model$phenol.start,
+      PIPHENYSF      = settings$model$phenol.end,
+      IPHENYF1       = settings$model$phenol.start,
+      IPHENYFF       = settings$model$phenol.end,
+      add_if_missing = TRUE,
+      check_paths    = check
+    )
   }
 
   ## -------------
@@ -183,14 +212,17 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
   # 
   if (!is.null(settings$state.data.assimilation)) {
     # Default values
-    sda_tags <- list(isoutput = 3,    # Save history state file
-                     unitstate = 1,   # History state frequency is days
-                     frqstate = 1)    # Write history file every 1 day
-
-    # Overwrite defaults with values from settings$model$ed2in list
-    sda_tags <- modifyList(sda_tags, settings$model$ed2in[names(sda_tags)])
-    ed2in.text <- ed2in_set_value_list(sda_tags, ed2in.text, 
-                                       "PEcAn: configured for SDA")
+    sda_tags <- list(
+      ISOUTPUT = 3,     # Save history state file
+      UNITSTATE = 3,    # History state frequency is years
+      FRQSTATE = 1      # Write history file every 1 year
+    )
+    
+    # Overwrite defaults with values from settings$model$ed2in_tags list
+    if(!is.null(settings$model$ed2in_tags)){
+      sda_tags <- modifyList(sda_tags, settings$model$ed2in_tags[names(sda_tags)])
+    }
+    ed2in.text <- modify_ed2in(ed2in.text, .dots = sda_tags, add_if_missing = TRUE, check_paths = check)
   }
 
   ##----------------------------------------------------------------------
@@ -198,10 +230,16 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
   # Assumes pattern 'DIR/PREFIX.lat<REMAINDER OF FILENAME>'
   # Slightly overcomplicated to avoid error if path name happened to contain .lat'
   
+  
   # when pss or css not exists, case 0
   if (is.null(settings$run$inputs$pss$path) | is.null(settings$run$inputs$css$path)) {
-    ed2in.text <- gsub("@INIT_MODEL@", 0, ed2in.text)
-    ed2in.text <- gsub("@SITE_PSSCSS@", "", ed2in.text)
+    ed2in.text <- modify_ed2in(
+      ed2in.text,
+      IED_INIT_MODE = 0,
+      SFILIN = "",
+      add_if_missing = TRUE,
+      check_paths = check
+    )
   } else {
     lat_rxp <- "\\.lat.*lon.*\\.(css|pss|site)"
     prefix.css <- sub(lat_rxp, "", settings$run$inputs$css$path)
@@ -211,53 +249,47 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
       PEcAn.logger::logger.info(paste("pss prefix:", prefix.pss))
       PEcAn.logger::logger.info(paste("css prefix:", prefix.css))
       PEcAn.logger::logger.severe("ED2 css/pss/ files have different prefix")
-    } else {
-      # pss and css are both present
-      value <- 2
-      # site exists
-      if (!is.null(settings$run$inputs$site$path)) {
-        prefix.site <- sub(lat_rxp, "", settings$run$inputs$site$path)
-        # sites and pss have different prefix name, kill
-        if (!identical(prefix.site, prefix.pss)) {
-          PEcAn.logger::logger.info(paste("site prefix:", prefix.site))
-          PEcAn.logger::logger.info(paste("pss prefix:", prefix.pss))
-          PEcAn.logger::logger.severe("ED2 sites/pss/ files have different prefix")
-        } else {
-          # sites and pass same prefix name, case 3
-          value <- 3
-        }
+    }
+    # pss and css are both present
+    value <- 2
+    # site exists
+    if (!is.null(settings$run$inputs$site$path)) {
+      prefix.site <- sub(lat_rxp, "", settings$run$inputs$site$path)
+      # sites and pss have different prefix name, kill
+      if (!identical(prefix.site, prefix.pss)) {
+        PEcAn.logger::logger.info(paste("site prefix:", prefix.site))
+        PEcAn.logger::logger.info(paste("pss prefix:", prefix.pss))
+        PEcAn.logger::logger.severe("ED2 sites/pss/ files have different prefix")
+      } else {
+        # sites and pass same prefix name, case 3
+        value <- 3
       }
+      
     }
-    ed2in.text <- gsub("@INIT_MODEL@", value, ed2in.text)
-    ed2in.text <- gsub("@SITE_PSSCSS@", paste0(prefix.pss, "."), ed2in.text)
+    ed2in.text <- modify_ed2in(
+      ed2in.text,
+      IED_INIT_MODE = value,
+      SFILIN = paste0(prefix.pss, "."),
+      add_if_missing = TRUE,
+      check_paths = check
+    )
   }
   
-  ##----------------------------------------------------------------------
-  
-  ed2in.text <- gsub("@ED_VEG@", settings$run$inputs$veg$path, ed2in.text)
-  ed2in.text <- gsub("@ED_SOIL@", settings$run$inputs$soil$path, ed2in.text)
-  ed2in.text <- gsub("@ED_LU@", settings$run$inputs$lu$path, ed2in.text)
-  ed2in.text <- gsub("@ED_THSUM@", ifelse(stringr::str_sub(settings$run$inputs$thsum$path, -1) == "/", settings$run$inputs$thsum$path, 
-                                          paste0(settings$run$inputs$thsum$path, "/")), ed2in.text)
-  
-  ##----------------------------------------------------------------------
-  ed2in.text <- gsub("@START_MONTH@", format(startdate, "%m"), ed2in.text)
-  ed2in.text <- gsub("@START_DAY@", format(startdate, "%d"), ed2in.text)
-  ed2in.text <- gsub("@START_YEAR@", format(startdate, "%Y"), ed2in.text)
-  ed2in.text <- gsub("@END_MONTH@", format(enddate, "%m"), ed2in.text)
-  ed2in.text <- gsub("@END_DAY@", format(enddate, "%d"), ed2in.text)
-  ed2in.text <- gsub("@END_YEAR@", format(enddate, "%Y"), ed2in.text)
-  
-  ##-----------------------------------------------------------------------
-  # Set The flag for IMETAVG telling ED what to do given how input radiation was originally
-  # averaged
-  # -1 = I don't know, use linear interpolation
-  # 0 = No average, the values are instantaneous
-  # 1 = Averages ending at the reference time
-  # 2 = Averages beginning at the reference time
-  # 3 = Averages centered at the reference time Deafult is -1
-  
-  ed2in.text <- gsub("@MET_SOURCE@", -1, ed2in.text)
+
+  thsum <- settings$run$inputs$thsum$path
+  if (!grepl("/$", thsum)) {
+    thsum <- paste0(thsum, "/")
+  }
+
+  ed2in.text <- modify_ed2in(
+    ed2in.text,
+    VEG_DATABASE = settings$run$inputs$veg$path,
+    SOIL_DATABASE = settings$run$inputs$soil$path,
+    LU_DATABASE = settings$run$inputs$lu$path,
+    THSUMS_DATABASE = thsum,
+    add_if_missing = TRUE,
+    check_paths = check
+  )
   
   ##----------------------------------------------------------------------
   if (is.null(settings$host$scratchdir)) {
@@ -265,23 +297,24 @@ write.config.ED2 <- function(trait.values, settings, run.id, defaults = settings
   } else {
     modeloutdir <- file.path(settings$host$scratchdir, settings$workflow$id, run.id)
   }
-  ed2in.text <- gsub("@OUTDIR@", modeloutdir, ed2in.text)
-  ed2in.text <- gsub("@ENSNAME@", run.id, ed2in.text)
-  ed2in.text <- gsub("@CONFIGFILE@", file.path(settings$host$rundir, run.id, "config.xml"), ed2in.text)
-  # ed2in.text <- gsub('@CONFIGFILE@','config.xml', ed2in.text) # for ED2.r81 on Kang.  Temporary
-  # hack
+  ed2in.text <- modify_ed2in(
+    ed2in.text,
+    run_name = paste0("ED2 v", revision, " PEcAn ", run.id),
+    run_dir = file.path(settings$host$rundir, run.id),    # For `config.xml`
+    output_dir = modeloutdir,   # Sets analysis and history paths
+    add_if_missing = TRUE,
+    check_paths = check
+  )
   
-  ##----------------------------------------------------------------------
-  ed2in.text <- gsub("@FFILOUT@", file.path(modeloutdir, "analysis"), ed2in.text)
-  ed2in.text <- gsub("@SFILOUT@", file.path(modeloutdir, "history"), ed2in.text)
-
   ##---------------------------------------------------------------------
-  # Modify any additional tags provided in settings$model$ed2in
-  ed2in.text <- ed2in_set_value_list(settings$model$ed2in, ed2in.text, 
-                                     "PEcAn: Custom argument from pecan.xml")
+  # Modify any additional tags provided in settings$model$ed2in_tags
+  ed2in.text <- modify_ed2in(ed2in.text, .dots = settings$model$ed2in_tags, add_if_missing = TRUE, check_paths = check)
   
   ##----------------------------------------------------------------------
-  writeLines(ed2in.text, con = file.path(settings$rundir, run.id, "ED2IN"))
+  if (check) {
+    check_ed2in(ed2in.text)
+  }
+  write_ed2in(ed2in.text, file.path(settings$rundir, run.id, "ED2IN"))
 } # write.config.ED2
 # ==================================================================================================#
 
diff --git a/models/ed/R/write_ed2in.R b/models/ed/R/write_ed2in.R
new file mode 100644
index 00000000000..bcec31eb505
--- /dev/null
+++ b/models/ed/R/write_ed2in.R
@@ -0,0 +1,75 @@
+#' Write ED2IN list to file
+#'
+#' This writes a ED2IN file from an `ed2in` list. Default method writes a 
+#' barebones file without comments. S3 method for `ed2in` objects extracts 
+#' comments and their locations from the object attributes (if `barebones` is 
+#' `FALSE`).
+#'
+#' @param ed2in Named list of ED2IN tag-value pairs. See [read_ed2in].
+#' @param filename Target file name
+#' @param custom_header Character vector for additional header comments. Each 
+#' item gets its own line.
+#' @param barebones Logical. If `TRUE`, omit comments and only write tag-value pairs.
+#' @export
+write_ed2in <- function(ed2in, filename, custom_header = character(), barebones = FALSE) {
+  UseMethod("write_ed2in", ed2in)
+}
+
+#' @rdname write_ed2in
+#' @export
+write_ed2in.ed2in <- function(ed2in, filename, custom_header = character(), barebones = FALSE) {
+  tags_values_vec <- tags2char(ed2in)
+  if (barebones) {
+    write_ed2in.default(ed2in, filename, custom_header, barebones)
+    return(NULL)
+  }
+  nvalues <- length(tags_values_vec)
+  ncomments <- length(attr(ed2in, "comment_values"))
+  file_body <- character(nvalues + ncomments)
+  file_body[attr(ed2in, "comment_linenos")] <- attr(ed2in, "comment_values")
+  file_body[attr(ed2in, "value_linenos")] <- tags_values_vec
+  header <- c(
+    "!=======================================",
+    "!=======================================",
+    "!  ED2 namelist file",
+    "!  Generated by `PEcAn.ED2::write_ed2in.ed2in`",
+    "!  Additional user comments below: ",
+    paste0("!   ", custom_header),
+    "!---------------------------------------"
+  )
+  output_lines <- c(header, file_body)
+  writeLines(output_lines, filename)
+}
+
+#' @rdname write_ed2in
+#' @export
+write_ed2in.default <- function(ed2in, filename, custom_header = character(), barebones = FALSE) {
+  tags_values_vec <- tags2char(ed2in)
+  header <- c(
+    "!=======================================",
+    "!=======================================",
+    "!  ED2 namelist file",
+    "!  Generated by `PEcAn.ED2::write_ed2in.default`",
+    "!  Additional user comments below: ",
+    paste0("!   ", custom_header),
+    "!---------------------------------------"
+  )
+  output_lines <- c(header, "$ED_NL", tags_values_vec, "$END")
+  writeLines(output_lines, filename)
+}
+
+#' Format ED2IN tag-value list
+#'
+#' Converts an `ed2in`-like list to an ED2IN-formatted character vector.
+#'
+#' @inheritParams write_ed2in
+tags2char <- function(ed2in) {
+  char_values <- vapply(ed2in, is.character, logical(1))
+  na_values <- vapply(ed2in, function(x) all(is.na(x)), logical(1))
+  quoted_vals <- ed2in
+  quoted_vals[char_values] <- lapply(quoted_vals[char_values], shQuote)
+  quoted_vals[na_values] <- lapply(quoted_vals[na_values], function(x) "")
+  values_vec <- vapply(quoted_vals, paste, character(1), collapse = ",")
+  tags_values_vec <- sprintf("   NL%%%s = %s", names(values_vec), values_vec)
+  tags_values_vec
+}
diff --git a/models/ed/R/write_ed_metheader.R b/models/ed/R/write_ed_metheader.R
new file mode 100644
index 00000000000..e93986517f9
--- /dev/null
+++ b/models/ed/R/write_ed_metheader.R
@@ -0,0 +1,43 @@
+#' Write ED meteorlogy header
+#'
+#' Write ED met driver header from R met driver list object
+#'
+#' @param ed_metheader ED meteorlogy header object (see [read_ed_metheader])
+#' @param filename Full file name (including path) of ED met header
+#' @param header_line Character string for top line of output file. Default is 
+#' `'header'`.
+#' @export
+write_ed_metheader <- function(ed_metheader, filename,
+                               header_line = shQuote("header")) {
+  nformats <- length(ed_metheader)
+  blocks <- vector("list", nformats)
+  for (i in seq_len(nformats)) {
+    metformat <- ed_metheader[[i]]
+    block_lines <- character(6)
+    prefix <- normalizePath(metformat$path_prefix, mustWork = FALSE)
+    if (file.exists(prefix) && file.info(prefix)$isdir) {
+      # ED doesn't treat directories specially.
+      # Need to add trailing slash.
+      prefix <- paste0(prefix, "/")
+    }
+    block_lines[1] <- prefix
+    block_lines[2] <- paste(
+      metformat$nlon,
+      metformat$nlat,
+      metformat$dx,
+      metformat$dy,
+      metformat$xmin,
+      metformat$ymin
+    )
+    block_lines[3] <- nrow(metformat$variables)
+    block_lines[4] <- paste(metformat$variables$variable, collapse = " ")
+    block_lines[5] <- paste(metformat$variables$update_frequency, collapse = " ")
+    block_lines[6] <- paste(metformat$variables$flag, collapse = " ")
+    blocks[[i]] <- block_lines
+  }
+  file_lines <- c(header_line, as.character(nformats), Reduce(c, blocks))
+  writeLines(file_lines, filename)
+}
+
+# TODO: First line does actually matter -- maybe a list of format names?
+# Regardless, need to set it to something
diff --git a/models/ed/R/write_ed_veg.R b/models/ed/R/write_ed_veg.R
new file mode 100644
index 00000000000..be0af1eb7ff
--- /dev/null
+++ b/models/ed/R/write_ed_veg.R
@@ -0,0 +1,104 @@
+#' Write ED inputs to directory
+#'
+#' Write a complete [ED inputs object][read_ed_veg] to disk. `css`, `pss`, and 
+#' `site` files are automatically named and correctly formatted.
+#'
+#' @param ed_veg ED vegetation inputs object (see [read_ed_veg]).
+#' @param path_prefix Desired path and prefix (without latitude and longitude)
+#' @return Named list (`css`, `pss`, `site`) of full file paths, invisibly
+#' @export
+write_ed_veg <- function(ed_veg, path_prefix) {
+  css_file <- write_css(ed_veg$css, path_prefix, ed_veg$latitude, ed_veg$longitude)
+  pss_file <- write_pss(ed_veg$pss, path_prefix, ed_veg$latitude, ed_veg$longitude)
+  site_file <- write_site(ed_veg$site, path_prefix, ed_veg$latitude, ed_veg$longitude)
+  invisible(
+    list(
+      css = css_file,
+      pss = pss_file,
+      site = site_file
+    )
+  )
+}
+
+#' Write individual ED inputs
+#'
+#' Functions for writing css, pss, and site files from their respective objects.
+#'
+#' Latitude and longitude coordinates will be converted directly to character, 
+#' without any changes to their precision. If they are `NULL` (default), the 
+#' function assumes that `lat` and `lon` are already in the `path_prefix`, and 
+#' if they are absent, the function will throw an error.
+#'
+#' @param css css object (see [read_css])
+#' @param pss pss object (see [read_pss])
+#' @param site site object (see [read_site])
+#' @param latitude Site latitude coordinate (default = `NULL`)
+#' @param longitude Site longitude coordinate (default = `NULL`)
+#' @inheritParams write_ed_veg
+#' @return Full file path as character, invisibly
+#' @export
+write_css <- function(css, path_prefix, latitude = NULL, longitude = NULL) {
+  css_fname <- prepare_ed_veg_filename(path_prefix, ".css", latitude, longitude)
+  write.table(css, css_fname, quote = FALSE, row.names = FALSE)
+  invisible(css_fname)
+}
+
+#' @rdname write_css
+#' @export
+write_pss <- function(pss, path_prefix, latitude = NULL, longitude = NULL) {
+  pss_fname <- prepare_ed_veg_filename(path_prefix, ".pss", latitude, longitude)
+  write.table(pss, pss_fname, quote = FALSE, row.names = FALSE)
+  invisible(pss_fname)
+}
+
+#' @rdname write_css
+#' @export
+write_site <- function(site, path_prefix, latitude = NULL, longitude = NULL) {
+  site_fname <- prepare_ed_veg_filename(path_prefix, ".site", latitude, longitude)
+  first_line <- sprintf(
+    "nsite %d file_format %d",
+    attr(site, "nsite"),
+    attr(site, "file_format")
+  )
+  writeLines(first_line, site_fname)
+  write.table(site, site_fname, quote = FALSE, row.names = FALSE, append = TRUE)
+  invisible(site_fname)
+}
+
+#' Format file name for ED vegetation inputs
+#'
+#' Adds the latitude and longitude, or checks if they are formatted correctly. 
+#' Then, splits the prefix into the directory and base name, appends the suffix 
+#' to the base name (adding a starting dot, if necessary), and returns the 
+#' filename as a character.
+#'
+#' @param suffix Character string of filename suffix.
+#' @inheritParams write_css
+#' @return Character string of full formatted file path
+prepare_ed_veg_filename <- function(path_prefix, suffix, latitude = NULL, longitude = NULL) {
+  if (!is.null(latitude) && !is.null(longitude)) {
+    path_prefix_full <- paste0(
+      path_prefix, ".",
+      "lat", as.character(latitude),
+      "lon", as.character(longitude)
+    )
+  } else {
+    testthat::test_that(
+      "Latitude and longitude are already present in `path_prefix`",
+      {
+        testthat::expect_true(
+          grepl("lat[[:digit:]]+(\\.[[:digit:]]+)?lon[[:digit:]]+(\\.[[:digit:]]+)?", path_prefix)
+        )
+      }
+    )
+    path_prefix_full <- path_prefix
+  }
+  base_name <- basename(path_prefix_full)
+  dir_name <- dirname(path_prefix_full)
+  dir.create(dir_name, showWarnings = FALSE)
+
+  if (!grepl("^\\.", suffix)) {
+    suffix <- paste0(".", suffix)
+  }
+  file.path(dir_name, paste0(base_name, suffix))
+}
diff --git a/models/ed/R/write_restart.ED2.R b/models/ed/R/write_restart.ED2.R
index 5c284215083..bc57d917046 100644
--- a/models/ed/R/write_restart.ED2.R
+++ b/models/ed/R/write_restart.ED2.R
@@ -1,157 +1,263 @@
 #' @title Write ED2 restart file from SDA results
 #' 
-#' @author Alexey Shiklomanov
+#' @author Alexey Shiklomanov, Istem Fer
 #' @inheritParams PEcAn.ModelName::write_restart.ModelName
 #' @return TRUE if successful
 #' @export
-write_restart.ED2 <- function(outdir,
-                              runid,
-                              start.time,
-                              stop.time,
-                              settings,
-                              new.state) {
-
-  rundir <- settings$host$rundir
-  mod_outdir <- settings$host$outdir
-
-  sda_datestr <- strftime(start.time, "%Y-%m-%d-%H%M%S")
-  sda_suffix <- paste0("SDA.", sda_datestr)
-
-  # Get history restart file path
-  histfile <- get_restartfile.ED2(mod_outdir, runid, start.time)
-  if (is.null(histfile)) {
-    PEcAn.logger::logger.severe("Failed to find ED2 history restart file.")
-  }
-
+write_restart.ED2 <- function(outdir, runid, start.time, stop.time,
+                              settings, new.state, RENAME = TRUE, new.params, inputs) {
+  
+  restart <- new.params$restart
+  
+  # IMPORTANT NOTE: in the future, things that are passed via "restart" list need to be confined to old states that will be used
+  # to carry out deternimistic relationships, no other read/write restart should copy this logic
+  histfile  <- restart$histfile # Get history restart file path
+  restart   <- restart$restart
+  
+  # remote or not remote?
+  # rundir <- settings$host$rundir
+  # mod_outdir <- settings$host$outdir 
+  rundir <- settings$rundir
+  mod_outdir <- settings$modeloutdir # same as outdir?
+  
+  sda_datestr  <- gregexpr("-S-", histfile)[[1]]
+  sda_suffix   <- paste0("SDA.", substr(histfile, sda_datestr[1] + 3, sda_datestr[1] + 19))
+  hyear        <- substr(histfile, sda_datestr[1] + 3, sda_datestr[1] + 6)
+  
+  # check these dirs for local vs remote
   #### Backup old run files to date directory
   runfiles <- list.files.nodir(file.path(rundir, runid))
-  modoutfiles <- list.files.nodir(file.path(mod_outdir, runid))
-  other_files <- grep("history-.*.h5", modoutfiles, value = TRUE, invert = TRUE)
-  copy_files <- c(basename(histfile), other_files)
-
+  modoutfiles <- list.files.nodir(file.path(mod_outdir, runid), hyear) # copy only current year, otherwise it cumulatively copies everything
+  
   dir.create(file.path(rundir, runid, sda_suffix))
   dir.create(file.path(mod_outdir, runid, sda_suffix))
   file.copy(file.path(rundir, runid, runfiles),
             file.path(rundir, runid, sda_suffix, runfiles), 
             overwrite = TRUE)
-  file.copy(file.path(mod_outdir, runid, copy_files),
-            file.path(mod_outdir, runid, sda_suffix, copy_files),
+  file.copy(file.path(mod_outdir, runid, modoutfiles),
+            file.path(mod_outdir, runid, sda_suffix, modoutfiles),
             overwrite = TRUE)
-
-  confxml <- get_configxml.ED2(rundir, runid)
-
-  #### Identify PFTs
-  # This assumes that PFT order is the same between pecan.xml and ED's 
-  # config.xml.  A better solution would set the PFT numbers in the 
-  # pecan.xml, or names in config.xml.
-  pftnums <- sapply(confxml, '[[', 'num')
-  pftnames <- sapply(settings$pfts, '[[', 'name')
-  names(pftnames) <- pftnums
-  names(pftnums) <- pftnames
-
-
-  nc <- ncdf4::nc_open(histfile)
-
-  #### Read common variables
+  
+  
+  remote_histfile  <- file.path(settings$host$outdir, runid, basename(histfile))
+  
+  #### Get common variables
   # PFT by cohort
-  pft_co <- ncdf4::ncvar_get(nc, 'PFT')
-
+  pft_co <- restart$PFT 
+  
+  # Plant density
+  plant_dens <- restart$NPLANT
+  
   # Patch area
-  patch_area <- ncdf4::ncvar_get(nc, 'AREA')
-
+  patch_area <- restart$AREA 
+  
   #### Create a patch index indicator vector
-  patch_index <- patch_cohort_index(nc)
-
-  ncdf4::nc_close(nc)
-
-  varname_regex <- '(^[^.]*)\\.([^.]*)\\.(.*)$'
-  var.names <- unique(gsub(varname_regex, "\\1", names(new.state)))
-
-  old.state <- read.restart.ED2(outdir = outdir,
-                                runid = runid,
-                                stop.time = start.time,
-                                settings = settings,
-                                var.names = var.names,
-                                params = NULL) ## TODO: new.params???
-
+  paco_n      <- restart$PACO_N  # number of cohorts per patch
+  patch_index <- rep(1:length(paco_n), times = paco_n)
+  
+  # read xml to extract allometric coeffs later
+  configfile <- file.path(rundir, runid,"config.xml")
+  pars <- XML::xmlToList(XML::xmlParse(configfile))
+  # remove non-pft sublists
+  pars[names(pars)!="pft"] <- NULL
+  
+  #### Write new state to file
+  # Default mode of H5File$new is "a", which is read + write and create file if it doesn't exist
+  histfile_h5 <- hdf5r::H5File$new(histfile)
+  
   for (var_name in var.names) {
-    if (var_name == "AGB") {
-
-      #### Disaggregate AGB down to cohort vector
+    # var_name <- "AbvGrndWood"
+    if (var_name == "AbvGrndWood") {
+      
+      #### Disaggregate AbvGrndWood down to cohort vector
       # NOTE: This is currently naive -- it just calculates the 
-      # AGB ratio between the old and new states and applies it to each 
+      # AbvGrndWood ratio between the old and new states and applies it to each 
       # cohort based on its PFT. No patch information is involved because 
       # none is provided in `new.state`.
-
-      new.agb_pft <- new.state[grep(var_name, names(new.state))]
-      old.agb_pft <- old.state[grep(var_name, names(old.state))]
-      new2old.agb_pft <- new.agb_pft / old.agb_pft
-      new2old_pftnames <- gsub(paste0(var_name, ".pft."), '', 
-                               names(new2old.agb_pft))
-      names(new2old.agb_pft) <- as.character(pftnums[new2old_pftnames])
-
-      agb_co_ratios <- new2old.agb_pft[as.character(pft_co)]
-
-      nc <- ncdf4::nc_open(histfile)
-      nplant_co_plant <- ncdf4::ncvar_get(nc, "NPLANT")
-      ncdf4::nc_close(nc)
-
-      # The only AGB-related state variables read by ED's history restart 
-      # subroutine are BDEAD, DBH, and NPLANT. The remaining states 
-      # (including cohort and patch-level AGB) are recalculated from 
-      # these variables.
-      #
+      
+      new_tmp <- new.state[grep(var_name, names(new.state))]
+      new_tmp <- udunits2::ud.convert(new_tmp, "Mg/ha/yr", "kg/m^2/yr")
+      
+      agb_co <- restart$AGB_CO
+      # reaggregate old state
+      plant2cohort <- agb_co * plant_dens
+      cohort2patch <- tapply(plant2cohort, list("patch" = patch_index), sum, na.rm = TRUE)
+      
+      agw_ratios <- new_tmp / sum(cohort2patch*patch_area, na.rm = TRUE)
+      
+      # when nudging a carbon pool, we need to nudge relevant pools
+      # maybe in the future if we are assimilating these or if they're in the state matrix also check if it's in the var.names before nudging proportionally
+      bdead    <- restart$BDEAD
+      #bstorage <- restart$BSTORAGE # storage is a thing in itself
+      bleaf     <- restart$BLEAF
+      broot     <- restart$BROOT
+      balive    <- restart$BALIVE
+      bseeds    <- restart$BSEEDS_CO
+      bsapwooda <- restart$BSAPWOODA
+      bsapwoodb <- restart$BSAPWOODB
+      
+      new_bdead     <- bdead  * agw_ratios[1,1]
+      new_agb       <- agb_co * agw_ratios[1,1]
+      new_bleaf     <- bleaf * agw_ratios[1,1]
+      new_broot     <- broot * agw_ratios[1,1]
+      new_balive    <- balive * agw_ratios[1,1]
+      new_bseeds    <- bseeds * agw_ratios[1,1]
+      new_bsapwooda <- bsapwooda * agw_ratios[1,1]
+      new_bsapwoodb <- bsapwoodb * agw_ratios[1,1]
+      
+      # # if you're nudging bdead, update bstorage and dbh too
+      # new_bstorage <- bstorage * agw_ratios[1,1]
+      
+      # what else to nudge?
+      # soil C : FAST_SOIL_C, SLOW_SOIL_C, STRUCTURAL_SOIL_C
+      # NPLANT
+      
+      pft_nums <- as.numeric(sapply(pars,`[[`, "num"))
+      # use ED2's allometric eqns to dtermine dbh from new bdead
+      C2B <- 2
+      new_dbh <- new_bdead
+      for(pn in seq_along(pft_nums)){
+        ind <- pft_co == pft_nums[pn]
+        
+        crit <- new_bdead[ind] <= pars[[pn]]$bdead_crit
+        new_dbh[ind][crit] = (new_bdead[ind][crit] / as.numeric(pars[[pn]]$b1Bs_small) * C2B)**(1.0/ as.numeric(pars[[pn]]$b2Bs_small))
+        new_dbh[ind][!crit] = (new_bdead[ind][!crit] / as.numeric(pars[[pn]]$b1Bs_large) * C2B)**(1.0/as.numeric(pars[[pn]]$b2Bs_large))
+        
+      }
+      
+      # AbvGrndWood in state matrix is not per PFT but total
+      # but leaving this bit as a reminder
+      
+      # new2old.agb_pft <- new.agb_pft / old.agb_pft
+      # new2old_pftnames <- gsub(paste0(var_name, ".pft."), '', 
+      #                          names(new2old.agb_pft))
+      # names(new2old.agb_pft) <- as.character(pftnums[new2old_pftnames])
+      # agb_co_ratios <- new2old.agb_pft[as.character(pft_co)]
+      
+      #nplant_co_plant <- restart$NPLANT
+      
+      
       # Here, we adjust cohort-level AGB by adjusting the stand density 
       # (NPLANT) proportional to the change in biomass computed above.
-      new.nplant_co_plant <- nplant_co_plant * agb_co_ratios
+      #new.nplant_co_plant <- nplant_co_plant * agb_co_ratios[1,1]
       # An alternative is to modify DBH and BDEAD, which requires solving 
       # the following allometric equation for DBH and then using ED 
       # allometric equations to recalculate BDEAD.
       # 
       # AGB = b1L*DBH^(b2L) * (1 + qsw * agf_bs * 
       #     (h0 + a * (1-exp(b*DBH))) + b1d*DBH^(b2d)
-
-      #### Write new state to file
-      # Default mode of H5File$new is "a", which is read + write and create file if it doesn't exist
-      histfile_h5 <- hdf5r::H5File$new(histfile)
+      
+      
       # The empty brackets (`[]`) indicate the whole vector is replaced.
       # This is necessary to overwrite an existing dataset
-      histfile_h5[["NPLANT"]][] <- new.nplant_co_plant
-      # This closes the file and all objects related to the file.
-      histfile_h5$close_all()
+      #histfile_h5[["NPLANT"]][] <- new.nplant_co_plant
+      histfile_h5[["BDEAD"]][] <- new_bdead
+      #histfile_h5[["BSTORAGE"]][] <- new_bstorage
+      histfile_h5[["DBH"]][] <- new_dbh
+      
+      # overwrite the keepers, not critical (these will be re-calculated within ED2)
+      histfile_h5[["AGB_CO"]][]    <- new_agb
+      histfile_h5[["TOTAL_AGB"]][] <- new_tmp
+      
+      histfile_h5[["BLEAF"]][]     <- new_bleaf
+      histfile_h5[["BROOT"]][]     <- new_broot
+      histfile_h5[["BALIVE"]][]    <- new_balive
+      histfile_h5[["BSEEDS_CO"]][] <- new_bseeds
+      histfile_h5[["BSAPWOODA"]][] <- new_bsapwooda
+      histfile_h5[["BSAPWOODB"]][] <- new_bsapwoodb
+      
+      
+      
+    } else if(var_name == "GWBI"){
+      
+      # zero cumulative rate keepers, nothing is calculated back from these
+      # so zeroing only the rate you're reading back is fine
+      histfile_h5[["TOTAL_AGB_GROWTH"]][] <- 0
+      # zero both
+      histfile_h5[["DDBH_DT"]][] <- rep(0, length(restart$DDBH_DT))
+      histfile_h5[["DAGB_DT"]][] <- rep(0, length(restart$DAGB_DT))
+      
+    }  else if(var_name == "storage_carbon_content"){
+      
+      bstorage <- restart$BSTORAGE
+      # reaggregate old state
+      plant2cohort <- bstorage * plant_dens
+      cohort2patch <- tapply(plant2cohort, list("patch" = patch_index), sum, na.rm = TRUE)
+      
+      bstorage_ratio   <- new.state$storage_carbon_content / sum(cohort2patch*patch_area, na.rm = TRUE)
+      
+      histfile_h5[["BSTORAGE"]][] <- bstorage*bstorage_ratio
+      
+    } else if(var_name == "fast_soil_pool_carbon_content"){
+      
+      fast_soil_c <- restart$FAST_SOIL_C
+      fsc_ratio   <- new.state$fast_soil_pool_carbon_content / sum(fast_soil_c*patch_area)
+      
+      histfile_h5[["FAST_SOIL_C"]][] <- fast_soil_c*fsc_ratio
+      
+    } else if(var_name == "structural_soil_pool_carbon_content"){
+      
+      structural_soil_c   <- restart$STRUCTURAL_SOIL_C
+      structural_sc_ratio <- new.state$structural_soil_pool_carbon_content / sum(structural_soil_c*patch_area)
+      
+      histfile_h5[["STRUCTURAL_SOIL_C"]][] <- structural_soil_c*structural_sc_ratio
+      
     } else {
       PEcAn.logger::logger.error("Variable ", var_name,
-                                " not currently supported",
-                                " by write.restart.ED2")
+                                 " not currently supported",
+                                 " by write.restart.ED2")
     }
   }
-
+  
+  # This closes the file and all objects related to the file.
+  histfile_h5$close_all()
+  
+  # copy the history file with new states and new timestamp to remote 
+  # it's OK, because we backed up the original above
+  PEcAn.remote::remote.copy.to(settings$host, histfile, remote_histfile)
+  
   ##### Modify ED2IN
   ed2in_path <- file.path(rundir, runid, "ED2IN")
-  ed2in_orig <- readLines(ed2in_path)
-  ed2in_new <- ed2in_orig
-
-  ## IED_INIT_MODE = 5 --> Run from history.h5 file
-  tag_val_list <- list("RUNTYPE" = "history",
-                       "IED_INIT_MODE" = 5,
-                       "SFILIN" = file.path(mod_outdir, runid, "history"),
-                       "IMONTHA" = strftime(start.time, "%m"), 
-                       "IDATEA" = strftime(start.time, "%d"),
-                       "IYEARA" = strftime(start.time, "%Y"),
-                       "ITIMEA" = strftime(start.time, "%H%M"),
-                       "IMONTHZ" = strftime(stop.time, "%m"),
-                       "IDATEZ" = strftime(stop.time, "%d"),
-                       "IYEARZ" = strftime(stop.time, "%Y"),
-                       "ITIMEZ" = strftime(stop.time, "%H%M"))
-
-  modstr <- 'Modified by write.restart.ED2'
-  ed2in_new <- ed2in_set_value_list(tag_val_list, ed2in_orig, modstr)
-
-  writeLines(ed2in_new, file.path(ed2in_path))
-
+  ed2in_orig <- read_ed2in(ed2in_path)
+  
+  
+  ed2in_new <- modify_ed2in(
+    ed2in_orig,
+    start_date = lubridate::ceiling_date(start.time, "1 day"),
+    end_date   = lubridate::ceiling_date(stop.time, "1 day"), # ED2 writes annual history files at the same month as initial
+    RUNTYPE    = "HISTORY",
+    IED_INIT_MODE = 4,
+    SFILIN = file.path(settings$host$outdir, runid, "history")
+  )
+  
+  
+  if(settings$host$name == "localhost") check_ed2in(ed2in_new)
+  write_ed2in(ed2in_new, ed2in_path)
+  
   # Remove old history.xml file, which job.sh looks for
-  file.remove(file.path(mod_outdir, runid, "history.xml"))
-
+  file.remove(file.path(mod_outdir, runid, "history.xml"))  # this is local
+  
+  # read the jobsh in the rundir
+  jobsh <- readLines(file.path(rundir, runid, "job.sh"),-1)
+  remote_remove_cmd <- paste0("rm -f ", file.path(settings$host$outdir, runid, "history.xml"))
+  jobsh[grep("@REMOVE_HISTXML@", jobsh)+1] <- remote_remove_cmd
+  
+  # also update mode2netcdf.ED2 call
+  mod2cf_line    <- grep("model2netcdf.ED2", jobsh)
+  mod2cf_string  <- jobsh[mod2cf_line]
+  begin_from     <- paste0("'", lubridate::year(start.time), "/")
+  begin_to       <- paste0("'", hyear,"/")   
+  end_from       <- begin_to 
+  end_to         <- paste0("'", as.numeric(hyear)+1,"/") 
+  # this order matters
+  mod2cf_string      <- gsub(end_from,   end_to,   mod2cf_string) # e.g. change from (...'1961/01/01', '1962/01/01'...) to (...'1961/01/01', '1963/01/01'...)
+  mod2cf_string      <- gsub(begin_from, begin_to, mod2cf_string) # e.g. change from (...'1961/01/01', '1963/01/01'...) to (...'1962/01/01', '1963/01/01'...)
+  jobsh[mod2cf_line] <- mod2cf_string
+  
+  writeLines(jobsh, file.path(rundir, runid, "job.sh"))
+  
+  PEcAn.logger::logger.info("Finished --", runid)
+  
   return(TRUE)
 } # write_restart.ED2
 
diff --git a/models/ed/R/zz.imports.R b/models/ed/R/zz.imports.R
new file mode 100644
index 00000000000..7cb141d451c
--- /dev/null
+++ b/models/ed/R/zz.imports.R
@@ -0,0 +1,5 @@
+#' Imports from other packages
+#'
+#' @name zz.imports
+#' @importFrom magrittr %>%
+NULL
diff --git a/models/ed/data/history.csv b/models/ed/data/history.csv
index f22f41eaf20..34df7dc36af 100644
--- a/models/ed/data/history.csv
+++ b/models/ed/data/history.csv
@@ -1,18 +1,18 @@
- num; is_tropical; is_grass; include_pft; include_pft_ag; include_pft_fp;        clumping_factor;    orient_factor;         leaf_emiss_tir;         wood_emiss_tir;       leaf_reflect_vis;       leaf_reflect_nir;       wood_reflect_vis;       wood_reflect_nir;         leaf_trans_vis;         leaf_trans_nir;         wood_trans_vis;         wood_trans_nir;   leaf_backscatter_vis;   leaf_backscatter_nir;   leaf_backscatter_tir;   wood_backscatter_vis;   wood_backscatter_nir;   wood_backscatter_tir;       leaf_scatter_vis;       leaf_scatter_nir;       wood_scatter_vis;       wood_scatter_nir;                   phi1;                   phi2;                 mu_bar; photosyn_pathway; quantum_efficiency;           Vm0;  Vm_low_temp;  Vm_high_temp;   Vm_decay_e;        Vm_decay_a;     Vm_decay_b;          vm_hor;       vm_q10; dark_respiration_factor;  Rd_low_temp;  Rd_high_temp;   Rd_decay_e;          Rd_hor;       Rd_q10;          Rd0;           D0; stomatal_slope;   cuticular_cond; water_conductance;   leaf_width; growth_resp_factor; leaf_turnover_rate; root_turnover_rate; storage_turnover_rate;     f_labile; root_respiration_factor; rrf_low_temp; rrf_high_temp;  rrf_decay_e;         rrf_hor;      rrf_q10;   frost_mort;         mort0;        mort1;         mort2;        mort3; cbr_severe_stress; seedling_mortality; treefall_s_gt; treefall_s_lt;    fire_s_gt;    fire_s_lt; plant_min_temp;          rho;           SLA; horiz_branch;            q;   sapwood_ratio;          qsw; init_density;          b1Ht;          b2Ht;       hgt_ref;      hgt_min;       hgt_max;      min_dbh;      dbh_crit;     dbh_adult;   dbh_bigleaf;   b1Bl_small;   b1Bl_large;   b2Bl_small;   b2Bl_large;  bleaf_adult;   b1Bs_small;   b1Bs_large;   b2Bs_small;   b2Bs_large;    min_bdead;      bdead_crit;         b1Ca;         b2Ca;        b1WAI;        b2WAI;       brf_wd;       agf_bs;        b1Vol;        b2Vol;          b1Rd;         b2Rd;       c2n_leaf;    c2n_recruit; phenology;  c_grn_leaf_dry; wat_dry_ratio_grn; wat_dry_ratio_ngrn; c_ngrn_biom_dry;         delta_c;         b1Cl;         b2Cl;      r_fract;     st_fract; nonlocal_dispersal;   repro_min_h;  one_plant_c; min_recruit_size; min_cohort_size;    seed_rain; negligible_nplant;  veg_hcap_min
-   1;           1;        1;           1;              0;              0; 1.00000000000000000000;     0.0000000000; 0.95999999999999996447; 0.95999999999999996447; 0.10000000149011611938; 0.10000000149011611938; 0.10000000149011611938; 0.10000000149011611938; 0.10000000149011611938; 0.10000000149011611938; 0.10000000149011611938; 0.10000000149011611938; 0.00000000000000000000; 0.00000000000000000000; 0.62500000000000000000; 0.00000000000000000000; 0.00000000000000000000; 0.62500000000000000000; 0.00000000000000000000; 0.00000000000000000000; 0.00000000000000000000; 0.00000000000000000000; 0.00000000000000000000; 0.00000000000000000000; 0.00000000000000000000;                4;       0.0549999997; 12.5000000000; 8.0000000000; 45.0000000000; 0.4000000060; 220000.0000000000; 690.0000000000; 3000.0000000000; 2.4000000954;            0.0350000001; 8.0000000000; 45.0000000000; 0.4000000060; 3000.0000000000; 2.4000000954; 0.4375000000; 0.0160000008;   5.1999998093; 10000.0000000000;      0.0000285199; 0.0500000007;       0.3330000043;       2.0000000000;       2.0000000000;          0.3333333433; 1.0000000000;            0.2800000012; 8.0000000000; 45.0000000000; 0.4000000060; 3000.0000000000; 2.4000000954; 3.0000000000; -0.3499999940; 2.0000000000; 15.0000000000; 0.0000000000;     -1.0628256798;       0.9499999881;  0.0000000000;  0.2500000000; 0.0000000000; 0.0000000000; 275.6499938965; 0.2000000030; 22.7000007629; 0.5000000000; 1.0000000000; 3900.0000000000; 0.0058205132; 0.1000000015;  0.0351999998;  0.6940000057; 61.7000007629; 0.5000000000;  1.5000000000; 0.1211817637;  0.5971379876; 10.0000000000;  0.5971379876; 0.1576947272; 0.1576947272; 0.9749494195; 0.9749494195; 0.7442804575; 0.0627227873; 0.0647229999; 2.4323608875; 2.4255735874; 0.0001849201;    0.0089480467; 1.1257275343; 1.0521197319; 0.0096000005; 2.0947000980; 0.1599999964; 0.6999999881; 0.0247086249; 2.0000000000; -1.1140580177; 0.4223014116;  25.4454765320;  25.6388263702;         1; 3218.0000000000;      1.8500000238;       0.6999999881; 1217.3759765625; -225.1618652344; 0.9900000095; 1.0000000000; 0.3000000119; 0.0000000000;       1.0000000000;  0.0000000000; 0.0203614440;     0.0002036145;    0.0000203614; 0.0100000007;      0.0000148253;  3.6809282303
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diff --git a/models/ed/data/history.r46.csv b/models/ed/data/history.r46.csv
index 52f46e57d86..64359bfba7f 100644
--- a/models/ed/data/history.r46.csv
+++ b/models/ed/data/history.r46.csv
@@ -1,16 +1,16 @@
 num;include_pft_ag;include_pft;SLA;b1Bl;b2Bl;b1Bs;b2Bs;b1Ht;b2Ht;Vm0;phenology;q;clumping;leaf_width;hgt_min;plant_min_temp;mort3;nonlocal_dispersal;seed_rain;stomatal_slope;growth_resp_factor;r_fract;repro_min_h;treefall_gt;treefall_lt;dark_respiration_factor;qsw;c2n_leaf;c2n_recruit;max_dbh;rho;D0;mort1;mort2;Vm_low_temp;cuticular_cond;quantum_efficiency;photosyn_pathway;leaf_turnover_rate;root_turnover_rate;storage_turnover_rate;root_respiration_factor;seedling_mortality;water_conductance;leaf_scatter_vis;diffuse_backscatter_vis;emis_v;f_labile
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diff --git a/models/ed/data/history.r81.csv b/models/ed/data/history.r81.csv
index 812b944c0f1..fb7c101dd51 100644
--- a/models/ed/data/history.r81.csv
+++ b/models/ed/data/history.r81.csv
@@ -1,8 +1,8 @@
 num;include_pft_ag;include_pft;SLA;b1Bl;b2Bl;b1Bs;b2Bs;b1Ht;b2Ht;Vm0;phenology;q;clumping;leaf_width;vm_q10;hgt_min;plant_min_temp;mort3;nonlocal_dispersal;seed_rain;stomatal_slope;growth_resp_factor;r_fract;repro_min_h;treefall_gt;treefall_lt;dark_respiration_factor;qsw;c2n_leaf;c2n_recruit;dbh_crit;rho;D0;mort1;mort2;Vm_low_temp;cuticular_cond;quantum_efficiency;photosyn_pathway;leaf_turnover_rate;root_turnover_rate;storage_turnover_rate;root_respiration_factor;seedling_mortality;water_conductance;leaf_scatter_vis;diffuse_backscatter_vis;emis_v;f_labile;leaf_reflect_vis;leaf_reflect_nir;leaf_trans_vis;leaf_trans_nir;wood_reflect_vis;wood_reflect_nir;wood_trans_vis;wood_trans_nir
-1;1;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;2.4000000954;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3330000043;0.3000000119;0;0;0.25;0.0399999991;0;0;0;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0.3333333433;0.2800000012;0.9499999881;900;0;0;0.96;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.16;0.25;0.028;0.248
-2;2;0;1;16.0179424286;0.4178909957;0.9749494195;0.1662153751;2.4323608875;0.0351999998;0.6940000057;18.75;1;1;0.800000011920929;0.1000000015;2.4000000954;0.5;275.6499938965;0.0616666712;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;96.2577896118;0.5299999714;0.0160000008;5;10;8;10000;0.0799999982;3;1;1;0.1666666716;0.2800000012;0.9499999881;600;0;0;0.95;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.001;0.001
-3;3;0;1;11.6448221207;0.5598162413;0.9749494195;0.222665906;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;0.800000011920929;0.1000000015;2.4000000954;0.5;275.6499938965;0.03166667;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;96.2577896118;0.7099999785;0.0160000008;5;10;8;10000;0.0799999982;3;0.5;0.5;0.1666666716;0.2800000012;0.9499999881;600;0;0;0.95;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.001;0.001
-4;4;0;1;9.6634206772;0.7096262574;0.9749494195;0.2822525501;2.4323608875;0.0351999998;0.6940000057;6.25;1;1;0.800000011920929;0.1000000015;2.4000000954;0.5;275.6499938965;0;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;96.2577896118;0.8999999762;0.0160000008;5;10;8;10000;0.0799999982;3;0.3333333433;0.3333333433;0.1666666716;0.2800000012;0.9499999881;600;0;0;0.95;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.001;0.001
+1;1;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;2.4000000954;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3330000043;0.3000000119;0;0;0.25;0.0399999991;0;0;0;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0;0.2800000012;0.9499999881;900;0;0;0.96;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.16;0.25;0.028;0.248
+2;2;0;1;16.0179424286;0.4178909957;0.9749494195;0.1662153751;2.4323608875;0.0351999998;0.6940000057;18.75;1;1;0.800000011920929;0.1000000015;2.4000000954;0.5;275.6499938965;0.0616666712;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;96.2577896118;0.5299999714;0.0160000008;5;10;8;10000;0.0799999982;3;1;1;0;0.2800000012;0.9499999881;600;0;0;0.95;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.001;0.001
+3;3;0;1;11.6448221207;0.5598162413;0.9749494195;0.222665906;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;0.800000011920929;0.1000000015;2.4000000954;0.5;275.6499938965;0.03166667;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;96.2577896118;0.7099999785;0.0160000008;5;10;8;10000;0.0799999982;3;0.5;0.5;0;0.2800000012;0.9499999881;600;0;0;0.95;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.001;0.001
+4;4;0;1;9.6634206772;0.7096262574;0.9749494195;0.2822525501;2.4323608875;0.0351999998;0.6940000057;6.25;1;1;0.800000011920929;0.1000000015;2.4000000954;0.5;275.6499938965;0;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;96.2577896118;0.8999999762;0.0160000008;5;10;8;10000;0.0799999982;3;0.3333333433;0.3333333433;0;0.2800000012;0.9499999881;600;0;0;0.95;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.001;0.001
 5;5;1;1;22;0.0799999982;1;1e-05;1;0.4778000116;-0.75;18.2999992371;1;1;0.84;0.0500000007;2.4000000954;0.150000006;193.1499938965;0.0659999996;1;0.0099999998;9;0.3333333433;0.3000000119;0;0;0.25;0.0149999997;0;0;0;3.9943094254;0.200000003;0.0160000008;1;20;4.7136998177;10000;0.0799999982;3;2;2;0;0.2800000012;0.9499999881;900;0;0;0.96;1;0.11;0.577;0.16;0.248;0.16;0.25;0.028;0.248
 6;6;0;1;6;0.0240000002;1.8990000486;0.1469999999;2.2379999161;27.1399993896;-0.0388399996;11.3500003815;0;0.3463000059;0.735;0.0500000007;2.4000000954;1.5;193.1499938965;0.0033928;0.7659999728;0.0099999998;7.1999998093;0.4503000081;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;77.7029876709;0;0.0160000008;1;20;4.7136998177;1000;0.0799999982;3;0.3333333433;3.9272179604;0;0.2800000012;0.9499999881;600;0;0;0.97;0.7900000215;0.11;0.577;0.16;0.248;0.11;0.25;0.001;0.001
 7;7;0;1;9;0.0240000002;1.8990000486;0.1469999999;2.2379999161;27.1399993896;-0.0388399996;11.3500003815;0;0.3463000059;0.735;0.0500000007;2.4000000954;1.5;263.1499938965;0.0043000001;0.7659999728;0.0099999998;7.1999998093;0.4503000081;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;77.7029876709;0;0.0160000008;1;20;4.7136998177;1000;0.0799999982;3;0.3333333433;4.1178469658;0;0.2800000012;0.9499999881;600;0;0;0.97;0.7900000215;0.11;0.577;0.16;0.248;0.11;0.25;0.001;0.001
@@ -12,7 +12,7 @@ num;include_pft_ag;include_pft;SLA;b1Bl;b2Bl;b1Bs;b2Bs;b1Ht;b2Ht;Vm0;phenology;q
 11;11;0;1;60;0.0170000009;1.7309999466;0.2349999994;2.2518000603;23.3873996735;-0.0540399998;6.9818749428;2;1.1274000406;0.84;0.1000000015;2.4000000954;1.5;-80;0.00428;0.074000001;0.0099999998;7.1999998093;0;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;53.145866394;0;0.0160000008;1;20;4.7136998177;10000;0.0799999982;3;0;5.070991993;0;0.2800000012;0.9499999881;600;0;0;0.95;0.7900000215;0.11;0.577;0.16;0.248;0.11;0.25;0.001;0.001
 12;12;1;1;22;0.0799999982;1;1e-05;1;0.4778000116;-0.75;18.2999992371;1;1;0.84;0.0500000007;2.4000000954;0.150000006;193.1499938965;0.0659999996;1;0.0099999998;9;0.3333333433;0.3000000119;0;0;0.25;0.0149999997;0;0;0;3.9943094254;0.200000003;0.0160000008;1;20;4.7136998177;10000;0.0799999982;3;2;0.3333333433;0;0.2800000012;0.9499999881;900;0;0;0.96;1;0.11;0.577;0.16;0.248;0.16;0.25;0.22;0.248
 13;13;1;1;22;0.0799999982;1;1e-05;1;0.4778000116;-0.75;18.2999992371;1;1;0.84;0.0500000007;2.4000000954;0.150000006;193.1499938965;0.0659999996;1;0.0099999998;9;0.3333333433;0.3000000119;0;0;0.25;0.0149999997;0;0;0;3.9943094254;0.200000003;0.0160000008;1;20;4.7136998177;10000;0.0799999982;3;2;0.3333333433;0;0.2800000012;0.9499999881;900;0;0;0.96;1;0.11;0.577;0.16;0.248;0.16;0.25;0.22;0.248
-14;14;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;2.4000000954;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3333333433;0.3000000119;0;0;0.25;0.0399999991;0;0;0;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0.3333333433;0.2800000012;0.9499999881;900;0;0;0.96;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.22;0.248
-15;15;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;2.4000000954;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3333333433;0.3000000119;0;0;0.25;0.0399999991;0;0;0;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0.3333333433;0.2800000012;0.9499999881;900;0;0;0.96;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.22;0.248
-16;16;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;20.8333320618;1;1;1;0.0500000007;2.4000000954;0.5;253.1499938965;0.1166666746;1;0.0099999998;9;0.3330000043;0.3000000119;0;0;0.25;0.0149999997;0;0;0;0.5971379876;0.200000003;0.0160000008;5;10;4.7136998177;10000;0.0799999982;3;2;2;0.3333333433;0.2800000012;0.9499999881;900;0;0;0.96;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.16;0.25;0.028;0.248
-17;17;0;1;10;0.4257757664;0.9749494195;0.1693515331;2.4323608875;0.0351999998;0.6940000057;15.625;0;1;0.735;0.0500000007;2.4000000954;0.5;258.1499938965;0.0043000001;0.7659999728;0.0099999998;7.1999998093;0.4503000081;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;96.2577896118;0.5400000215;0.0160000008;5;10;4.7136998177;1000;0.0799999982;3;0.1666666716;0.1666666716;0.1666666716;0.2800000012;0.9499999881;600;0;0;0.97;0.7900000215;0.09;0.577;0.05;0.248;0.11;0.25;0.001;0.001
+14;14;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;2.4000000954;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3333333433;0.3000000119;0;0;0.25;0.0399999991;0;0;0;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0;0.2800000012;0.9499999881;900;0;0;0.96;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.22;0.248
+15;15;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;2.4000000954;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3333333433;0.3000000119;0;0;0.25;0.0399999991;0;0;0;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0;0.2800000012;0.9499999881;900;0;0;0.96;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.11;0.25;0.22;0.248
+16;16;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;20.8333320618;1;1;1;0.0500000007;2.4000000954;0.5;253.1499938965;0.1166666746;1;0.0099999998;9;0.3330000043;0.3000000119;0;0;0.25;0.0149999997;0;0;0;0.5971379876;0.200000003;0.0160000008;5;10;4.7136998177;10000;0.0799999982;3;2;2;0;0.2800000012;0.9499999881;900;0;0;0.96;1;0.100000001490116;0.540000021457672;0.0500000007450581;0.270000010728836;0.16;0.25;0.028;0.248
+17;17;0;1;10;0.4257757664;0.9749494195;0.1693515331;2.4323608875;0.0351999998;0.6940000057;15.625;0;1;0.735;0.0500000007;2.4000000954;0.5;258.1499938965;0.0043000001;0.7659999728;0.0099999998;7.1999998093;0.4503000081;0.3000000119;5;0;0.1000000015;0.0149999997;0;0;0;96.2577896118;0.5400000215;0.0160000008;5;10;4.7136998177;1000;0.0799999982;3;0.1666666716;0.1666666716;0;0.2800000012;0.9499999881;600;0;0;0.97;0.7900000215;0.09;0.577;0.05;0.248;0.11;0.25;0.001;0.001
diff --git a/models/ed/data/history.r82.csv b/models/ed/data/history.r82.csv
index 5baf25dddf0..09676a3de79 100644
--- a/models/ed/data/history.r82.csv
+++ b/models/ed/data/history.r82.csv
@@ -1,18 +1,18 @@
 num;include_pft_ag;include_pft;SLA;b1Bl;b2Bl;b1Bs;b2Bs;b1Ht;b2Ht;Vm0;phenology;q;clumping;leaf_width;hgt_min;plant_min_temp;mort3;nonlocal_dispersal;seed_rain;stomatal_slope;growth_resp_factor;r_fract;repro_min_h;treefall_gt;treefall_lt;dark_respiration_factor;qsw;c2n_leaf;c2n_recruit;dbh_crit;rho;D0;mort1;mort2;Vm_low_temp;cuticular_cond;quantum_efficiency;photosyn_pathway;leaf_turnover_rate;root_turnover_rate;storage_turnover_rate;root_respiration_factor;seedling_mortality;water_conductance;leaf_scatter_vis;diffuse_backscatter_vis;emis_v;f_labile
-1;1;1;33.4669990540;0.0346058160;1.5942586660;0.0501835719;2.3597955704;0.8519564867;0.6399999857;17.5961399078;2;0.7422149181;1.00000000000000000000;0.0049999999;2.0000000000;-100.0000000000;0.1166666746;0.2140000015;0.0099999998;3.4500000477;0.2561094761;0.2468371987;0.0000000000;0.0000000000;0.2500000000;0.0149999997;0.0000000000;25.4454765320;25.4454765320;0.4977572262;0.2000000030;0.0149999997;1.0000000000;27.8999996185;10.0000000000;8000.0000000000;0.0560000017;4;5.7870283127;0.6600000262;0.0000000000;0.5279999971;0.9700000286;0.0000095066;0.20000000670552253723;0.54515625020780134058;0.95999999999999996447;1.0000000000
-2;0;1;16.0179424286;0.0591472238;1.5705568790;0.1243378818;2.3470983505;0.8519564867;0.6399999857;23.4375000000;1;1.0000000000;1.00000000000000000000;0.1000000015;0.5000000000;275.6499938965;0.0616666712;1.0000000000;0.0099999998;9.0000000000;0.3333333433;0.3000000119;5.0000000000;0.0000000000;0.1000000015;0.0149999997;0.0041071647;19.8357734680;22.5503253937;68.3095474243;0.5299999714;0.0149999997;10.0000000000;20.0000000000;8.0000000000;10000.0000000000;0.0799999982;3;1.0000000000;1.0000000000;0.0000000000;0.5279999971;0.9499999881;0.0000095066;0.20000000670552253723;0.58265625239640939093;0.94999999999999995559;1.0000000000
-3;0;1;11.6448221207;0.0694663823;1.5634458065;0.1632390916;2.3432888985;0.8519564867;0.6399999857;15.6250000000;1;1.0000000000;1.00000000000000000000;0.1000000015;0.5000000000;275.6499938965;0.0316666700;1.0000000000;0.0099999998;9.0000000000;0.3333333433;0.3000000119;5.0000000000;0.0000000000;0.1000000015;0.0149999997;0.0029858518;40.2063484192;45.2240753174;68.3095474243;0.7099999785;0.0149999997;10.0000000000;20.0000000000;8.0000000000;10000.0000000000;0.0799999982;3;0.5000000000;0.5000000000;0.0000000000;0.5279999971;0.9499999881;0.0000095066;0.20000000670552253723;0.58265625239640939093;0.94999999999999995559;1.0000000000
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+17;17;0;1;10;0.0597584434;1.570102334;0.1265206039;2.3468546867;0.8519564867;0.6399999857;19.53125;0;1;0.735;0.0500000007;0.5;258.1499938965;0.0043000001;0.7659999728;0.0099999998;7.1999998093;0.4503000081;0.3000000119;5;0;0.1000000015;0.0180000011;0.0025641026;37.8558273315;49.7729492188;68.3095474243;0.5400000215;0.0149999997;10;20;4.7136998177;1000;0.0799999982;3;0.1666666716;0.1666666716;0;0.5279999971;0.9499999881;9.5066e-06;0.14;0.536432142857143;0.97;0.7900000215
diff --git a/models/ed/data/history.r85.csv b/models/ed/data/history.r85.csv
index 0214eda049f..008120633e2 100644
--- a/models/ed/data/history.r85.csv
+++ b/models/ed/data/history.r85.csv
@@ -1,8 +1,8 @@
 num;include_pft_ag;include_pft;SLA;b1Bl;b2Bl;b1Bs;b2Bs;b1Ht;b2Ht;Vm0;phenology;q;clumping;leaf_width;hgt_min;plant_min_temp;mort3;nonlocal_dispersal;seed_rain;stomatal_slope;growth_resp_factor;r_fract;repro_min_h;treefall_gt;treefall_lt;dark_respiration_factor;Rd0;qsw;c2n_leaf;c2n_recruit;dbh_crit;rho;D0;mort1;mort2;Vm_low_temp;cuticular_cond;quantum_efficiency;photosyn_pathway;leaf_turnover_rate;root_turnover_rate;storage_turnover_rate;root_respiration_factor;seedling_mortality;water_conductance;leaf_scatter_vis;diffuse_backscatter_vis;emis_v;f_labile
-1;1;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3330000043;0.3000000119;0;0;0.25;0.0399999991;0.5;0.0058205132;25.445476532;25.6388263702;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0.3333333433;0.5279999971;0.9499999881;2.85199e-05;0.150000002235174;0.533749999888241;0.96;1
-2;2;0;1;16.0179424286;0.4178909957;0.9749494195;0.1662153751;2.4323608875;0.0351999998;0.6940000057;18.75;1;1;0.800000011920929;0.1000000015;0.5;275.6499938965;0.0616666712;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0.28125;0.0041071647;24.5743560791;24.7624835968;96.2577896118;0.5299999714;0.0160000008;5;10;8;10000;0.0799999982;3;1;1;0.1666666716;0.5279999971;0.9499999881;1.90132e-05;0.150000002235174;0.550416666803261;0.95;1
-3;3;0;1;11.6448221207;0.5598162413;0.9749494195;0.222665906;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;0.800000011920929;0.1000000015;0.5;275.6499938965;0.03166667;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0.1875;0.0029858518;49.6025009155;49.9060745239;96.2577896118;0.7099999785;0.0160000008;5;10;8;10000;0.0799999982;3;0.5;0.5;0.1666666716;0.5279999971;0.9499999881;1.90132e-05;0.150000002235174;0.550416666803261;0.95;1
-4;4;0;1;9.6634206772;0.7096262574;0.9749494195;0.2822525501;2.4323608875;0.0351999998;0.6940000057;6.25;1;1;0.800000011920929;0.1000000015;0.5;275.6499938965;0;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0.09375;0.0024778002;112.2281112671;112.4855804443;96.2577896118;0.8999999762;0.0160000008;5;10;8;10000;0.0799999982;3;0.3333333433;0.3333333433;0.1666666716;0.5279999971;0.9499999881;1.90132e-05;0.150000002235174;0.550416666803261;0.95;1
+1;1;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3330000043;0.3000000119;0;0;0.25;0.0399999991;0.5;0.0058205132;25.445476532;25.6388263702;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0;0.5279999971;0.9499999881;2.85199e-05;0.150000002235174;0.533749999888241;0.96;1
+2;2;0;1;16.0179424286;0.4178909957;0.9749494195;0.1662153751;2.4323608875;0.0351999998;0.6940000057;18.75;1;1;0.800000011920929;0.1000000015;0.5;275.6499938965;0.0616666712;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0.28125;0.0041071647;24.5743560791;24.7624835968;96.2577896118;0.5299999714;0.0160000008;5;10;8;10000;0.0799999982;3;1;1;0;0.5279999971;0.9499999881;1.90132e-05;0.150000002235174;0.550416666803261;0.95;1
+3;3;0;1;11.6448221207;0.5598162413;0.9749494195;0.222665906;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;0.800000011920929;0.1000000015;0.5;275.6499938965;0.03166667;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0.1875;0.0029858518;49.6025009155;49.9060745239;96.2577896118;0.7099999785;0.0160000008;5;10;8;10000;0.0799999982;3;0.5;0.5;0;0.5279999971;0.9499999881;1.90132e-05;0.150000002235174;0.550416666803261;0.95;1
+4;4;0;1;9.6634206772;0.7096262574;0.9749494195;0.2822525501;2.4323608875;0.0351999998;0.6940000057;6.25;1;1;0.800000011920929;0.1000000015;0.5;275.6499938965;0;1;0.0099999998;9;0.3330000043;0.3000000119;5;0;0.1000000015;0.0149999997;0.09375;0.0024778002;112.2281112671;112.4855804443;96.2577896118;0.8999999762;0.0160000008;5;10;8;10000;0.0799999982;3;0.3333333433;0.3333333433;0;0.5279999971;0.9499999881;1.90132e-05;0.150000002235174;0.550416666803261;0.95;1
 5;5;1;1;22;0.0799999982;1;1e-05;1;0.4778000116;-0.75;18.2999992371;1;1;0.84;0.0500000007;0.150000006;193.1499938965;0.0659999996;1;0.0099999998;9;0.3333333433;0.3000000119;0;0;0.25;0.0149999997;0.2744999826;0.0056410255;18.3122673035;18.3132705688;3.9943094254;0.200000003;0.0160000008;1;20;4.7136998177;10000;0.0799999982;3;2;2;0;0.5279999971;0.9499999881;2.85199e-05;0.27;0.476851851851852;0.96;1
 6;6;0;1;6;0.0240000002;1.8990000486;0.1469999999;2.2379999161;27.1399993896;-0.0388399996;11.3500003815;0;0.3463000059;0.735;0.0500000007;1.5;193.1499938965;0.0033928;0.7659999728;0.0099999998;7.1999998093;0.4503000081;0.3000000119;5;0;0.1000000015;0.0149999997;0.1702499986;0.0015384615;78.032623291;124.6847686768;77.7029876709;0;0.0160000008;1;20;4.7136998177;1000;0.0799999982;3;0.3333333433;3.9272179604;0;0.5279999971;0.9499999881;1.90132e-05;0.27;0.476851851851852;0.97;0.7900000215
 7;7;0;1;9;0.0240000002;1.8990000486;0.1469999999;2.2379999161;27.1399993896;-0.0388399996;11.3500003815;0;0.3463000059;0.735;0.0500000007;1.5;263.1499938965;0.0043000001;0.7659999728;0.0099999998;7.1999998093;0.4503000081;0.3000000119;5;0;0.1000000015;0.0149999997;0.1702499986;0.0023076923;52.0217514038;106.0161056519;77.7029876709;0;0.0160000008;1;20;4.7136998177;1000;0.0799999982;3;0.3333333433;4.1178469658;0;0.5279999971;0.9499999881;1.90132e-05;0.27;0.476851851851852;0.97;0.7900000215
@@ -12,7 +12,7 @@ num;include_pft_ag;include_pft;SLA;b1Bl;b2Bl;b1Bs;b2Bs;b1Ht;b2Ht;Vm0;phenology;q
 11;11;0;1;35.1331596375;0.0170000009;1.7309999466;0.2349999994;2.2518000603;23.3873996735;-0.0540399998;43.3195915222;2;1.082343936;0.84;0.1000000015;2;-80;0.00428;0.074000001;0.0099999998;5.7846779823;0.3519981802;0.3154290915;5;0;0.1000000015;0.0355941243;0.5;0.0153846154;18.0751247406;56.3194046021;53.145866394;0;0.0160000008;1;20.1296615601;4.9695806503;10000;0.0671692118;3;0;0.6832925081;0;2.9513967037;0.9499999881;0.004550749;0.27;0.476851851851852;0.95;0.7900000215
 12;12;1;1;22;0.0799999982;1;1e-05;1;0.4778000116;-0.75;18.2999992371;1;1;0.84;0.0500000007;0.150000006;193.1499938965;0.0659999996;1;0.0099999998;9;0.3333333433;0.3000000119;0;0;0.25;0.0149999997;0.2744999826;0.0056410255;18.3122673035;18.3132705688;3.9943094254;0.200000003;0.0160000008;1;20;4.7136998177;10000;0.0799999982;3;2;0.3333333433;0;0.5279999971;0.9499999881;2.85199e-05;0.27;0.476851851851852;0.96;1
 13;13;1;1;22;0.0799999982;1;1e-05;1;0.4778000116;-0.75;18.2999992371;1;1;0.84;0.0500000007;0.150000006;193.1499938965;0.0659999996;1;0.0099999998;9;0.3333333433;0.3000000119;0;0;0.25;0.0149999997;0.2744999826;0.0056410255;18.3122673035;18.3132705688;3.9943094254;0.200000003;0.0160000008;1;20;4.7136998177;10000;0.0799999982;3;2;0.3333333433;0;0.5279999971;0.9499999881;2.85199e-05;0.27;0.476851851851852;0.96;1
-14;14;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3333333433;0.3000000119;0;0;0.25;0.0399999991;0.5;0.0058205132;25.445476532;25.6388263702;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0.3333333433;0.5279999971;0.9499999881;2.85199e-05;0.150000002235174;0.533749999888241;0.96;1
-15;15;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3333333433;0.3000000119;0;0;0.25;0.0399999991;0.5;0.0058205132;25.445476532;25.6388263702;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0.3333333433;0.5279999971;0.9499999881;2.85199e-05;0.150000002235174;0.533749999888241;0.96;1
-16;16;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;20.8333320618;1;1;1;0.0500000007;0.5;253.1499938965;0.1166666746;1;0.0099999998;9;0.3330000043;0.3000000119;0;0;0.25;0.0149999997;0.3124999702;0.0058205132;15.6761617661;15.8046960831;0.5971379876;0.200000003;0.0160000008;5;10;4.7136998177;10000;0.0799999982;3;2;2;0.3333333433;0.5279999971;0.9499999881;2.85199e-05;0.150000002235174;0.533749999888241;0.96;1
-17;17;0;1;10;0.4257757664;0.9749494195;0.1693515331;2.4323608875;0.0351999998;0.6940000057;15.625;0;1;0.735;0.0500000007;0.5;258.1499938965;0.0043000001;0.7659999728;0.0099999998;7.1999998093;0.4503000081;0.3000000119;5;0;0.1000000015;0.0149999997;0.234375;0.0025641026;46.8195762634;55.0424690247;96.2577896118;0.5400000215;0.0160000008;5;10;4.7136998177;1000;0.0799999982;3;0.1666666716;0.1666666716;0.1666666716;0.5279999971;0.9499999881;1.90132e-05;0.14;0.536432142857143;0.97;0.7900000215
+14;14;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3333333433;0.3000000119;0;0;0.25;0.0399999991;0.5;0.0058205132;25.445476532;25.6388263702;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0;0.5279999971;0.9499999881;2.85199e-05;0.150000002235174;0.533749999888241;0.96;1
+15;15;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;12.5;1;1;1;0.0500000007;0.5;275.6499938965;0.1166666746;1;0.0099999998;5.1999998093;0.3333333433;0.3000000119;0;0;0.25;0.0399999991;0.5;0.0058205132;25.445476532;25.6388263702;0.5971379876;0.200000003;0.0160000008;5;10;8;10000;0.0549999997;4;2;2;0;0.5279999971;0.9499999881;2.85199e-05;0.150000002235174;0.533749999888241;0.96;1
+16;16;1;1;22.7000007629;0.1576947272;0.9749494195;0.0627227873;2.4323608875;0.0351999998;0.6940000057;20.8333320618;1;1;1;0.0500000007;0.5;253.1499938965;0.1166666746;1;0.0099999998;9;0.3330000043;0.3000000119;0;0;0.25;0.0149999997;0.3124999702;0.0058205132;15.6761617661;15.8046960831;0.5971379876;0.200000003;0.0160000008;5;10;4.7136998177;10000;0.0799999982;3;2;2;0;0.5279999971;0.9499999881;2.85199e-05;0.150000002235174;0.533749999888241;0.96;1
+17;17;0;1;10;0.4257757664;0.9749494195;0.1693515331;2.4323608875;0.0351999998;0.6940000057;15.625;0;1;0.735;0.0500000007;0.5;258.1499938965;0.0043000001;0.7659999728;0.0099999998;7.1999998093;0.4503000081;0.3000000119;5;0;0.1000000015;0.0149999997;0.234375;0.0025641026;46.8195762634;55.0424690247;96.2577896118;0.5400000215;0.0160000008;5;10;4.7136998177;1000;0.0799999982;3;0.1666666716;0.1666666716;0;0.5279999971;0.9499999881;1.90132e-05;0.14;0.536432142857143;0.97;0.7900000215
diff --git a/models/ed/data/history.rgit.csv b/models/ed/data/history.rgit.csv
index 8cdff7d2517..e9d2e7afcc5 100644
--- a/models/ed/data/history.rgit.csv
+++ b/models/ed/data/history.rgit.csv
@@ -1,18 +1,18 @@
-"num";"is_tropical";"is_grass";"include_pft";"include_pft_ag";"include_pft_fp";"clumping_factor";"orient_factor";"leaf_emiss_tir";"wood_emiss_tir";"leaf_reflect_vis";"leaf_reflect_nir";"wood_reflect_vis";"wood_reflect_nir";"leaf_trans_vis";"leaf_trans_nir";"wood_trans_vis";"wood_trans_nir";"leaf_backscatter_vis";"leaf_backscatter_nir";"leaf_backscatter_tir";"wood_backscatter_vis";"wood_backscatter_nir";"wood_backscatter_tir";"leaf_scatter_vis";"leaf_scatter_nir";"wood_scatter_vis";"wood_scatter_nir";"phi1";"phi2";"mu_bar";"photosyn_pathway";"quantum_efficiency";"Vm0";"Vm_low_temp";"Vm_high_temp";"Vm_decay_e";"Vm_decay_a";"Vm_decay_b";"vm_hor";"vm_q10";"dark_respiration_factor";"Rd_low_temp";"Rd_high_temp";"Rd_decay_e";"Rd_hor";"Rd_q10";"Rd0";"D0";"stomatal_slope";"cuticular_cond";"water_conductance";"leaf_width";"growth_resp_factor";"leaf_turnover_rate";"root_turnover_rate";"storage_turnover_rate";"f_labile";"root_respiration_factor";"rrf_low_temp";"rrf_high_temp";"rrf_decay_e";"rrf_hor";"rrf_q10";"frost_mort";"mort0";"mort1";"mort2";"mort3";"cbr_severe_stress";"seedling_mortality";"treefall_s_gt";"treefall_s_lt";"fire_s_gt";"fire_s_lt";"plant_min_temp";"rho";"SLA";"horiz_branch";"q";"sapwood_ratio";"qsw";"init_density";"b1Ht";"b2Ht";"hgt_ref";"hgt_min";"hgt_max";"min_dbh";"dbh_crit";"dbh_adult";"dbh_bigleaf";"b1Bl_small";"b1Bl_large";"b2Bl_small";"b2Bl_large";"bleaf_adult";"b1Bs_small";"b1Bs_large";"b2Bs_small";"b2Bs_large";"min_bdead";"bdead_crit";"b1Ca";"b2Ca";"b1WAI";"b2WAI";"brf_wd";"agf_bs";"b1Vol";"b2Vol";"b1Rd";"b2Rd";"c2n_leaf";"c2n_recruit";"phenology";"c_grn_leaf_dry";"wat_dry_ratio_grn";"wat_dry_ratio_ngrn";"c_ngrn_biom_dry";"delta_c";"b1Cl";"b2Cl";"r_fract";"st_fract";"nonlocal_dispersal";"repro_min_h";"one_plant_c";"min_recruit_size";"min_cohort_size";"seed_rain";"negligible_nplant";"veg_hcap_min"
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+14;14;1;1;1;0;0;1;0;0.96;0.96;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0;0;0.625;0;0;0.625;0;0;0;0;0;0;0;4;0.0549999997;12.5;8;45;0.400000006;220000;690;3000;2.4000000954;0.0350000001;8;45;0.400000006;3000;2.4000000954;0.4375;0.0160000008;5.1999998093;10000;2.85199e-05;0.0500000007;0.3333333433;2;2;0;1;0.2800000012;8;45;0.400000006;3000;2.4000000954;3;-0.349999994;2;15;0;-1.0628256798;0.9499999881;0;0.25;0;0;275.6499938965;0.200000003;22.7000007629;0.5;1;3900;0.0058205132;0.1000000015;0.0351999998;0.6940000057;61.7000007629;0.5;1.5;0.1211817637;0.5971379876;10;0.5971379876;0.1576947272;0.1576947272;0.9749494195;0.9749494195;0.7442804575;0.0627227873;0.0647229999;2.4323608875;2.4255735874;0.0001849201;0.0089480467;1.1257275343;1.0521197319;0.0096000005;2.094700098;0.1599999964;0.6999999881;0.0247086249;2;-1.1140580177;0.4223014116;25.445476532;25.6388263702;1;3218;1.8500000238;0.6999999881;1217.3759765625;-225.1618652344;0.9900000095;1;0.3000000119;0;1;0;0.020361444;0.0002036145;2.03614e-05;0.0100000007;1.48253e-05;3.6809282303
+15;15;1;1;1;0;0;1;0;0.96;0.96;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0;0;0.625;0;0;0.625;0;0;0;0;0;0;0;4;0.0549999997;12.5;8;45;0.400000006;220000;690;3000;2.4000000954;0.0350000001;8;45;0.400000006;3000;2.4000000954;0.4375;0.0160000008;5.1999998093;10000;2.85199e-05;0.0500000007;0.3333333433;2;2;0;1;0.2800000012;8;45;0.400000006;3000;2.4000000954;3;-0.349999994;2;15;0;-1.0628256798;0.9499999881;0;0.25;0;0;275.6499938965;0.200000003;22.7000007629;0.5;1;3900;0.0058205132;0.1000000015;0.0351999998;0.6940000057;61.7000007629;0.5;1.5;0.1211817637;0.5971379876;10;0.5971379876;0.1576947272;0.1576947272;0.9749494195;0.9749494195;0.7442804575;0.0627227873;0.0647229999;2.4323608875;2.4255735874;0.0001849201;0.0089480467;1.1257275343;1.0521197319;0.0096000005;2.094700098;0.1599999964;0.6999999881;0.0247086249;2;-1.1140580177;0.4223014116;25.445476532;25.6388263702;1;3218;1.8500000238;0.6999999881;1217.3759765625;-225.1618652344;0.9900000095;1;0.3000000119;0;1;0;0.020361444;0.0002036145;2.03614e-05;0.0100000007;1.48253e-05;3.6809282303
+16;16;1;1;1;0;0;1;0;0.96;0.96;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0.100000001490116;0;0;0.625;0;0;0.625;0;0;0;0;0;0;0;3;0.0799999982;18.75;4.7136998177;45;0.400000006;220000;690;3000;2.4000000954;0.0144999996;4.7136998177;45;0.400000006;3000;2.4000000954;0.271874994;0.0160000008;9;10000;2.85199e-05;0.0500000007;0.3330000043;2;2;0;1;0.2800000012;4.7136998177;45;0.400000006;3000;2.4000000954;3;-0.349999994;2;15;0;-1.0628256798;0.9499999881;0;0.25;0;0;253.1499938965;0.200000003;22.7000007629;0.5;1;3900;0.0058205132;0.1000000015;0.0351999998;0.6940000057;61.7000007629;0.5;1.5;0.1211817637;0.5971379876;10;0.5971379876;0.1576947272;0.1576947272;0.9749494195;0.9749494195;0.7442804575;0.0627227873;0.0647229999;2.4323608875;2.4255735874;0.0001849201;0.0089480467;1.1257275343;1.0521197319;0.0096000005;2.094700098;0.1599999964;0.6999999881;0.0247086249;2;-1.1140580177;0.4223014116;17.340555191;17.4809608459;1;3218;1.8500000238;0.6999999881;1217.3759765625;-225.1618652344;0.9900000095;1;0.3000000119;0;1;0;0.020361444;0.0002036145;2.03614e-05;0.0100000007;1.48253e-05;3.6809282303
+17;17;1;0;1;0;0;0.735;89128.9609375;0.97;0.9;0.09;0.09;0.09;0.09;0.09;0.09;0.09;0.09;0;0;0.6275125;0;0;0.6275125;0;0;0;0;0;0;0;3;0.0799999982;15.625;4.7136998177;45;0.400000006;220000;690;3000;2.4000000954;0.0144999996;4.7136998177;45;0.400000006;3000;2.4000000954;0.2265625149;0.0160000008;7.1999998093;1000;1.90132e-05;0.0500000007;0.4503000081;0.1666666716;0.1666666716;0;0.7900000215;0.2800000012;4.7136998177;45;0.400000006;3000;2.4000000954;3;-0.349999994;2;15;0.0043000001;-1.0628256798;0.9499999881;0;0.1000000015;0;0;258.1499938965;0.5400000215;10;0.6100000143;1;3900;0.0025641026;0.1000000015;0.0351999998;0.6940000057;61.7000007629;0.5;35;0.1211817637;96.2577896118;10;30;0.4257757664;0.4257757664;0.9749494195;0.9749494195;2.0095572472;0.1693515331;0.1747521162;2.4323608875;2.4255735874;0.0004992842;5651.8544921875;1.1257275343;1.0521197319;0.0276500005;1.9768999815;0.1599999964;0.6999999881;0.0247086249;2;-1.1140580177;0.4223014116;46.8195762634;55.0424690247;0;3218;1.8500000238;0.6999999881;1217.3759765625;-225.1618652344;0.3106774986;1.0980000496;0.3000000119;0;0.7659999728;18;0.0549316183;0.0005493162;5.49316e-05;0.0100000007;1e-10;9.9385070801
diff --git a/models/ed/inst/ED2IN.rgit b/models/ed/inst/ED2IN.rgit
index 0a5d59f13e4..fd1a9e4b3d5 100644
--- a/models/ed/inst/ED2IN.rgit
+++ b/models/ed/inst/ED2IN.rgit
@@ -1288,12 +1288,6 @@ $ED_NL
    !---------------------------------------------------------------------------------------!
    NL%STORAGE_RESP_SCHEME = 0
    !---------------------------------------------------------------------------------------!
-
-   !---------------------------------------------------------------------------------------!
-   ! IOPTINPT -- Optimization configuration. (Currently not used)                          !
-   !---------------------------------------------------------------------------------------!
-   NL%IOPTINPT = ''
-   !---------------------------------------------------------------------------------------!
 $END
 !==========================================================================================!
 !==========================================================================================!
diff --git a/models/ed/inst/template.job b/models/ed/inst/template.job
index aed8b59792b..07a89da0df0 100644
--- a/models/ed/inst/template.job
+++ b/models/ed/inst/template.job
@@ -14,6 +14,9 @@ echo "Logging on "$TIMESTAMP
 mkdir -p "@OUTDIR@"
 @SCRATCH_MKDIR@
 
+# @REMOVE_HISTXML@ : tag to remove "history.xml" on remote for restarts, commented out on purpose
+
+
 # flag needed for ubuntu
 export GFORTRAN_UNBUFFERED_PRECONNECTED=yes
 
diff --git a/models/ed/man/between.Rd b/models/ed/man/between.Rd
new file mode 100644
index 00000000000..6fcb8dc63d5
--- /dev/null
+++ b/models/ed/man/between.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_ed2in.R
+\name{between}
+\alias{between}
+\title{Check if value is between (inclusive) a range}
+\usage{
+between(x, lower, upper)
+}
+\arguments{
+\item{x}{Value to check}
+
+\item{lower}{Lower limit}
+
+\item{upper}{Upper limit}
+}
+\description{
+Check if value is between (inclusive) a range
+}
diff --git a/models/ed/man/check_css.Rd b/models/ed/man/check_css.Rd
new file mode 100644
index 00000000000..e6511a674cc
--- /dev/null
+++ b/models/ed/man/check_css.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_veg.R
+\name{check_css}
+\alias{check_css}
+\alias{check_pss}
+\alias{check_site}
+\title{Check individual ED input files}
+\usage{
+check_css(css, pss = NULL)
+
+check_pss(pss, site = NULL)
+
+check_site(site)
+}
+\arguments{
+\item{css}{css data object (see \link{read_css})}
+
+\item{pss}{pss data object (see \link{read_pss})}
+
+\item{site}{site data object (see \link{read_site})}
+}
+\value{
+\code{NULL} (invisibly)
+}
+\description{
+Check internal file formatting, and optionally check for compatibility
+against related files.
+}
diff --git a/models/ed/man/check_ed2in.Rd b/models/ed/man/check_ed2in.Rd
new file mode 100644
index 00000000000..8a2e8d032cc
--- /dev/null
+++ b/models/ed/man/check_ed2in.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_ed2in.R
+\name{check_ed2in}
+\alias{check_ed2in}
+\title{Check ED2IN}
+\usage{
+check_ed2in(ed2in)
+}
+\arguments{
+\item{ed2in}{Named list of ED2IN tag-value pairs. See \link{read_ed2in}.}
+}
+\description{
+Check the basic structure of \code{ed2in} object, as well as consistency among
+arguments (e.g. run dates and coordinates are within the range of vegetation
+and meteorology data).
+}
diff --git a/models/ed/man/check_ed_metfile.Rd b/models/ed/man/check_ed_metfile.Rd
new file mode 100644
index 00000000000..9bc159472fc
--- /dev/null
+++ b/models/ed/man/check_ed_metfile.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_ed_metheader.R
+\name{check_ed_metfile}
+\alias{check_ed_metfile}
+\title{Check individual ED metfile}
+\usage{
+check_ed_metfile(metfile, variables)
+}
+\arguments{
+\item{metfile}{Path to meteorology file}
+
+\item{variables}{Variables table from \link[=read_ed_metheader]{ed_metheader} object}
+}
+\value{
+\code{NULL}, invisibly, if successful or throw an error
+}
+\description{
+Check individual ED metfile
+}
diff --git a/models/ed/man/check_ed_metheader.Rd b/models/ed/man/check_ed_metheader.Rd
new file mode 100644
index 00000000000..6bcc256454f
--- /dev/null
+++ b/models/ed/man/check_ed_metheader.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_ed_metheader.R
+\name{check_ed_metheader}
+\alias{check_ed_metheader}
+\alias{check_ed_metheader_format}
+\title{Check ED met header object}
+\usage{
+check_ed_metheader(ed_metheader, check_files = TRUE)
+
+check_ed_metheader_format(ed_metheader_format, check_files = TRUE)
+}
+\arguments{
+\item{ed_metheader}{ED meteorology header object (see \link{read_ed_metheader})}
+
+\item{check_files}{Logical. If \code{TRUE}, perform basic diagnostics on met
+files as well.}
+
+\item{ed_metheader_format}{A single format inside the met header object}
+}
+\description{
+Check that the object has all components, and throw an error if anything is
+wrong. Optionally, do some basic checks of actualy meteorology files as
+well.
+}
+\details{
+\code{check_ed_metheader_format} checks an individual format (one item in the
+\code{ed_metheader} list). \code{check_ed_metheader} applies these checks to each item
+in the format list.
+}
diff --git a/models/ed/man/convert.samples.ED.Rd b/models/ed/man/convert.samples.ED.Rd
index 4540a0d42ed..00378c24c27 100644
--- a/models/ed/man/convert.samples.ED.Rd
+++ b/models/ed/man/convert.samples.ED.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/write.configs.ed.R
 \name{convert.samples.ED}
 \alias{convert.samples.ED}
-\title{Convert samples for ed}
+\title{convert parameters from PEcAn database default units to ED defaults}
 \usage{
 convert.samples.ED(trait.samples)
 }
@@ -13,9 +13,6 @@ convert.samples.ED(trait.samples)
 matrix or dataframe with values transformed
 }
 \description{
-convert parameters from PEcAn database default units to ED defaults
-}
-\details{
 Performs model specific unit conversions on a a list of trait values,
 such as those provided to write.config
 }
diff --git a/models/ed/man/create_css.Rd b/models/ed/man/create_css.Rd
new file mode 100644
index 00000000000..8b6ab5a8d73
--- /dev/null
+++ b/models/ed/man/create_css.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_veg.R
+\name{create_css}
+\alias{create_css}
+\alias{create_pss}
+\alias{create_site}
+\title{Create css, pss, and site files from examples}
+\usage{
+create_css(input, check = TRUE)
+
+create_pss(input, check = TRUE)
+
+create_site(input, check = TRUE)
+}
+\arguments{
+\item{input}{Named \code{list} or \code{data.frame} containing columns to replace in examples}
+
+\item{check}{Logical. If \code{TRUE} (default), also check files for validity.}
+}
+\value{
+css, pss, or site object (\code{data.frame}, possibly with attributes)
+}
+\description{
+Create css, pss, and site files from examples
+}
diff --git a/models/ed/man/create_ed_veg.Rd b/models/ed/man/create_ed_veg.Rd
new file mode 100644
index 00000000000..af8ba0fb2f8
--- /dev/null
+++ b/models/ed/man/create_ed_veg.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_veg.R
+\name{create_ed_veg}
+\alias{create_ed_veg}
+\title{Create full ED vegetation input object}
+\usage{
+create_ed_veg(css, pss, site, latitude, longitude, check = TRUE, ...)
+}
+\arguments{
+\item{css}{\link[=read_css]{css} object (\code{data.frame})}
+
+\item{pss}{\link[=read_pss]{pss} object (\code{data.frame})}
+
+\item{site}{\link[=read_site]{site} object (\code{data.frame})}
+
+\item{latitude}{Latitude coordinate}
+
+\item{longitude}{Longitude coordinate}
+
+\item{check}{Logical. If \code{TRUE} (default), also check files for validity.}
+
+\item{...}{Additional objects to store in list}
+}
+\description{
+Create full ED vegetation input object
+}
diff --git a/models/ed/man/dates_in_month.Rd b/models/ed/man/dates_in_month.Rd
new file mode 100644
index 00000000000..71161e1ef61
--- /dev/null
+++ b/models/ed/man/dates_in_month.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_met_dates.R
+\name{dates_in_month}
+\alias{dates_in_month}
+\title{Get all the dates in a month}
+\usage{
+dates_in_month(date)
+}
+\arguments{
+\item{date}{Date as string or date object}
+}
+\value{
+Sequence of dates from the first to the last day of the month.
+}
+\description{
+For a given date, figure out its month and return all of the dates for that
+month.
+}
diff --git a/models/ed/man/download_edi.Rd b/models/ed/man/download_edi.Rd
new file mode 100644
index 00000000000..fe62f82787e
--- /dev/null
+++ b/models/ed/man/download_edi.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download_edi.R
+\name{download_edi}
+\alias{download_edi}
+\title{Download ED inputs}
+\usage{
+download_edi(directory)
+}
+\arguments{
+\item{directory}{Target directory for unzipping files. Will be created if it
+doesn't exist.}
+}
+\value{
+\code{TRUE}, invisibly
+}
+\description{
+Download and unzip common ED inputs from a public Open Science Framework
+(OSF) repository (https://osf.io/b6umf). Inputs include the Olson Global
+Ecosystems (OGE) database (\code{oge2OLD}) and the \code{chd} and \code{dgd} databases.
+}
+\details{
+The total download size around 28 MB.
+}
diff --git a/models/ed/man/ed.var.Rd b/models/ed/man/ed.var.Rd
new file mode 100644
index 00000000000..fd79d0e2ba8
--- /dev/null
+++ b/models/ed/man/ed.var.Rd
@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ed_varlookup.R
+\name{ed.var}
+\alias{ed.var}
+\title{Lookup function for translating commonly used ED variables
+returns out list, readvar variables to read from file, expr if any derivation is needed}
+\usage{
+ed.var(varname)
+}
+\description{
+Lookup function for translating commonly used ED variables
+returns out list, readvar variables to read from file, expr if any derivation is needed
+}
diff --git a/models/ed/man/ed2in2time.Rd b/models/ed/man/ed2in2time.Rd
new file mode 100644
index 00000000000..3c0b8c87b8c
--- /dev/null
+++ b/models/ed/man/ed2in2time.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_ed2in_dates.R
+\name{ed2in2time}
+\alias{ed2in2time}
+\title{Convert ED2IN \code{ITIMEA/Z} string to hour and minute}
+\usage{
+ed2in2time(itimea)
+}
+\arguments{
+\item{itimea}{ED2IN time string, e.g. "1200"}
+}
+\value{
+List containing numeric values of hour and minute
+}
+\description{
+Convert ED2IN \code{ITIMEA/Z} string to hour and minute
+}
diff --git a/models/ed/man/ed2in_set_value.Rd b/models/ed/man/ed2in_set_value.Rd
deleted file mode 100644
index 3d320469a1f..00000000000
--- a/models/ed/man/ed2in_set_value.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ed2in_set_value.R
-\name{ed2in_set_value}
-\alias{ed2in_set_value}
-\title{Substitute single value into ED2IN}
-\usage{
-ed2in_set_value(tag, value, ed2in, modstring = "Modified by PEcAn")
-}
-\arguments{
-\item{tag}{ED2IN tag, e.g. "SFILIN"}
-
-\item{value}{Value for setting the tag}
-
-\item{ed2in}{Character vector containing ED2IN file, usually generated by 
-\code{readLines}.}
-}
-\description{
-Given a tag, find that tag in the provided ED2IN character 
-vector and change its value. If the tag is not found, do nothing.
-}
-\author{
-Alexey Shiklomanov
-}
diff --git a/models/ed/man/ed2in_set_value_list.Rd b/models/ed/man/ed2in_set_value_list.Rd
deleted file mode 100644
index 28f5c451fb1..00000000000
--- a/models/ed/man/ed2in_set_value_list.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ed2in_set_value.R
-\name{ed2in_set_value_list}
-\alias{ed2in_set_value_list}
-\title{Substitute list of tag-value pairs into ED2IN}
-\usage{
-ed2in_set_value_list(tag_val_list, ed2in, ...)
-}
-\arguments{
-\item{tag_val_list}{Named list of tag-value pairs. List names should match 
-ed2in tags.}
-
-\item{ed2in}{Character vector containing ED2IN file, usually generated by 
-\code{readLines}.}
-
-\item{...}{Other parameters to \code{ed2in_set_value}}
-}
-\author{
-Alexey Shiklomanov
-}
diff --git a/models/ed/man/example_css.Rd b/models/ed/man/example_css.Rd
new file mode 100644
index 00000000000..6d4e7ce8b06
--- /dev/null
+++ b/models/ed/man/example_css.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/example_veg.R
+\docType{data}
+\name{example_css}
+\alias{example_css}
+\alias{example_pss}
+\alias{example_site}
+\title{Example css, pss, and site objects}
+\format{An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 1 rows and 10 columns.}
+\usage{
+example_css
+
+example_pss
+
+example_site
+}
+\description{
+Example css, pss, and site objects
+}
+\keyword{datasets}
diff --git a/models/ed/man/get_configxml.ED2.Rd b/models/ed/man/get_configxml.ED2.Rd
index 1bfb1d3f72b..2475d073e83 100644
--- a/models/ed/man/get_configxml.ED2.Rd
+++ b/models/ed/man/get_configxml.ED2.Rd
@@ -11,6 +11,9 @@ get_configxml.ED2(rundir, runid)
 
 \item{runid}{PEcAn run ID}
 }
+\description{
+Get ED2 config.xml file
+}
 \author{
 Alexey Shiklomanov
 }
diff --git a/models/ed/man/get_ed2in_dates.Rd b/models/ed/man/get_ed2in_dates.Rd
new file mode 100644
index 00000000000..c6fe2f44d66
--- /dev/null
+++ b/models/ed/man/get_ed2in_dates.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_ed2in_dates.R
+\name{get_ed2in_dates}
+\alias{get_ed2in_dates}
+\title{Extract sequence of dates from ED2IN file}
+\usage{
+get_ed2in_dates(ed2in)
+}
+\arguments{
+\item{ed2in}{Named list of ED2IN tag-value pairs. See \link{read_ed2in}.}
+}
+\value{
+Vector of dates from start date to end date by 1 day
+}
+\description{
+Extract sequence of dates from ED2IN file
+}
diff --git a/models/ed/man/get_latlon.Rd b/models/ed/man/get_latlon.Rd
new file mode 100644
index 00000000000..434158b6b6e
--- /dev/null
+++ b/models/ed/man/get_latlon.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_ed_veg.R
+\name{get_latlon}
+\alias{get_latlon}
+\title{Parse latitude or longitude}
+\usage{
+get_latlon(filepath, latlon)
+}
+\arguments{
+\item{filepath}{Path to a css, pss, or site file}
+
+\item{latlon}{Which value to retrieve, either "lat" for latitude or "lon"
+for longitude}
+}
+\value{
+Numeric value of latitude or longitude
+}
+\description{
+Automatically determine latitude or longitude from an ED input filepath. If
+the latitude/longitude regular expression isn't matched, this will throw an
+error.
+}
diff --git a/models/ed/man/get_met_dates.Rd b/models/ed/man/get_met_dates.Rd
new file mode 100644
index 00000000000..2cd632dc0c3
--- /dev/null
+++ b/models/ed/man/get_met_dates.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_met_dates.R
+\name{get_met_dates}
+\alias{get_met_dates}
+\title{Get meteorology dates}
+\usage{
+get_met_dates(ed_metheader)
+}
+\arguments{
+\item{ed_metheader}{ED meteorlogy header object (see \link{read_ed_metheader})}
+}
+\value{
+Vector of dates for a run
+}
+\description{
+Figure out the dates for which a given meteorology is available by parsing
+the matching file names.
+}
diff --git a/models/ed/man/get_restartfile.ED2.Rd b/models/ed/man/get_restartfile.ED2.Rd
index 750359b737f..f4605ec385b 100644
--- a/models/ed/man/get_restartfile.ED2.Rd
+++ b/models/ed/man/get_restartfile.ED2.Rd
@@ -7,13 +7,16 @@
 get_restartfile.ED2(mod_outdir, runid, file.time)
 }
 \arguments{
-\item{mod_outdir}{Directory where PEcAn stores ensemble outputs. Usually 
+\item{mod_outdir}{Directory where PEcAn stores ensemble outputs. Usually
 \code{<workflowID>/out}}
 
 \item{runid}{PEcAn run ID}
 
 \item{file.time}{Start or end time from SDA analysis}
 }
+\description{
+Get ED history restart file path
+}
 \author{
 Alexey Shiklomanov
 }
diff --git a/models/ed/man/is.ed2in.Rd b/models/ed/man/is.ed2in.Rd
new file mode 100644
index 00000000000..6a55088e3a4
--- /dev/null
+++ b/models/ed/man/is.ed2in.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_ed2in.R
+\name{is.ed2in}
+\alias{is.ed2in}
+\title{Check if object is \code{ed2in}}
+\usage{
+is.ed2in(x)
+}
+\arguments{
+\item{x}{Object to be tested}
+}
+\description{
+Simple test if object inheirts from class \code{"ed2in"}.
+}
diff --git a/models/ed/man/list.files.nodir.Rd b/models/ed/man/list.files.nodir.Rd
index 242dad9efc2..8cd27fb51a9 100644
--- a/models/ed/man/list.files.nodir.Rd
+++ b/models/ed/man/list.files.nodir.Rd
@@ -12,6 +12,9 @@ list.files.nodir(path, ...)
     expansion (see \code{\link{path.expand}}) is performed.  Missing
     values will be ignored.}
 }
+\description{
+List only files in a directory
+}
 \author{
 Alexey Shiklomanov
 }
diff --git a/models/ed/man/met2model.ED2.Rd b/models/ed/man/met2model.ED2.Rd
index 3ee0be1e989..f79c77540d7 100644
--- a/models/ed/man/met2model.ED2.Rd
+++ b/models/ed/man/met2model.ED2.Rd
@@ -2,10 +2,11 @@
 % Please edit documentation in R/met2model.ED2.R
 \name{met2model.ED2}
 \alias{met2model.ED2}
-\title{met2model for ED2}
+\title{met2model wrapper for ED2}
 \usage{
-met2model.ED2(in.path, in.prefix, outfolder, start_date, end_date, lst = 0,
-  lat = NA, lon = NA, overwrite = FALSE, verbose = FALSE, ...)
+met2model.ED2(in.path, in.prefix, outfolder, start_date, end_date,
+  lst = 0, lat = NA, lon = NA, overwrite = FALSE,
+  verbose = FALSE, leap_year = TRUE, ...)
 }
 \arguments{
 \item{in.path}{location on disk where inputs are stored}
@@ -23,7 +24,12 @@ met2model.ED2(in.path, in.prefix, outfolder, start_date, end_date, lst = 0,
 \item{overwrite}{should existing files be overwritten}
 
 \item{verbose}{should the function be very verbose}
+
+\item{leap_year}{Enforce Leap-years? If set to TRUE, will require leap years to have 366 days. If set to false, will require all years to have 365 days. Default = TRUE.}
 }
 \description{
-met2model wrapper for ED2
+If files already exist in 'Outfolder', the default function is NOT to
+overwrite them and only gives user the notice that file already exists. If
+user wants to overwrite the existing files, just change overwrite statement
+below to TRUE.
 }
diff --git a/models/ed/man/met_flag_description.Rd b/models/ed/man/met_flag_description.Rd
new file mode 100644
index 00000000000..16b211bf3f6
--- /dev/null
+++ b/models/ed/man/met_flag_description.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_ed_metheader.R
+\docType{data}
+\name{met_flag_description}
+\alias{met_flag_description}
+\title{Description of meteorology flags}
+\format{An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 5 rows and 2 columns.}
+\usage{
+met_flag_description
+}
+\description{
+Descriptions of ED met header variable flags.
+}
+\details{
+\code{data.frame} with the following columns:
+\itemize{
+\item \code{flag} -- Numeric flag (in header file)
+\item \code{flag_description} -- Description of flag
+}
+}
+\keyword{datasets}
diff --git a/models/ed/man/met_variable_description.Rd b/models/ed/man/met_variable_description.Rd
new file mode 100644
index 00000000000..f252e6673cc
--- /dev/null
+++ b/models/ed/man/met_variable_description.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_ed_metheader.R
+\docType{data}
+\name{met_variable_description}
+\alias{met_variable_description}
+\title{Description of meteorology variables}
+\format{An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 15 rows and 3 columns.}
+\usage{
+met_variable_description
+}
+\description{
+Helpful information about ED_MET_DRIVER files.
+}
+\details{
+\code{data.frame} with the following columns:
+\itemize{
+\item \code{variable} -- Variable name
+\item \code{description} -- Variable description
+\item \code{unit} -- Variable unit (character, parse-able by \code{udunints2})
+}
+}
+\keyword{datasets}
diff --git a/models/ed/man/modify_df.Rd b/models/ed/man/modify_df.Rd
new file mode 100644
index 00000000000..30a353c6722
--- /dev/null
+++ b/models/ed/man/modify_df.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_veg.R
+\name{modify_df}
+\alias{modify_df}
+\title{Modify a reference \code{data.frame}}
+\usage{
+modify_df(input, base)
+}
+\arguments{
+\item{input}{Named \code{list} or \code{data.frame} containing columns to replace in \code{base}}
+
+\item{base}{Reference object to modify}
+}
+\value{
+Modified \code{data.frame}
+}
+\description{
+Wrapper around \code{modifyList} to allow expanding a \code{data.frame} by modifying
+only a single column.
+}
diff --git a/models/ed/man/modify_ed2in.Rd b/models/ed/man/modify_ed2in.Rd
new file mode 100644
index 00000000000..12870bc0fe2
--- /dev/null
+++ b/models/ed/man/modify_ed2in.Rd
@@ -0,0 +1,90 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/modify_ed2in.R
+\name{modify_ed2in}
+\alias{modify_ed2in}
+\title{Modify an ED2IN object}
+\usage{
+modify_ed2in(ed2in, ..., veg_prefix = NULL, latitude = NULL,
+  longitude = NULL, met_driver = NULL, start_date = NULL,
+  end_date = NULL, EDI_path = NULL, output_types = NULL,
+  output_dir = NULL, run_dir = NULL, runtype = NULL,
+  run_name = NULL, pecan_defaults = FALSE, add_if_missing = FALSE,
+  check_paths = TRUE, .dots = list())
+}
+\arguments{
+\item{...}{Namelist arguments (see Description and Details)}
+
+\item{veg_prefix}{Vegetation file prefix (\code{SFILIN}). If \code{lat} and \code{lon} are part of the prefix,}
+
+\item{latitude}{Run latitude coordinate. If \code{veg_prefix} is also provided,
+pass to \link{read_ed_veg}, otherwise set in ED2IN directly. Should be omitted if
+\code{lat} and \code{lon} are already part of \code{veg_prefix}.}
+
+\item{longitude}{Run longitude coordinate. If \code{veg_prefix} is also provided,
+pass to \link{read_ed_veg}, otherwise set in ED2IN directly. Should be omitted if
+\code{lat} and \code{lon} are already part of \code{veg_prefix}.}
+
+\item{met_driver}{Path and filename of met driver header
+(\code{ED_MET_DRIVER_DB})}
+
+\item{start_date}{Run start date (\code{IMONTHA}, \code{IDATEA}, \code{IYEARA}, \code{ITIMEA})}
+
+\item{end_date}{Run end date (\code{IMONTHZ}, \code{IDATEZ}, \code{IYEARZ} \code{ITIMEZ})}
+
+\item{EDI_path}{Path to \code{EDI} directory, which often has the \code{VEG_DATABASE}
+and \code{THSUMS_DATABASE} files.}
+
+\item{output_types}{Character vector of output types (see Details)}
+
+\item{output_dir}{Output directory, for \code{FFILOUT} (analysis) and \code{SFILOUT}
+(history) files}
+
+\item{run_dir}{Directory in which to store run-related config files (e.g. \code{config.xml}).}
+
+\item{runtype}{ED initialization mode; either "INITIAL" or "HISTORY"}
+
+\item{pecan_defaults}{Logical. If \code{TRUE}, set common \code{ED2IN} defaults.}
+
+\item{add_if_missing}{Logical. If \code{TRUE}, all-caps arguments not found in
+existing \code{ed2in} list will be added to the end.  Default = \code{FALSE}.}
+
+\item{check_paths}{Logical. If \code{TRUE} (default), for any parameters that
+expect files, check that files exist and throw an error if they don't.}
+
+\item{.dots}{A list of \code{...} arguments.}
+}
+\value{
+Modified \code{ed2in} list object. See \link{read_ed2in}.
+}
+\description{
+This is a convenience function for modifying an \code{ed2in} list object.
+Arguments passed in all caps are assumed to be ED2IN namelist parameters and
+are inserted directly into the \code{ed2in} list objects. Lowercase arguments are
+defined explicitly (see "Parameters"), and those that do not match explicit
+arguments will be ignored with a warning. Because the lowercase arguments
+come with additional validity checks, they are recommended over modifying
+the ED2IN file directly via uppercase arguments.
+}
+\details{
+Namelist arguments are applied last, and will silently overwrite any
+arguments set by special case arguments.
+
+Namelist arguments can be stored in a list and passed in via the \code{.dots}
+argument (e.g. \code{.dots = list(SFILIN = "/path/prefix_", ...)}), or using the
+\code{rlang::!!!} splicing operator. If both are provided, they will be spliced
+together, with the \code{...} taking precedence.
+
+For \code{output_types}, select one or more of the following:
+\itemize{
+\item "fast" -- Fast analysis; mostly polygon-level averages (\code{IFOUTPUT})
+\item "daily -- Daily means (one file per day) (\code{IDOUTPUT})
+\item "monthly" -- Monthly means (one file per month) (\code{IMOUTPUT})
+\item "monthly_diurnal" -- Monthly means of the diurnal cycle (one file per
+month) (\code{IQOUTPUT})
+\item "annual" -- Annual (one file per year) (\code{IYOUTPUT})
+\item "instant" -- Instantaneous fluxes, mostly polygon-level variables, one
+file per year (\code{ITOUTPUT})
+\item "restart" -- Restart file for HISTORY runs. (\code{ISOUTPUT})
+\item "all" -- All output types
+}
+}
diff --git a/models/ed/man/patch_cohort_index.Rd b/models/ed/man/patch_cohort_index.Rd
index 2689b18afe5..5c6e2df25e9 100644
--- a/models/ed/man/patch_cohort_index.Rd
+++ b/models/ed/man/patch_cohort_index.Rd
@@ -10,7 +10,7 @@ patch_cohort_index(nc)
 \item{nc}{\code{ncdf4} object for ED history restart file.}
 }
 \description{
-Generate a vector of integer indices for mapping ED state 
+Generate a vector of integer indices for mapping ED state
 cohort vectors onto patches, for instance for use with \code{tapply}.
 }
 \author{
diff --git a/models/ed/man/prepare_ed_veg_filename.Rd b/models/ed/man/prepare_ed_veg_filename.Rd
new file mode 100644
index 00000000000..ef5a98ebcc1
--- /dev/null
+++ b/models/ed/man/prepare_ed_veg_filename.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/write_ed_veg.R
+\name{prepare_ed_veg_filename}
+\alias{prepare_ed_veg_filename}
+\title{Format file name for ED vegetation inputs}
+\usage{
+prepare_ed_veg_filename(path_prefix, suffix, latitude = NULL,
+  longitude = NULL)
+}
+\arguments{
+\item{path_prefix}{Desired path and prefix (without latitude and longitude)}
+
+\item{suffix}{Character string of filename suffix.}
+
+\item{latitude}{Site latitude coordinate (default = \code{NULL})}
+
+\item{longitude}{Site longitude coordinate (default = \code{NULL})}
+}
+\value{
+Character string of full formatted file path
+}
+\description{
+Adds the latitude and longitude, or checks if they are formatted correctly.
+Then, splits the prefix into the directory and base name, appends the suffix
+to the base name (adding a starting dot, if necessary), and returns the
+filename as a character.
+}
diff --git a/models/ed/man/print.ed2in.Rd b/models/ed/man/print.ed2in.Rd
new file mode 100644
index 00000000000..a53e2af25f2
--- /dev/null
+++ b/models/ed/man/print.ed2in.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_ed2in.R
+\name{print.ed2in}
+\alias{print.ed2in}
+\title{Print method for \code{ed2in}}
+\usage{
+\method{print}{ed2in}(x, ...)
+}
+\arguments{
+\item{x}{an object used to select a method.}
+
+\item{...}{further arguments passed to or from other methods.}
+}
+\description{
+Sets attributes to \code{NULL} before printing, so the output isn't as messy.
+}
diff --git a/models/ed/man/read.output.ED2.Rd b/models/ed/man/read.output.ED2.Rd
index f52ff93b4d6..0ea392e589d 100644
--- a/models/ed/man/read.output.ED2.Rd
+++ b/models/ed/man/read.output.ED2.Rd
@@ -14,7 +14,7 @@ read.output.ED2(run.id, outdir, start.year = NA, end.year = NA,
 
 \item{start.year}{}
 
-\item{output.type}{type of output file to read, can be '-Y-' for annual output, '-M-' for monthly means, '-D-' for daily means, '-T-' for instantaneous fluxes. Output types are set in the ED2IN namelist as NL%I[DMYT]OUTPUT}
+\item{output.type}{type of output file to read, can be '-Y-' for annual output, '-M-' for monthly means, '-D-' for daily means, '-T-' for instantaneous fluxes. Output types are set in the ED2IN namelist as NL%I\link{DMYT}OUTPUT}
 }
 \value{
 vector of output variable for all runs within ensemble
diff --git a/models/ed/man/read_E_files.Rd b/models/ed/man/read_E_files.Rd
index 30724157e38..c89ffd8e1a0 100644
--- a/models/ed/man/read_E_files.Rd
+++ b/models/ed/man/read_E_files.Rd
@@ -4,21 +4,26 @@
 \alias{read_E_files}
 \title{Function for reading -E- files}
 \usage{
-read_E_files(yr, yfiles, efiles, outdir, start_date, end_date, pft_names, ...)
+read_E_files(yr, yfiles, efiles, outdir, start_date, end_date, pft_names,
+  ...)
+}
+\arguments{
+\item{yr}{the year being processed}
+
+\item{yfiles}{the years on the filenames, will be used to matched efiles for that year}
 }
 \description{
-yr      : the year being processed
-yfiles  : the years on the filenames, will be used to matched efiles for that year
+Function for reading -E- files
 }
 \details{
 e.g.     yr = 1999
-     yfiles = 1999 1999 1999 1999 1999 1999 1999 2000 2000 2000 2000
-     efiles = "analysis-E-1999-06-00-000000-g01.h5" "analysis-E-1999-07-00-000000-g01.h5"
-              "analysis-E-1999-08-00-000000-g01.h5" "analysis-E-1999-09-00-000000-g01.h5"
-              "analysis-E-1999-10-00-000000-g01.h5" "analysis-E-1999-11-00-000000-g01.h5"
-              "analysis-E-1999-12-00-000000-g01.h5" "analysis-E-2000-01-00-000000-g01.h5"
-              "analysis-E-2000-02-00-000000-g01.h5" "analysis-E-2000-03-00-000000-g01.h5"
-              "analysis-E-2000-04-00-000000-g01.h5"
+yfiles = 1999 1999 1999 1999 1999 1999 1999 2000 2000 2000 2000
+efiles = "analysis-E-1999-06-00-000000-g01.h5" "analysis-E-1999-07-00-000000-g01.h5"
+"analysis-E-1999-08-00-000000-g01.h5" "analysis-E-1999-09-00-000000-g01.h5"
+"analysis-E-1999-10-00-000000-g01.h5" "analysis-E-1999-11-00-000000-g01.h5"
+"analysis-E-1999-12-00-000000-g01.h5" "analysis-E-2000-01-00-000000-g01.h5"
+"analysis-E-2000-02-00-000000-g01.h5" "analysis-E-2000-03-00-000000-g01.h5"
+"analysis-E-2000-04-00-000000-g01.h5"
 
 pft_names  : character vector with names of PFTs
 pft_names <- c("temperate.Early_Hardwood", "temperate.Late_Hardwood")
diff --git a/models/ed/man/read_S_files.Rd b/models/ed/man/read_S_files.Rd
new file mode 100644
index 00000000000..41e709cbfd6
--- /dev/null
+++ b/models/ed/man/read_S_files.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/model2netcdf.ED2.R
+\name{read_S_files}
+\alias{read_S_files}
+\title{S-file contents are not written to standard netcdfs but are used by read_restart
+from SDA's perspective it doesn't make sense to write and read to ncdfs because ED restarts from history files}
+\usage{
+read_S_files(sfile, outdir, pft_names, pecan_names = NULL)
+}
+\arguments{
+\item{sfile}{history file name e.g. "history-S-1961-01-01-000000-g01.h5"}
+
+\item{outdir}{path to run outdir, where the -S- file is}
+
+\item{pft_names}{string vector, names of ED2 pfts in the run, e.g. c("temperate.Early_Hardwood", "temperate.Late_Conifer")}
+
+\item{pecan_names}{string vector, pecan names of requested variables, e.g. c("AGB", "AbvGrndWood")}
+}
+\description{
+S-file contents are not written to standard netcdfs but are used by read_restart
+from SDA's perspective it doesn't make sense to write and read to ncdfs because ED restarts from history files
+}
diff --git a/models/ed/man/read_T_files.Rd b/models/ed/man/read_T_files.Rd
index d8104269d3b..baf333e8af3 100644
--- a/models/ed/man/read_T_files.Rd
+++ b/models/ed/man/read_T_files.Rd
@@ -6,12 +6,16 @@
 \usage{
 read_T_files(yr, yfiles, tfiles, outdir, start_date, end_date, ...)
 }
+\arguments{
+\item{yr}{the year being processed}
+
+\item{yfiles}{the years on the filenames, will be used to matched tfiles for that year}
+}
 \description{
-yr     : the year being processed
-yfiles : the years on the filenames, will be used to matched tfiles for that year
+Function for reading -T- files
 }
 \details{
 e.g.    yr = 1999
-     yfiles = 1999 2000
-     tfiles = "analysis-T-1999-00-00-000000-g01.h5" "analysis-T-2000-00-00-000000-g01.h5"
+yfiles = 1999 2000
+tfiles = "analysis-T-1999-00-00-000000-g01.h5" "analysis-T-2000-00-00-000000-g01.h5"
 }
diff --git a/models/ed/man/read_css.Rd b/models/ed/man/read_css.Rd
new file mode 100644
index 00000000000..38d6efa99d3
--- /dev/null
+++ b/models/ed/man/read_css.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_ed_veg.R
+\name{read_css}
+\alias{read_css}
+\alias{read_pss}
+\alias{read_site}
+\title{Read individual css, pss, and site files}
+\usage{
+read_css(filepath, check = TRUE, ...)
+
+read_pss(filepath, check = TRUE)
+
+read_site(filepath, check = TRUE, ...)
+}
+\arguments{
+\item{filepath}{Full path to css, pss, or site file}
+
+\item{check}{Logical. If \code{TRUE} (default), \link[=check_css]{check} that file is valid.}
+
+\item{...}{Additional arguments to \link[=check_css]{check functions}.}
+}
+\value{
+\code{data.frame} containing
+}
+\description{
+Read files into objects usable by other PEcAn.ED2 utilities, and optionally check for errors.
+}
diff --git a/models/ed/man/read_ed2in.Rd b/models/ed/man/read_ed2in.Rd
new file mode 100644
index 00000000000..1606c12b025
--- /dev/null
+++ b/models/ed/man/read_ed2in.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_ed2in.R
+\name{read_ed2in}
+\alias{read_ed2in}
+\title{Read ED2IN file to named list}
+\usage{
+read_ed2in(filename)
+}
+\arguments{
+\item{filename}{Full path to ED2IN file}
+}
+\value{
+Named list of \code{tag = value}
+}
+\description{
+Parse an ED2IN file to a named list.
+}
diff --git a/models/ed/man/read_ed_metheader.Rd b/models/ed/man/read_ed_metheader.Rd
new file mode 100644
index 00000000000..832c2d3192d
--- /dev/null
+++ b/models/ed/man/read_ed_metheader.Rd
@@ -0,0 +1,61 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_ed_metheader.R
+\name{read_ed_metheader}
+\alias{read_ed_metheader}
+\title{Read ED meteorology header file}
+\usage{
+read_ed_metheader(filename, check = TRUE, check_files = TRUE)
+}
+\arguments{
+\item{filename}{File name (including path) of met driver header file, as
+character}
+
+\item{check}{Logical, whether or not to check file for correctness (default
+= \code{TRUE})}
+
+\item{check_files}{Logical. If \code{TRUE}, perform basic diagnostics on met
+files as well.}
+}
+\value{
+List of ED met input parameters. See Details.
+}
+\description{
+Read a ED_MET_DRIVER_HEADER file into a list-like object that can be
+manipulated within R. Returns a list of file formats.
+}
+\details{
+The output is an unnamed list with each element corresponding to a single
+file format. Each file format contains the following elements:
+\itemize{
+\item \code{path_prefix} -- Path and prefix of files
+\item \code{nlon} -- Number of longitude grid cells
+\item \code{nlat} -- Number of latitude grid cells
+\item \code{dx} -- Size of longitude grid cell
+\item \code{dy} -- Size of latitude grid cell
+\item \code{xmin} -- Minimum longitude
+\item \code{ymin} -- Minimum latitude
+\item \code{variables} -- Data frame of variables, with the columns described below.
+Starred columns are required for writing. This table is left joined with
+\link{met_variable_description} and \link{met_flag_description}.
+\itemize{
+\item \code{variable} -- Variable name
+\item \code{description} -- Variable description
+\item \code{unit} -- Variable unit
+\item \code{update_frequency} -- Update frequency (seconds) or scalar values if
+\code{flag=4}
+\item \code{flag} -- Variable flags.
+\item \code{flag_description} -- Description of variable flag
+}
+}
+
+The formatting of a meteorlogy header file is as follows (from the \link[=https://github.com/EDmodel/ED2/wiki/Drivers]{ED GitHub Wiki}):\preformatted{<number of file formats>    # Repeat lines below this number of times
+<path and prefix of files>
+<nlon>, <nlat>, <dx>, <dy>, <xmin>, <ymin>
+<number of variables>
+<list of variable names>
+<list of update frequencies (seconds) or scalar values if flag=4>
+<list of variable flags>
+}
+
+The variables in the third row are defined as follows:
+}
diff --git a/models/ed/man/read_ed_veg.Rd b/models/ed/man/read_ed_veg.Rd
new file mode 100644
index 00000000000..35a6c315333
--- /dev/null
+++ b/models/ed/man/read_ed_veg.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_ed_veg.R
+\name{read_ed_veg}
+\alias{read_ed_veg}
+\title{Read ED2 vegetation inputs}
+\usage{
+read_ed_veg(path_prefix, latitude = NULL, longitude = NULL,
+  check = TRUE)
+}
+\arguments{
+\item{path_prefix}{Full path and prefix to initial condition files.}
+
+\item{latitude}{Run latitude (default = \code{NULL}). If \code{NULL}, deduced from file name.}
+
+\item{longitude}{Run longitude (default = \code{NULL}). If \code{NULL}, deduced from file name.}
+
+\item{check}{Whether or not to check css, pss, and site files for validity.
+Default = \code{TRUE}.}
+}
+\value{
+List containing \code{css}, \code{pss}, and \code{site} objects, \code{latitude} and
+\code{longitude}, and \code{orig_paths}, a list of paths to the original \code{css}, \code{pss},
+and \code{site} files.
+}
+\description{
+Read ED2 css, pss, and site files into a single ED input object.
+}
diff --git a/models/ed/man/read_restart.ED2.Rd b/models/ed/man/read_restart.ED2.Rd
index 43865a948aa..eff0cdcebd8 100644
--- a/models/ed/man/read_restart.ED2.Rd
+++ b/models/ed/man/read_restart.ED2.Rd
@@ -19,6 +19,9 @@ read_restart.ED2(outdir, runid, stop.time, settings, var.names, params)
 
 \item{params}{Any parameters required for state calculations}
 }
+\description{
+State data assimilation read-restart for ED2
+}
 \examples{
 \dontrun{
   outdir <- "~/sda-hackathon/outputs"
@@ -30,5 +33,5 @@ read_restart.ED2(outdir, runid, stop.time, settings, var.names, params)
 
 }
 \author{
-Alexey Shiklomanov
+Alexey Shiklomanov, Istem Fer
 }
diff --git a/models/ed/man/run_ed_singularity.Rd b/models/ed/man/run_ed_singularity.Rd
new file mode 100644
index 00000000000..7fdb3462d30
--- /dev/null
+++ b/models/ed/man/run_ed_singularity.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_ed_singularity.R
+\name{run_ed_singularity}
+\alias{run_ed_singularity}
+\title{Run ED singularity container}
+\usage{
+run_ed_singularity(img_path, ed2in_path, app = "ED",
+  singularity_args = NULL, ...)
+}
+\arguments{
+\item{img_path}{Path to Singularity container (usually a \code{.simg} file)}
+
+\item{ed2in_path}{Path to ED2IN file.}
+
+\item{app}{Singularity "app" to run. Either "ED" or "EDR".}
+
+\item{singularity_args}{Additional arguments to be passed to \code{singularity run} (before)}
+
+\item{Additional}{arguments to \link[base:system2]{base::system2}}
+}
+\description{
+Uses \link[base:system2]{base::system2} to run ED or EDR via a Singularity container.
+}
+\details{
+On some systems, to run Singularity properly, you will need to bind
+additional paths. To do this, pass the arguments as a character vector to
+\code{singularity_args}. For instance:\preformatted{bindpaths <- c("/scratch", "/data")
+run_ed_singularity(..., singularity_args = paste("--bind", bindpaths))
+}
+
+By default, \link[base:system2]{base::system2} prints the output to the console. To store
+standard ED output in a variable as a character vector, set \code{stdout = TRUE}.
+To redirect all output to the variable, including GCC exceptions, use
+\code{stderr = TRUE} (this will automatically set \code{stdout = TRUE} as well).
+Output can also be redirected to a file via \code{stderr = "/path/to/file.log"}.
+}
diff --git a/models/ed/man/tags2char.Rd b/models/ed/man/tags2char.Rd
new file mode 100644
index 00000000000..455bbd62d69
--- /dev/null
+++ b/models/ed/man/tags2char.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/write_ed2in.R
+\name{tags2char}
+\alias{tags2char}
+\title{Format ED2IN tag-value list}
+\usage{
+tags2char(ed2in)
+}
+\arguments{
+\item{ed2in}{Named list of ED2IN tag-value pairs. See \link{read_ed2in}.}
+}
+\description{
+Converts an \code{ed2in}-like list to an ED2IN-formatted character vector.
+}
diff --git a/models/ed/man/translate_vars_ed.Rd b/models/ed/man/translate_vars_ed.Rd
new file mode 100644
index 00000000000..c0a2c705888
--- /dev/null
+++ b/models/ed/man/translate_vars_ed.Rd
@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/other.helpers.ED2.R
+\name{translate_vars_ed}
+\alias{translate_vars_ed}
+\title{Function translating pecan vars to ED vars
+var.names <- c("DBH", "AGB", "AbvGrndWood")}
+\usage{
+translate_vars_ed(varnames)
+}
+\description{
+Function translating pecan vars to ED vars
+var.names <- c("DBH", "AGB", "AbvGrndWood")
+}
diff --git a/models/ed/man/write.config.ED2.Rd b/models/ed/man/write.config.ED2.Rd
index ed6029b12e1..2bcbe2e8e68 100644
--- a/models/ed/man/write.config.ED2.Rd
+++ b/models/ed/man/write.config.ED2.Rd
@@ -5,7 +5,7 @@
 \title{Write ED configuration files}
 \usage{
 write.config.ED2(trait.values, settings, run.id,
-  defaults = settings$constants)
+  defaults = settings$constants, check = FALSE, ...)
 }
 \arguments{
 \item{trait.values}{Named list of trait values, with names corresponding to PFT}
@@ -15,17 +15,18 @@ write.config.ED2(trait.values, settings, run.id,
 \item{run.id}{id of run}
 
 \item{defaults}{list of defaults to process. Default=settings$constants}
+
+\item{check}{Logical. If \code{TRUE}, check ED2IN validity before running and
+throw an error if anything is wrong (default = \code{FALSE})}
 }
 \value{
 configuration file and ED2IN namelist for given run
 }
 \description{
-Writes an xml and ED2IN config files for use with the Ecological Demography model.
-}
-\details{
-Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create
+Writes an xml and ED2IN config files for use with the Ecological Demography
+model. Requires a pft xml object, a list of trait values for a single model
+run, and the name of the file to create
 }
 \author{
-David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov
+David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov, Istem Fer
 }
diff --git a/models/ed/man/write.config.xml.ED2.Rd b/models/ed/man/write.config.xml.ED2.Rd
index eef6447d27b..fd8f90be6a7 100644
--- a/models/ed/man/write.config.xml.ED2.Rd
+++ b/models/ed/man/write.config.xml.ED2.Rd
@@ -4,7 +4,8 @@
 \alias{write.config.xml.ED2}
 \title{Write ED2 config.xml file}
 \usage{
-write.config.xml.ED2(settings, trait.values, defaults = settings$constants)
+write.config.xml.ED2(settings, trait.values,
+  defaults = settings$constants)
 }
 \arguments{
 \item{settings}{PEcAn settings file. Settings required for this script are: model$revision, model$config.header, constants}
@@ -16,6 +17,9 @@ write.config.xml.ED2(settings, trait.values, defaults = settings$constants)
 \value{
 R XML object containing full ED2 XML file
 }
+\description{
+Write ED2 config.xml file
+}
 \details{
 Refactored by Alexey Shiklomanov to allow use in PEcAn RTM module.
 }
diff --git a/models/ed/man/write_css.Rd b/models/ed/man/write_css.Rd
new file mode 100644
index 00000000000..b580aca4759
--- /dev/null
+++ b/models/ed/man/write_css.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/write_ed_veg.R
+\name{write_css}
+\alias{write_css}
+\alias{write_pss}
+\alias{write_site}
+\title{Write individual ED inputs}
+\usage{
+write_css(css, path_prefix, latitude = NULL, longitude = NULL)
+
+write_pss(pss, path_prefix, latitude = NULL, longitude = NULL)
+
+write_site(site, path_prefix, latitude = NULL, longitude = NULL)
+}
+\arguments{
+\item{css}{css object (see \link{read_css})}
+
+\item{path_prefix}{Desired path and prefix (without latitude and longitude)}
+
+\item{latitude}{Site latitude coordinate (default = \code{NULL})}
+
+\item{longitude}{Site longitude coordinate (default = \code{NULL})}
+
+\item{pss}{pss object (see \link{read_pss})}
+
+\item{site}{site object (see \link{read_site})}
+}
+\value{
+Full file path as character, invisibly
+}
+\description{
+Functions for writing css, pss, and site files from their respective objects.
+}
+\details{
+Latitude and longitude coordinates will be converted directly to character,
+without any changes to their precision. If they are \code{NULL} (default), the
+function assumes that \code{lat} and \code{lon} are already in the \code{path_prefix}, and
+if they are absent, the function will throw an error.
+}
diff --git a/models/ed/man/write_ed2in.Rd b/models/ed/man/write_ed2in.Rd
new file mode 100644
index 00000000000..d51cfd83fba
--- /dev/null
+++ b/models/ed/man/write_ed2in.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/write_ed2in.R
+\name{write_ed2in}
+\alias{write_ed2in}
+\alias{write_ed2in.ed2in}
+\alias{write_ed2in.default}
+\title{Write ED2IN list to file}
+\usage{
+write_ed2in(ed2in, filename, custom_header = character(),
+  barebones = FALSE)
+
+\method{write_ed2in}{ed2in}(ed2in, filename, custom_header = character(),
+  barebones = FALSE)
+
+\method{write_ed2in}{default}(ed2in, filename,
+  custom_header = character(), barebones = FALSE)
+}
+\arguments{
+\item{ed2in}{Named list of ED2IN tag-value pairs. See \link{read_ed2in}.}
+
+\item{filename}{Target file name}
+
+\item{custom_header}{Character vector for additional header comments. Each
+item gets its own line.}
+
+\item{barebones}{Logical. If \code{TRUE}, omit comments and only write tag-value pairs.}
+}
+\description{
+This writes a ED2IN file from an \code{ed2in} list. Default method writes a
+barebones file without comments. S3 method for \code{ed2in} objects extracts
+comments and their locations from the object attributes (if \code{barebones} is
+\code{FALSE}).
+}
diff --git a/models/ed/man/write_ed_metheader.Rd b/models/ed/man/write_ed_metheader.Rd
new file mode 100644
index 00000000000..ad2bcdb8fd5
--- /dev/null
+++ b/models/ed/man/write_ed_metheader.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/write_ed_metheader.R
+\name{write_ed_metheader}
+\alias{write_ed_metheader}
+\title{Write ED meteorlogy header}
+\usage{
+write_ed_metheader(ed_metheader, filename,
+  header_line = shQuote("header"))
+}
+\arguments{
+\item{ed_metheader}{ED meteorlogy header object (see \link{read_ed_metheader})}
+
+\item{filename}{Full file name (including path) of ED met header}
+
+\item{header_line}{Character string for top line of output file. Default is
+\code{'header'}.}
+}
+\description{
+Write ED met driver header from R met driver list object
+}
diff --git a/models/ed/man/write_ed_veg.Rd b/models/ed/man/write_ed_veg.Rd
new file mode 100644
index 00000000000..4066dd368dc
--- /dev/null
+++ b/models/ed/man/write_ed_veg.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/write_ed_veg.R
+\name{write_ed_veg}
+\alias{write_ed_veg}
+\title{Write ED inputs to directory}
+\usage{
+write_ed_veg(ed_veg, path_prefix)
+}
+\arguments{
+\item{ed_veg}{ED vegetation inputs object (see \link{read_ed_veg}).}
+
+\item{path_prefix}{Desired path and prefix (without latitude and longitude)}
+}
+\value{
+Named list (\code{css}, \code{pss}, \code{site}) of full file paths, invisibly
+}
+\description{
+Write a complete \link[=read_ed_veg]{ED inputs object} to disk. \code{css}, \code{pss}, and
+\code{site} files are automatically named and correctly formatted.
+}
diff --git a/models/ed/man/write_restart.ED2.Rd b/models/ed/man/write_restart.ED2.Rd
index 159af30699d..26a6af45122 100644
--- a/models/ed/man/write_restart.ED2.Rd
+++ b/models/ed/man/write_restart.ED2.Rd
@@ -4,18 +4,34 @@
 \alias{write_restart.ED2}
 \title{Write ED2 restart file from SDA results}
 \usage{
-write_restart.ED2(outdir, runid, start.time, stop.time, settings, new.state)
+write_restart.ED2(outdir, runid, start.time, stop.time, settings,
+  new.state, RENAME = TRUE, new.params, inputs)
 }
 \arguments{
+\item{outdir}{outout directory}
+
+\item{runid}{run id}
+
 \item{start.time}{Time of current assimilation step}
 
 \item{stop.time}{Time of next assimilation step}
 
+\item{settings}{pecan settings list}
+
 \item{new.state}{Analysis state matrix returned by \code{sda.enkf}}
+
+\item{RENAME}{flag to either rename output file or not}
+
+\item{new.params}{optional, additionals params to pass write.configs that are deterministically related to the parameters updated by the analysis}
+
+\item{inputs}{new input paths updated by the SDA workflow, will be passed to write.configs}
 }
 \value{
 TRUE if successful
 }
+\description{
+Write ED2 restart file from SDA results
+}
 \author{
-Alexey Shiklomanov
+Alexey Shiklomanov, Istem Fer
 }
diff --git a/models/ed/man/zz.imports.Rd b/models/ed/man/zz.imports.Rd
new file mode 100644
index 00000000000..7feb762ec2b
--- /dev/null
+++ b/models/ed/man/zz.imports.Rd
@@ -0,0 +1,8 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zz.imports.R
+\name{zz.imports}
+\alias{zz.imports}
+\title{Imports from other packages}
+\description{
+Imports from other packages
+}
diff --git a/models/ed/scripts/zero_storage_resp.R b/models/ed/scripts/zero_storage_resp.R
new file mode 100644
index 00000000000..88af1fa0b47
--- /dev/null
+++ b/models/ed/scripts/zero_storage_resp.R
@@ -0,0 +1,11 @@
+histfiles <- list.files("data", "history.*.csv", full.names = TRUE)
+
+str_col <- "storage_turnover_rate"
+
+for (hf in histfiles) {
+  d <- read.table(hf, header = TRUE, sep = ";")
+  if (str_col %in% colnames(d)) {
+    d[, str_col] <- 0
+  }
+  write.table(d, hf, quote = FALSE, sep = ";")
+}
diff --git a/models/ed/tests/test_ed_integration.R b/models/ed/tests/test_ed_integration.R
index eabeb6b2cd1..96c271f7566 100644
--- a/models/ed/tests/test_ed_integration.R
+++ b/models/ed/tests/test_ed_integration.R
@@ -1,4 +1,7 @@
-devtools::load_all("models/ed")
+if(FALSE){
+  devtools::load_all("models/ed")
+  
+  commandArgs <- function(...) "~/pecan/tests/pecan64.ed.xml"
+  source("~/pecan/web/workflow.R")
+}
 
-commandArgs <- function(...) "~/pecan/tests/pecan64.ed.xml"
-source("~/pecan/web/workflow.R")
diff --git a/models/ed/tests/testthat/test.no_storage_resp.R b/models/ed/tests/testthat/test.no_storage_resp.R
new file mode 100644
index 00000000000..3e5b1f15f40
--- /dev/null
+++ b/models/ed/tests/testthat/test.no_storage_resp.R
@@ -0,0 +1,22 @@
+library(testthat)
+
+context("All storage respiration values are zero")
+
+l <- data(package = "PEcAn.ED2")
+histfiles <- grep("history", l$results[, "Item"], value = TRUE)
+myenv <- new.env()
+data(list = histfiles, package = "PEcAn.ED2", envir = myenv)
+
+for (hf in ls(envir = myenv)) {
+  test_that(
+    paste0("History file '", hf, "' has zero storage respiration."),
+    {
+      d <- get(hf, envir = myenv)
+      srcol <- grepl("storage", colnames(d))
+      if (any(srcol)) {
+        srvals <- d[, srcol]
+        expect_true(all(srvals == 0))
+      }
+    }
+  )
+}
diff --git a/models/ed/vignettes/running_ed_from_R.Rmd b/models/ed/vignettes/running_ed_from_R.Rmd
new file mode 100644
index 00000000000..a367d63d49d
--- /dev/null
+++ b/models/ed/vignettes/running_ed_from_R.Rmd
@@ -0,0 +1,193 @@
+---
+title: "Running ED from R"
+author: "Alexey Shiklomanov"
+---
+
+# Introduction
+
+The `PEcAn.ED2` package features a number of utilities to facilitate running the ED model from inside R, including
+working with input files,
+running the ED executable,
+and processing the outputs.
+This tutorial describes these utilites and provides examples of common use cases.
+
+# Basic ED run
+
+## Installing the R package
+
+The `PEcAn.ED2` package and its PEcAn dependencies can be installed from GitHub as follows (all CRAN package dependencies should be installed automatically):
+
+```{r install, eval = -(1:5)}
+devtools::install_github("pecanproject/pecan", ref = "develop", subdir = "base/logger")
+devtools::install_github("pecanproject/pecan", ref = "develop", subdir = "base/utils")
+devtools::install_github("pecanproject/pecan", ref = "develop", subdir = "base/settings")
+devtools::install_github("pecanproject/pecan", ref = "develop", subdir = "modules/data.atmosphere")
+devtools::install_github("pecanproject/pecan", ref = "develop", subdir = "models/ed")
+
+library(PEcAn.ED2)
+```
+
+## Installing the ED2 model
+
+The source code for the ED2 model is available [on GitHub](https://github.com/edmodel/ed2).
+
+Alternatively, if you have [Singularity](https://singularity.lbl.gov) container software installed, you can use a pre-built Singularity container available on [Singularity Hub](https://www.singularity-hub.org/collections/642):
+
+```
+singularity pull --name ed2.simg shub://ashiklom/ED2
+```
+
+## ED inputs
+
+### EDI
+
+ED requires a global land use database to determine its land-sea mask, as well as a vegetation "thermal sums" database.
+These can be customized to some extent, but this package provides a version of the most common inputs.
+These inputs, stored in an "EDI" directory, can be downloaded via the `download_edi` function:
+
+```{r get_edi}
+library(here)
+rundir <- here("vignettes", "ed_run_data")
+dir.create(rundir, showWarnings = FALSE)
+
+edi_dir <- file.path(rundir, "EDI")
+if (!file.exists(edi_dir)) {
+  download_edi(edi_dir)
+} else {
+  message("EDI directory already exists. Skipping download.")
+}
+```
+
+### Meteorological data
+
+To do the ED run described here, we'll need some meteorological data.
+ED meteorological data are typically stored in HDF5 format and are described by a plain text header file (typically called `ED_MET_DRIVER_HEADER`).
+
+To download the meteorological data, we'll use the `PEcAn.data.atmosphere` package.
+Here, we grab the data for the first week of July 2005 and Harvard Forest, for which we'll be running the simulation.
+
+```{r, download_met}
+start_date <- "2006-07-01"
+end_date <- "2006-07-08"
+latitude <- 42.53
+longitude <- -72.19
+
+raw_met <- PEcAn.data.atmosphere::download.CRUNCEP(
+  outfolder = file.path(rundir, "raw_met"),
+  start_date = start_date,
+  end_date = start_date,
+  site_id = NULL,
+  lat.in = latitude,
+  lon.in = longitude
+)
+```
+
+Next, we convert this raw data to the ED-specific format.
+
+```{r, met2model}
+ed_met <- met2model.ED2(
+  in.path = dirname(raw_met$file),
+  in.prefix = "CRUNCEP",
+  outfolder = file.path(rundir, "ed_met"),
+  start_date = start_date,
+  end_date = start_date,
+  lat = latitude,
+  lon = longitude,
+  overwrite = TRUE
+)
+```
+
+If you already have ED-specific meteorology available, `PEcAn.ED2` provides utilities to interact with that file directly:
+
+```{r met_driver, eval = FALSE}
+met_driver_raw <- "/path/to/ED_MET_DRIVER_HEADER"
+met_driver_obj <- read_ed_metheader(met_driver_raw, check = FALSE)
+met_driver_obj[[1]]$path_prefix <- "/path/to/new/location"
+met_driver_obj[[1]]$xmin <- -90
+met_driver_obj[[1]]$ymin <- 43
+
+met_driver_path <- file.path(rundir, "ED_MET_DRIVER_HEADER")
+write_ed_metheader(met_driver_obj, met_driver_path)
+```
+
+### Vegetation inputs
+
+A common way to initialize ED is through three interrelated vegetation initial condition files:
+
+* `css` -- Cohort file, which describes all plant cohorts located within a patch, including its PFT, DBH, and stand density
+* `pss` -- Patch file, which describes each patch within a site (single, plot-scale runs will often have only one patch)
+* `site` -- Site file, which describes each site (single, plot-scale runs will often have only one site)
+
+The package ships with simple functional examples of these objects (`example_css/pss/site`) and functions for quickly creating custom objects based on these examples (`create_css/pss/site`).
+Below, we create a `css` file with a single PFT with a specific DBH, but stick to the unmodified example `pss` and `site` files.
+
+```{r, veg_inputs}
+css <- create_css(list(pft = 11, dbh = 18.00))
+pss <- example_pss
+site <- example_site
+veg_input <- create_ed_veg(css, pss, site, latitude, longitude, check = TRUE)
+
+veg_prefix <- file.path(rundir, "veg_input", "test_veg")
+write_ed_veg(veg_input, veg_prefix)
+```
+
+As with meteorology, `PEcAn.ED2` also provides utilities for working with existing vegetation inputs.
+
+```{r veg_input, eval = FALSE}
+veg_prefix <- "/path/to/site/files/prefix"
+latitude <- 43.3724
+longitude <- -89.9071
+veg_input <- read_ed_veg(veg_prefix, latitude = latitude, longitude = longitude)
+```
+
+### ED configuration file
+
+Now that all inputs are taken care of, the final step is to create the ED configuration file (typically called `ED2IN`).
+
+First, read a `ED2IN` template file:
+
+```{r read_ed2in}
+ed2in_raw <- read_ed2in(system.file("ED2IN.rgit", package = "PEcAn.ED2"))
+```
+
+Then, set up the `ED2IN` with the required components.
+
+```{r modify_ed2in}
+ed2in <- modify_ed2in(
+  ed2in_raw,
+  veg_prefix = veg_prefix,
+  latitude = latitude,
+  longitude = longitude,
+  met_driver = ed_met$file,
+  EDI_path = file.path(rundir, "EDI"),
+  start_date = start_date,
+  end_date = end_date,
+  run_dir = file.path(rundir, "run"),
+  output_dir = file.path(rundir, "out"),
+  runtype = "INITIAL",
+  EXPNME = "ED test run"
+)
+```
+
+It is also a good idea to check the `ED2IN` file for internal consistency.
+
+```{r check_ed2in}
+check_ed2in(ed2in)
+```
+
+Assuming the `ed2in` object is valid, you then write it to a file to a desired directory.
+This doesn't have to be the run directory (nor does the file have to be named `ED2IN`), but it's a good idea to keep the `ED2IN` file close to the run outputs, as it provides useful metadata for the run.
+
+```{r write_ed2in}
+ed2in_path <- file.path(rundir, "ED2IN")
+write_ed2in(ed2in, ed2in_path)
+```
+
+### Running ED
+
+Assuming all of the inputs are correct, running ED is as simple as calling the `run_ed_singularity` function, which requires paths to the Singularity image and ED2IN file.
+
+```{r start_ed_run, eval = FALSE}
+img_path <- "~/Projects/ED2/ed2.simg"
+run_ed_singularity(img_path, ed2in_path)
+```
diff --git a/models/fates/DESCRIPTION b/models/fates/DESCRIPTION
index 1eaba6180f8..feb2433ab1c 100644
--- a/models/fates/DESCRIPTION
+++ b/models/fates/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.FATES
 Type: Package
 Title: PEcAn package for integration of FATES model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
@@ -24,4 +24,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/fates/R/model2netcdf.FATES.R b/models/fates/R/model2netcdf.FATES.R
index 09fb319ee2b..4eede2a3394 100644
--- a/models/fates/R/model2netcdf.FATES.R
+++ b/models/fates/R/model2netcdf.FATES.R
@@ -53,6 +53,7 @@ model2netcdf.FATES <- function(outdir) {
     files <- dir(outdir, "*clm2.h0.*.nc", full.names = TRUE)
     file.dates <- as.Date(sub(".nc", "", sub(".*clm2.h0.", "", files)))
     years <- lubridate::year(file.dates)
+    init_year <- unique(years)[1]
 
     ## Loop over years
     for (year in unique(years)) {
@@ -84,11 +85,11 @@ model2netcdf.FATES <- function(outdir) {
         sitelat <- ncdf4::ncvar_get(ncin,"lat")
         sitelon <- ncdf4::ncvar_get(ncin,"lon")
         ## time variable based on internal calc, nc$dim$time is the FATES output time
-        t <- ncdim_def(name = "time", units = paste0("days since ", year, "-01-01 00:00:00"),
-                       vals = as.vector(time), calendar = "standard", 
+        t <- ncdf4::ncdim_def(name = "time", units = paste0("days since ", init_year, "-01-01 00:00:00"),
+                       vals = as.vector(time), calendar = "noleap", 
                        unlim = TRUE)  # a direct analog of internal FATES output dim "time"
-        lat <- ncdim_def("lat", "degrees_north", vals = as.numeric(sitelat), longname = "coordinate_latitude")
-        lon <- ncdim_def("lon", "degrees_east", vals = as.numeric(sitelon), longname = "coordinate_longitude")
+        lat <- ncdf4::ncdim_def("lat", "degrees_north", vals = as.numeric(sitelat), longname = "coordinate_latitude")
+        lon <- ncdf4::ncdim_def("lon", "degrees_east", vals = as.numeric(sitelon), longname = "coordinate_longitude")
         xyt <- list(lon, lat, t)
         
         ### build netCDF data
diff --git a/models/fates/man/met2model.FATES.Rd b/models/fates/man/met2model.FATES.Rd
index b245826ebb8..3aae31813f6 100644
--- a/models/fates/man/met2model.FATES.Rd
+++ b/models/fates/man/met2model.FATES.Rd
@@ -4,8 +4,8 @@
 \alias{met2model.FATES}
 \title{met2model for FATES}
 \usage{
-met2model.FATES(in.path, in.prefix, outfolder, start_date, end_date, lst = 0,
-  lat, lon, overwrite = FALSE, verbose = FALSE, ...)
+met2model.FATES(in.path, in.prefix, outfolder, start_date, end_date,
+  lst = 0, lat, lon, overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
 \item{in.path}{location on disk where inputs are stored}
diff --git a/models/fates/man/model2netcdf.FATES.Rd b/models/fates/man/model2netcdf.FATES.Rd
index 5555c597cbf..b1338622936 100644
--- a/models/fates/man/model2netcdf.FATES.Rd
+++ b/models/fates/man/model2netcdf.FATES.Rd
@@ -9,6 +9,9 @@ model2netcdf.FATES(outdir)
 \arguments{
 \item{outdir}{Location of FATES model output}
 }
+\description{
+Code to convert FATES netcdf output into into CF standard
+}
 \examples{
  
 \dontrun{
diff --git a/models/gday/DESCRIPTION b/models/gday/DESCRIPTION
index 6857d5a2bb8..bfe722814cd 100644
--- a/models/gday/DESCRIPTION
+++ b/models/gday/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.GDAY
 Type: Package
 Title: PEcAn package for integration of the GDAY model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Martin De Kauwe
 Maintainer: Martin De Kauwe <mdekauwe@gmail.com>
 Description: This module provides functions to link the GDAY model to PEcAn.
@@ -21,4 +21,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: TRUE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/jules/DESCRIPTION b/models/jules/DESCRIPTION
index 4d8aa015caa..999a2883315 100644
--- a/models/jules/DESCRIPTION
+++ b/models/jules/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.JULES
 Type: Package
 Title: PEcAn package for integration of the JULES model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: This module provides functions to link the (JULES) to PEcAn.
@@ -21,4 +21,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/linkages/DESCRIPTION b/models/linkages/DESCRIPTION
index b70f7bd752d..a8250d06bd1 100644
--- a/models/linkages/DESCRIPTION
+++ b/models/linkages/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.LINKAGES
 Type: Package
 Title: PEcAn package for integration of the LINKAGES model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Ann Raiho, Mike Dietze
 Maintainer: Ann Raiho <araiho@nd.edu>
 Description: This module provides functions to link the (LINKAGES) to PEcAn.
@@ -23,5 +23,6 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
 Remotes: araiho/linkages_package
diff --git a/models/linkages/R/met2model.LINKAGES.R b/models/linkages/R/met2model.LINKAGES.R
index 3cbc2af19f9..075389d3eab 100644
--- a/models/linkages/R/met2model.LINKAGES.R
+++ b/models/linkages/R/met2model.LINKAGES.R
@@ -112,6 +112,8 @@ met2model.LINKAGES <- function(in.path, in.prefix, outfolder, start_date, end_da
 
   precip.mat <- month_matrix_precip
   temp.mat <- month_matrix_temp_mean
+  rownames(temp.mat) <- start_year:end_year
+  rownames(precip.mat) <- start_year:end_year
   save(precip.mat, temp.mat, file = out.file)
   return(invisible(results))
 } # met2model.LINKAGES
diff --git a/models/linkages/R/read_restart.LINKAGES.R b/models/linkages/R/read_restart.LINKAGES.R
index bf911a381d4..83e56c5e82b 100644
--- a/models/linkages/R/read_restart.LINKAGES.R
+++ b/models/linkages/R/read_restart.LINKAGES.R
@@ -36,29 +36,36 @@ read_restart.LINKAGES <- function(outdir, runid, stop.time, settings, var.names
   for (i in seq_along(settings$pfts)) {
     pft.names[i] <- settings$pfts[i]$pft$name
   }
-  ens.pft.names <- grep("pft", names(ens))
-  names(ens[[grep("pft", names(ens))]]) <- pft.names
+  #ens.pft.names <- grep("pft", names(ens))
+  #names(ens[[grep("pft", names(ens))]]) <- pft.names
   
   forecast <- list()
 
+  if ("Fcomp" %in% var.names) {
+    forecast[[length(forecast)+1]] <- ens$AGB.pft #already has C  #* unit.conv 
+    names(forecast[[length(forecast)+1]]) <- paste0('Fcomp.',pft.names)
+  }
+  
   if ("AGB.pft" %in% var.names) {
-    forecast[[1]] <- ens$AGB.pft #already has C  #* unit.conv 
-    names(forecast[[1]]) <- paste0('AGB.pft.',pft.names)
+    forecast[[length(forecast)+1]] <- ens$AGB.pft #already has C  #* unit.conv 
+    names(forecast[[length(forecast)+1]]) <- paste0('AGB.pft.',pft.names)
   }
     
   if ("TotSoilCarb" %in% var.names) {
-    forecast[[2]] <- udunits2::ud.convert(ens$TotSoilCarb, "kg/m^2", "Mg/ha") #* unit.conv 
-    names(forecast[[2]]) <- c("TotSoilCarb")
+    forecast[[length(forecast)+1]] <- ens$TotSoilCarb #udunits2::ud.convert(ens$TotSoilCarb, "kg/m^2", "Mg/ha") #* unit.conv 
+    names(forecast[[length(forecast)+1]]) <- c("TotSoilCarb")
   }
   
   }else{
     forecast <- list()
     if ("AGB.pft" %in% var.names) {
-      forecast[[1]] <- rep(NA,length(settings$pfts))
+      forecast[[length(forecast)+1]] <- rep(NA,length(settings$pfts))
+    }
+    if ("Fcomp" %in% var.names) {
+      forecast[[length(forecast)+1]] <- rep(NA,length(settings$pfts)) #already has C  #* unit.conv
     }
-    
     if ("TotSoilCarb" %in% var.names) {
-      forecast[[2]] <- NA
+      forecast[[length(forecast)+1]] <- NA
     }
   }
   # Put forecast into vector
diff --git a/models/linkages/R/write.config.LINKAGES.R b/models/linkages/R/write.config.LINKAGES.R
index c8604840d69..ce851f5d3e4 100644
--- a/models/linkages/R/write.config.LINKAGES.R
+++ b/models/linkages/R/write.config.LINKAGES.R
@@ -55,10 +55,11 @@ write.config.LINKAGES <- function(defaults = NULL, trait.values, settings, run.i
   
   iplot <- 1
   nyear <- length(year)
+  max.ind <- 1500
+  plat <- abs(as.numeric(settings$run$site$lat))
+  
   bgs <- 120
   egs <- 273
-  max.ind <- 15000
-  plat <- abs(as.numeric(settings$run$site$lat))
   
   texture <- read.csv(system.file("texture.csv", package = "PEcAn.LINKAGES"))
   
@@ -81,7 +82,7 @@ write.config.LINKAGES <- function(defaults = NULL, trait.values, settings, run.i
     soils <- db.query(paste("SELECT soil,som,sand_pct,clay_pct,soilnotes FROM sites WHERE id =", settings$run$site$id), 
                       con = dbcon)
     
-    soil.dat <- PEcAn.data.land::soil_params(sand = soils$sand_pct/100, clay = soils$clay_pct/100)
+    soil.dat <- PEcAn.data.land::soil_params(sand = soils$sand_pct/100, clay = soils$clay_pct/100, silt = 100 - soils$sand_pct - soils$clay_pct)
     
     fc <- soil.dat$volume_fraction_of_water_in_soil_at_field_capacity * 100
     dry <- soil.dat$volume_fraction_of_condensed_water_in_soil_at_wilting_point * 100
@@ -96,10 +97,9 @@ write.config.LINKAGES <- function(defaults = NULL, trait.values, settings, run.i
   
   climate_file <- settings$run$inputs$met$path
   load(climate_file)
-  #temp.mat <- temp.mat[start.year:end.year - start.year + 1, ]
-  temp.mat <- temp.mat[which(temp.mat[,13]%in%start.year:end.year),]
-  precip.mat <- precip.mat[which( precip.mat[,13]%in%start.year:end.year),]
-  #precip.mat <- precip.mat[start.year:end.year - start.year + 1, ]
+  
+  temp.mat <- temp.mat[which(rownames(temp.mat)%in%start.year:end.year),]
+  precip.mat <- precip.mat[which(rownames(precip.mat)%in%start.year:end.year),]
   
   basesc <- 74
   basesn <- 1.64
@@ -156,8 +156,8 @@ write.config.LINKAGES <- function(defaults = NULL, trait.values, settings, run.i
           if ("AGEMX" %in% names(vals)) {
             spp.params[spp.params$Spp_Name == group, ]$AGEMX <- vals$AGEMX
           }
-          if ("Gmax" %in% names(vals)) {
-            spp.params[spp.params$Spp_Name == group, ]$G <- vals$Gmax
+          if ("G" %in% names(vals)) {
+            spp.params[spp.params$Spp_Name == group, ]$G <- vals$G
           }
           if ("SPRTND" %in% names(vals)) {
             spp.params[spp.params$Spp_Name == group, ]$SPRTND <- vals$SPRTND
@@ -175,7 +175,7 @@ write.config.LINKAGES <- function(defaults = NULL, trait.values, settings, run.i
             spp.params[spp.params$Spp_Name == group, ]$D3 <- vals$D3
           }
           if ("FROST" %in% names(vals)) {
-             spp.params[spp.params$Spp_Name == group, ]$FROST <- vals$FROST
+            spp.params[spp.params$Spp_Name == group, ]$FROST <- vals$FROST
           }
           if ("CM1" %in% names(vals)) {
             spp.params[spp.params$Spp_Name == group, ]$CM1 <- vals$CM1
diff --git a/models/linkages/R/write_restart.LINKAGES.R b/models/linkages/R/write_restart.LINKAGES.R
index 145ac77db66..01095374239 100644
--- a/models/linkages/R/write_restart.LINKAGES.R
+++ b/models/linkages/R/write_restart.LINKAGES.R
@@ -30,7 +30,8 @@
 # outdir, runid, time, settings, new.state, variables, sample_parameters = FALSE, trait.values =
 # NA,met=NULL,RENAME = TRUE
 
-write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time, settings, new.state, 
+write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time,
+                                   settings, new.state, 
                                    RENAME = TRUE, new.params, inputs) {
   
   ### TO DO : needs to be vectorized to improve SDA speed for runs that are longer than 50 years
@@ -40,18 +41,15 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time, setting
   new.state[new.state < 0] <- 0
   
   names.keep <- names(new.state)
-  
   new.state <- as.matrix(new.state)
-  
   names(new.state) <- names.keep
   
-  if(sum(new.state)>1000) {
-    prop.stop <- new.state/sum(new.state)
-    new.state <- 1000 * prop.stop
-  }
   new.state.save <- new.state
-  new.state <- new.state.save[grep("pft", names(new.state.save))]
-  new.state.other <- new.state.save[grep("pft", names(new.state.save), invert = TRUE)]
+  
+  if(grep('Fcomp',names.keep)){
+    new.state <- new.state.save[grep("Fcomp", names(new.state.save))]
+    new.state.other <- new.state.save[grep("Fcomp", names(new.state.save), invert = TRUE)]
+  }
   
   variables <- names(new.state)
   ### Going to need to change this... ### Get some expert opinion
@@ -217,7 +215,7 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time, setting
   
   #making sure to stick with density dependence rules in linkages (< 198 trees per 800/m^2)
   #someday we could think about estimating this parameter from data
-  if(sum(new.ntrees) > 198) new.ntrees <- round((new.ntrees / sum(new.ntrees)) * runif(1,160,195))
+  if(sum(new.ntrees) > 98) new.ntrees <- round((new.ntrees / sum(new.ntrees)) * runif(1,95,98))
   
   print(paste0("new.ntrees =", new.ntrees))
   
@@ -226,9 +224,11 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time, setting
     new.n.index <- c(new.n.index, rep(i, new.ntrees[i]))
   }
   
-  dbh.temp <- numeric(200)
-  iage.temp <- numeric(200)
-  nogro.temp <- numeric(200)
+  n.ind <- 100
+  
+  dbh.temp <- numeric(n.ind)
+  iage.temp <- numeric(n.ind)
+  nogro.temp <- numeric(n.ind)
   
   # sample from individuals to construct new states
   for (s in seq_len(nspec)) {
@@ -290,8 +290,9 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time, setting
     
     b_obs[nl:nu] <- biomass_function(dbh.temp[nl:nu], 
                                      spp.biomass.params = spp.biomass.params) * as.numeric(bcorr[s])
+    bMax <- 200
     for (j in nl:nu) {
-      dbh.temp[j] <- optimize(merit, c(1, 200), b_obs = b_obs[j], 
+      dbh.temp[j] <- optimize(merit, c(1, bMax), b_obs = b_obs[j], 
                               spp.biomass.params = spp.biomass.params)$minimum
     }
     
@@ -304,7 +305,7 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time, setting
   iage <- iage.temp
   nogro <- nogro.temp  # numeric(200)#hack
   
-  nogro[nogro < (-2)] <- 1
+  #nogro[nogro < 1] <- 1
   
   ntrees <- new.ntrees
   
@@ -325,12 +326,16 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time, setting
   # optimize(merit, c(0,200),b_obs=b_obs)$minimum } } nu <- nl + ntrees[n] - 1 nl <- nu + 1 }
   
   ##### SOIL
-  if ("TotSoilCarb" %in% variables) {
+  if ("TotSoilCarb" %in% names(new.state.other)) {
     leaf.sum <- sum(tyl[1:12]) * 0.48
+    if(new.state.other["TotSoilCarb"] > 1000) new.state.other["TotSoilCarb"] = rnorm(1,1000,10)
     soil.org.mat <- new.state.other["TotSoilCarb"] - leaf.sum
-    soil.corr <- soil.org.mat/(sum(C.mat[C.mat[, 5], 1]) * 0.48)
-    C.mat[C.mat[, 5], 1] <- C.mat[C.mat[, 5], 1] * as.numeric(soil.corr)
-  }
+    soil.corr <- soil.org.mat / (sum(C.mat[C.mat[1:ncohrt, 5], 1]) * 0.48)
+    #if(soil.corr > 1) soil.corr <- 1
+    C.mat[C.mat[1:ncohrt, 5], 1] <- C.mat[C.mat[1:ncohrt, 5], 1] * as.numeric(soil.corr)
+    C.mat[is.na(C.mat[1:ncohrt,1]),1] <- 0
+    C.mat[C.mat[1:ncohrt,1] < 0,1] <- 0
+    }
   
   if (RENAME) {
     file.rename(file.path(settings$rundir, runid, "linkages.restart.Rdata"), 
@@ -343,8 +348,8 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time, setting
   
   # make a new settings with the right years min start date and end date - fail in informative way
   
-  settings$run$start.date <- paste0(start.time + 1, "/01/01")
-  settings$run$end.date <- paste0(stop.time + 1, "/12/31")
+  settings$run$start.date <- paste0(formatC(year(start.time + 1), width = 4, format = "d", flag = "0"), "/01/01")
+  settings$run$end.date <- paste0(formatC(year(stop.time), width = 4, format = "d", flag = "0"), "/12/31")
   
   do.call(write.config.LINKAGES, 
           args = list(trait.values = new.params, settings = settings, run.id = runid, 
diff --git a/models/linkages/man/read_restart.LINKAGES.Rd b/models/linkages/man/read_restart.LINKAGES.Rd
index 05c7511a35d..94b123f13bb 100644
--- a/models/linkages/man/read_restart.LINKAGES.Rd
+++ b/models/linkages/man/read_restart.LINKAGES.Rd
@@ -4,8 +4,8 @@
 \alias{read_restart.LINKAGES}
 \title{read_restart.LINKAGES}
 \usage{
-read_restart.LINKAGES(outdir, runid, stop.time, settings, var.names = NULL,
-  params = NULL)
+read_restart.LINKAGES(outdir, runid, stop.time, settings,
+  var.names = NULL, params = NULL)
 }
 \arguments{
 \item{outdir}{output directory}
diff --git a/models/lpjguess/DESCRIPTION b/models/lpjguess/DESCRIPTION
index 53e94e85ad6..63662202437 100644
--- a/models/lpjguess/DESCRIPTION
+++ b/models/lpjguess/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.LPJGUESS
 Type: Package
 Title: PEcAn package for integration of the LPJ-GUESS model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Istem Fer, Tony Gardella
 Maintainer: Istem Fer <fer.istem@gmail.com>
 Description: This module provides functions to link LPJ-GUESS to PEcAn.
@@ -21,4 +21,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/lpjguess/man/write.insfile.LPJGUESS.Rd b/models/lpjguess/man/write.insfile.LPJGUESS.Rd
index 4fdb588d0c2..6ad5a57f5c0 100644
--- a/models/lpjguess/man/write.insfile.LPJGUESS.Rd
+++ b/models/lpjguess/man/write.insfile.LPJGUESS.Rd
@@ -20,6 +20,9 @@ write.insfile.LPJGUESS(settings, trait.values, rundir, outdir, run.id)
 \value{
 settings Updated list
 }
+\description{
+Write LPJ-GUESS instruction script
+}
 \author{
 Istem Fer
 }
diff --git a/models/maat/DESCRIPTION b/models/maat/DESCRIPTION
index 6adfc5d9298..3dc1d63c9f7 100644
--- a/models/maat/DESCRIPTION
+++ b/models/maat/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.MAAT
 Type: Package
 Title: PEcAn package for integration of the MAAT model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Shawn Serbin, Anthony Walker
 Maintainer: Shawn Serbin <sserbin@bnl.gov>
 Description: This module provides functions to link the MAAT to PEcAn.
@@ -23,4 +23,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/maespa/DESCRIPTION b/models/maespa/DESCRIPTION
index 4b39cba0e6d..8916a00a37b 100644
--- a/models/maespa/DESCRIPTION
+++ b/models/maespa/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.MAESPA
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis using MAESPA
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Tony Gardella
 Maintainer: Tony Gardella <tonygard@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
@@ -30,4 +30,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Require: 
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/preles/DESCRIPTION b/models/preles/DESCRIPTION
index cf7f6e8aaf8..d0fd1d1a143 100644
--- a/models/preles/DESCRIPTION
+++ b/models/preles/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.PRELES
 Type: Package
 Title: PEcAn package for integration of the PRELES model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Tony Gardella, Mike Dietze
 Maintainer: Tony Gardella <tonygard@bu.edu>
 Description: This module provides functions to run the PREdict Light use
@@ -30,4 +30,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/preles/man/runPRELES.jobsh.Rd b/models/preles/man/runPRELES.jobsh.Rd
index f32c7e27f56..c85e859d2f0 100644
--- a/models/preles/man/runPRELES.jobsh.Rd
+++ b/models/preles/man/runPRELES.jobsh.Rd
@@ -18,6 +18,9 @@ runPRELES.jobsh(met.file, outdir, parameters, sitelat, sitelon, start.date,
 
 \item{end_date}{End time of the simulation}
 }
+\description{
+Function to process ncdf file, run PRELES model, and convert output .nc file in CF standard
+}
 \author{
 Tony Gardella, Michael Dietze
 }
diff --git a/models/sipnet/DESCRIPTION b/models/sipnet/DESCRIPTION
index b266e56987c..3f7ae2eb590 100644
--- a/models/sipnet/DESCRIPTION
+++ b/models/sipnet/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.SIPNET
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
@@ -28,5 +28,6 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
+Encoding: UTF-8
 Require: 
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
diff --git a/models/sipnet/R/met2model.SIPNET.R b/models/sipnet/R/met2model.SIPNET.R
index f70ad93954a..c5d4bc51c12 100644
--- a/models/sipnet/R/met2model.SIPNET.R
+++ b/models/sipnet/R/met2model.SIPNET.R
@@ -18,21 +18,50 @@
 ##' @title met2model.SIPNET
 ##' @export
 ##' @param in.path location on disk where inputs are stored
-##' @param in.prefix prefix of input and output files
+##' @param in.prefix prefix of input and output files OR the full file name if year.fragment = TRUE
 ##' @param outfolder location on disk where outputs will be stored
 ##' @param start_date the start date of the data to be downloaded (will only use the year part of the date)
 ##' @param end_date the end date of the data to be downloaded (will only use the year part of the date)
 ##' @param overwrite should existing files be overwritten
 ##' @param verbose should the function be very verbose
+##' @param year.fragment the function should ignore whether or not the data is stored as a set of complete years (such as for forecasts).
+##' @param in.prefix a data file to use for input - default behavior is to use all MET.year.nc files within the start and end year 
+##' range in the directory in.path.  If not null, overrides default behavior.
+##' @author Luke Dramko, Michael Dietze, Alexey Shiklomanov, Rob Kooper
 met2model.SIPNET <- function(in.path, in.prefix, outfolder, start_date, end_date,
-                             overwrite = FALSE, verbose = FALSE, ...) {
+                             overwrite = FALSE, verbose = FALSE, year.fragment = FALSE, ...) {
+  
   PEcAn.logger::logger.info("START met2model.SIPNET")
   start_date <- as.POSIXlt(start_date, tz = "UTC")
   end_date <- as.POSIXlt(end_date, tz = "UTC")
-  out.file <- paste(in.prefix, strptime(start_date, "%Y-%m-%d"),
-                    strptime(end_date, "%Y-%m-%d"),
-                    "clim",
-                    sep = ".")
+  if (year.fragment) { # in.prefix is not guaranteed to contain the file extension.
+    escaped <- gsub("(\\W)", "\\\\\\1", in.prefix) # The file name may contain special characters that could mess up the regular expression.
+    matching_files <- grep(escaped, list.files(in.path), value=TRUE) 
+    if (length(matching_files) == 0) {
+      PEcAn.logger::logger.severe(paste0("No files found matching ", in.prefix, "; cannot process data."))
+    }
+    
+    # This function is supposed to process netcdf files, so we'll search for files the the extension .nc and use those first.
+    nc_file = grep("\\.nc$", matching_files)
+    if (length(nc_file) > 0) {
+      if (grepl("\\.nc$", in.prefix)) {
+        out.file <- sub("\\.nc$", ".clim", in.prefix)
+      } else {
+        out.file <- paste0(in.prefix, ".clim")
+        in.prefix <- paste0(in.prefix, ".nc")
+      }
+    } else { # no .nc files found... it could be that the extension was left off, or some other problem
+      PEcAn.logger::logger.warn("No files found with extension '.nc'.  Using the first file in the list below:")
+      PEcAn.logger::logger.warn(matching_files)
+      in.prefix <- matching_files[i]
+    }
+  } else { # Default behavior
+    out.file <- paste(in.prefix, strptime(start_date, "%Y-%m-%d"),
+                      strptime(end_date, "%Y-%m-%d"),
+                      "clim",
+                      sep = ".")
+  }
+  
   out.file.full <- file.path(outfolder, out.file)
 
   results <- data.frame(file = out.file.full,
@@ -44,7 +73,7 @@ met2model.SIPNET <- function(in.path, in.prefix, outfolder, start_date, end_date
                         dbfile.name = out.file,
                         stringsAsFactors = FALSE)
   PEcAn.logger::logger.info("internal results")
-  print(results)
+  PEcAn.logger::logger.info(results)
 
   if (file.exists(out.file.full) && !overwrite) {
     PEcAn.logger::logger.debug("File '", out.file.full, "' already exists, skipping to next file.")
@@ -59,8 +88,14 @@ met2model.SIPNET <- function(in.path, in.prefix, outfolder, start_date, end_date
   out <- NULL
 
   # get start/end year since inputs are specified on year basis
+  # only if year.fragment = FALSE
   start_year <- lubridate::year(start_date)
-  end_year <- lubridate::year(end_date)
+  if (year.fragment) {
+    end_year <- lubridate::year(start_date) # Start year is listed twice because there's only one file. start_year and end_year only control
+                                            # the loop and file name, which are overriden for year.fragment
+  } else {
+    end_year <- lubridate::year(end_date)
+  }
 
   ## loop over files
   for (year in start_year:end_year) {
@@ -69,8 +104,12 @@ met2model.SIPNET <- function(in.path, in.prefix, outfolder, start_date, end_date
     PEcAn.logger::logger.info(year)
 
     diy <- PEcAn.utils::days_in_year(year)
-
-    old.file <- file.path(in.path, paste(in.prefix, year, "nc", sep = "."))
+    
+    if (!year.fragment) { # default behavior
+        old.file <- file.path(in.path, paste(in.prefix, year, "nc", sep = "."))
+    } else { # Use the supplied file name
+        old.file <- file.path(in.path, in.prefix)
+    }
 
     if (file.exists(old.file)) {
       ## open netcdf
@@ -79,8 +118,16 @@ met2model.SIPNET <- function(in.path, in.prefix, outfolder, start_date, end_date
       ## convert time to seconds
       sec <- nc$dim$time$vals
       sec <- udunits2::ud.convert(sec, unlist(strsplit(nc$dim$time$units, " "))[1], "seconds")
-
-      dt <- PEcAn.utils::seconds_in_year(year) / length(sec)
+      
+      # Calculate the delta time.  If using whole-year data, the appropriate length in seconds is 
+      # fetched; otherwise, it is assumed that the length of time provided in the time dimension of
+      # the input file is correct.
+      if (year.fragment) {
+        dt <- mean(diff(sec), na.rm=TRUE)
+        
+      } else {
+        dt <- PEcAn.utils::seconds_in_year(year) / length(sec)
+      }
       tstep <- round(86400 / dt)
       dt <- 86400 / tstep
 
@@ -110,7 +157,7 @@ met2model.SIPNET <- function(in.path, in.prefix, outfolder, start_date, end_date
 
       soilT <- try(ncdf4::ncvar_get(nc, "soil_temperature"))
       if (!is.numeric(soilT)) {
-        # approximation borrowed from SIPNET CRUNCEPpreprocessing's tsoil.py
+        # approximation borrowed from SIPNET CRUNCEP preprocessing's tsoil.py
         tau <- 15 * tstep
         filt <- exp(-(1:length(Tair)) / tau)
         filt <- (filt / sum(filt))
@@ -204,8 +251,9 @@ met2model.SIPNET <- function(in.path, in.prefix, outfolder, start_date, end_date
       tmp[hr.na, 4] <- tmp[hr.na - 1, 4] + dt/86400 * 24
     }
 
-    ##filter out days not included in start or end date
-    if(year == start_year){
+    ## filter out days not included in start or end date if not a year fragment. (This procedure would be nonsensible for a year
+    ## fragment, as it would filter out all of the days.)
+    if(year == start_year && !year.fragment){
       extra.days <- length(as.Date(paste0(start_year, "-01-01")):as.Date(start_date)) #extra days length includes the start date
       if (extra.days > 1){
         PEcAn.logger::logger.info("Subsetting SIPNET met to match start date")
@@ -213,7 +261,7 @@ met2model.SIPNET <- function(in.path, in.prefix, outfolder, start_date, end_date
         tmp <- tmp[start.row:nrow(tmp),]
       }
     }
-    if (year == end_year){
+    if (year == end_year && !year.fragment){
       if(year == start_year){
         extra.days  <- length(as.Date(start_date):as.Date(end_date))
         if (extra.days > 1){
diff --git a/models/sipnet/R/write.configs.SIPNET.R b/models/sipnet/R/write.configs.SIPNET.R
index 96ef340ec63..c3f4eba477e 100644
--- a/models/sipnet/R/write.configs.SIPNET.R
+++ b/models/sipnet/R/write.configs.SIPNET.R
@@ -15,19 +15,22 @@
 ##' @author Michael Dietze
 write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs = NULL, IC = NULL,
                                 restart = NULL, spinup = NULL) {
+  
   ### WRITE sipnet.in
   template.in <- system.file("sipnet.in", package = "PEcAn.SIPNET")
   config.text <- readLines(con = template.in, n = -1)
   writeLines(config.text, con = file.path(settings$rundir, run.id, "sipnet.in"))
 
   ### WRITE *.clim
-  template.clim <- settings$run$input$met$path  ## read from settings #typo in inputs?
+  template.clim <- settings$run$inputs$met$path  ## read from settings
   if (!is.null(inputs)) {
     ## override if specified in inputs
     if ("met" %in% names(inputs)) {
       template.clim <- inputs$met$path
     }
   }
+  
+  PEcAn.logger::logger.info(paste0("Writing SIPNET configs with input ", template.clim))
 
   # find out where to write run/ouput
   rundir <- file.path(settings$host$rundir, as.character(run.id))
diff --git a/models/sipnet/R/write_restart.SIPNET.R b/models/sipnet/R/write_restart.SIPNET.R
index 194bb3c4d9a..d2120e5529b 100644
--- a/models/sipnet/R/write_restart.SIPNET.R
+++ b/models/sipnet/R/write_restart.SIPNET.R
@@ -31,7 +31,6 @@ write_restart.SIPNET <- function(outdir, runid, start.time, stop.time, settings,
 
   rundir <- settings$host$rundir
   variables <- colnames(new.state)
-
   # values that will be used for updating other states deterministically depending on the SDA states
   IC_extra <- data.frame(t(new.params$restart))
   
diff --git a/models/sipnet/inst/template.job b/models/sipnet/inst/template.job
index ac491ec41a4..bc2d0b82550 100644
--- a/models/sipnet/inst/template.job
+++ b/models/sipnet/inst/template.job
@@ -30,7 +30,7 @@ if [ ! -e "@OUTDIR@/sipnet.out" ]; then
   # convert to MsTMIP
   echo "require (PEcAn.SIPNET)
     model2netcdf.SIPNET('@OUTDIR@', @SITE_LAT@, @SITE_LON@, '@START_DATE@', '@END_DATE@', @DELETE.RAW@, '@REVISION@')
-    " | R --vanilla
+    " | R --no-save
 fi
 
 # copy readme with specs to output
diff --git a/models/sipnet/man/met2model.SIPNET.Rd b/models/sipnet/man/met2model.SIPNET.Rd
index 32aaa240572..ad741df7bef 100644
--- a/models/sipnet/man/met2model.SIPNET.Rd
+++ b/models/sipnet/man/met2model.SIPNET.Rd
@@ -5,12 +5,12 @@
 \title{met2model.SIPNET}
 \usage{
 met2model.SIPNET(in.path, in.prefix, outfolder, start_date, end_date,
-  overwrite = FALSE, verbose = FALSE, ...)
+  overwrite = FALSE, verbose = FALSE, year.fragment = FALSE, ...)
 }
 \arguments{
 \item{in.path}{location on disk where inputs are stored}
 
-\item{in.prefix}{prefix of input and output files}
+\item{in.prefix}{prefix of input and output files OR the full file name if year.fragment = TRUE}
 
 \item{outfolder}{location on disk where outputs will be stored}
 
@@ -21,7 +21,15 @@ met2model.SIPNET(in.path, in.prefix, outfolder, start_date, end_date,
 \item{overwrite}{should existing files be overwritten}
 
 \item{verbose}{should the function be very verbose}
+
+\item{year.fragment}{the function should ignore whether or not the data is stored as a set of complete years (such as for forecasts).}
+
+\item{in.prefix}{a data file to use for input - default behavior is to use all MET.year.nc files within the start and end year 
+range in the directory in.path.  If not null, overrides default behavior.}
 }
 \description{
 met2model wrapper for SIPNET
 }
+\author{
+Luke Dramko, Michael Dietze, Alexey Shiklomanov, Rob Kooper
+}
diff --git a/models/sipnet/man/model2netcdf.SIPNET.Rd b/models/sipnet/man/model2netcdf.SIPNET.Rd
index c22676ab97c..e6aca9ebc46 100644
--- a/models/sipnet/man/model2netcdf.SIPNET.Rd
+++ b/models/sipnet/man/model2netcdf.SIPNET.Rd
@@ -4,8 +4,8 @@
 \alias{model2netcdf.SIPNET}
 \title{Function to convert SIPNET model output to standard netCDF format}
 \usage{
-model2netcdf.SIPNET(outdir, sitelat, sitelon, start_date, end_date, delete.raw,
-  revision, overwrite = FALSE)
+model2netcdf.SIPNET(outdir, sitelat, sitelon, start_date, end_date,
+  delete.raw, revision, overwrite = FALSE)
 }
 \arguments{
 \item{outdir}{Location of SIPNET model output}
diff --git a/models/sipnet/man/write.config.SIPNET.Rd b/models/sipnet/man/write.config.SIPNET.Rd
index cd04816396a..c16850cc6da 100644
--- a/models/sipnet/man/write.config.SIPNET.Rd
+++ b/models/sipnet/man/write.config.SIPNET.Rd
@@ -4,8 +4,8 @@
 \alias{write.config.SIPNET}
 \title{Writes a configuration files for SIPNET model}
 \usage{
-write.config.SIPNET(defaults, trait.values, settings, run.id, inputs = NULL,
-  IC = NULL, restart = NULL, spinup = NULL)
+write.config.SIPNET(defaults, trait.values, settings, run.id,
+  inputs = NULL, IC = NULL, restart = NULL, spinup = NULL)
 }
 \description{
 Writes a configuration files for your model
diff --git a/models/sipnet/man/write_restart.SIPNET.Rd b/models/sipnet/man/write_restart.SIPNET.Rd
index de341227793..eea1ee45f5f 100644
--- a/models/sipnet/man/write_restart.SIPNET.Rd
+++ b/models/sipnet/man/write_restart.SIPNET.Rd
@@ -4,8 +4,8 @@
 \alias{write_restart.SIPNET}
 \title{write_restart.SIPNET}
 \usage{
-write_restart.SIPNET(outdir, runid, start.time, stop.time, settings, new.state,
-  RENAME = TRUE, new.params = FALSE, inputs)
+write_restart.SIPNET(outdir, runid, start.time, stop.time, settings,
+  new.state, RENAME = TRUE, new.params = FALSE, inputs)
 }
 \arguments{
 \item{outdir}{output directory}
diff --git a/models/template/DESCRIPTION b/models/template/DESCRIPTION
index cfd37e19a01..8decc752fa0 100644
--- a/models/template/DESCRIPTION
+++ b/models/template/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.ModelName
 Type: Package
 Title: PEcAn package for integration of the ModelName model
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: John Doe, Jane Doe
 Maintainer: John Doe <jdoe@illinois.edu>
 Description: This module provides functions to link the (ModelName) to PEcAn.
@@ -17,4 +17,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/models/template/R/write_restart.ModelName.R b/models/template/R/write_restart.ModelName.R
index e51d89dbb72..eceed0450a1 100644
--- a/models/template/R/write_restart.ModelName.R
+++ b/models/template/R/write_restart.ModelName.R
@@ -2,10 +2,15 @@
 #' 
 #' @author Alexey Shiklomanov
 #' 
+#' @param outdir       outout directory
+#' @param runid        run id  
 #' @param start.time   Time of current assimilation step 
 #' @param stop.time    Time of next assimilation step
+#' @param settings     pecan settings list
 #' @param new.state    Analysis state matrix returned by \code{sda.enkf}
-#' @inheritParams read.restart.ModelName
+#' @param RENAME       flag to either rename output file or not
+#' @param new.params   optional, additionals params to pass write.configs that are deterministically related to the parameters updated by the analysis 
+#' @param inputs       new input paths updated by the SDA workflow, will be passed to write.configs
 #' 
 #' @description Write restart files for model
 #' 
@@ -15,4 +20,7 @@ write_restart.ModelName <- function(outdir,
                                     start.time,
                                     stop.time,
                                     settings,
-                                    new.state) {}
+                                    new.state,
+                                    RENAME,
+                                    new.params,
+                                    inputs) {}
diff --git a/models/template/man/read_restart.ModelName.Rd b/models/template/man/read_restart.ModelName.Rd
index b8c518b4b70..9a3792ff612 100644
--- a/models/template/man/read_restart.ModelName.Rd
+++ b/models/template/man/read_restart.ModelName.Rd
@@ -4,7 +4,8 @@
 \alias{read_restart.ModelName}
 \title{Read restart template for SDA}
 \usage{
-read_restart.ModelName(outdir, runid, stop.time, settings, var.names, params)
+read_restart.ModelName(outdir, runid, stop.time, settings, var.names,
+  params)
 }
 \arguments{
 \item{outdir}{Output directory}
diff --git a/models/template/man/write_restart.ModelName.Rd b/models/template/man/write_restart.ModelName.Rd
index 17d4ed7235a..78d0a4ecd62 100644
--- a/models/template/man/write_restart.ModelName.Rd
+++ b/models/template/man/write_restart.ModelName.Rd
@@ -5,14 +5,26 @@
 \title{Write restart template for SDA}
 \usage{
 write_restart.ModelName(outdir, runid, start.time, stop.time, settings,
-  new.state)
+  new.state, RENAME, new.params, inputs)
 }
 \arguments{
+\item{outdir}{outout directory}
+
+\item{runid}{run id}
+
 \item{start.time}{Time of current assimilation step}
 
 \item{stop.time}{Time of next assimilation step}
 
+\item{settings}{pecan settings list}
+
 \item{new.state}{Analysis state matrix returned by \code{sda.enkf}}
+
+\item{RENAME}{flag to either rename output file or not}
+
+\item{new.params}{optional, additionals params to pass write.configs that are deterministically related to the parameters updated by the analysis}
+
+\item{inputs}{new input paths updated by the SDA workflow, will be passed to write.configs}
 }
 \description{
 Write restart files for model
diff --git a/modules/allometry/DESCRIPTION b/modules/allometry/DESCRIPTION
index bc2cedd1d2a..79180830908 100644
--- a/modules/allometry/DESCRIPTION
+++ b/modules/allometry/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.allometry
 Type: Package
 Title: PEcAn allometry functions
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze <dietze@bu.edu>
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: Synthesize allometric equations or fit allometries to data
@@ -22,4 +22,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/allometry/man/AllomAve.Rd b/modules/allometry/man/AllomAve.Rd
index 2ac51a21e87..90dce68be2e 100644
--- a/modules/allometry/man/AllomAve.Rd
+++ b/modules/allometry/man/AllomAve.Rd
@@ -4,9 +4,10 @@
 \alias{AllomAve}
 \title{AllomAve}
 \usage{
-AllomAve(pfts, components = 6, outdir = NULL, con = NULL, field = NULL,
-  parm = system.file("data/Table3_GTR-NE-319.v2.csv", package =
-  "PEcAn.allometry"), ngibbs = 5000, nchain = 3, dmin = 0.1, dmax = 500)
+AllomAve(pfts, components = 6, outdir = NULL, con = NULL,
+  field = NULL, parm = system.file("data/Table3_GTR-NE-319.v2.csv",
+  package = "PEcAn.allometry"), ngibbs = 5000, nchain = 3,
+  dmin = 0.1, dmax = 500)
 }
 \arguments{
 \item{pfts}{pft list from PEcAn settings (if con) OR list of pft spcd's
diff --git a/modules/assim.batch/DESCRIPTION b/modules/assim.batch/DESCRIPTION
index 0d57c494e8a..ad52c26cd70 100644
--- a/modules/assim.batch/DESCRIPTION
+++ b/modules/assim.batch/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.assim.batch
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
@@ -37,4 +37,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/assim.batch/NAMESPACE b/modules/assim.batch/NAMESPACE
index 630ac2f28ba..cca9ea728d1 100644
--- a/modules/assim.batch/NAMESPACE
+++ b/modules/assim.batch/NAMESPACE
@@ -38,6 +38,7 @@ export(pda.settings.bt)
 export(return.bias)
 export(return_hyperpars)
 export(runModule.assim.batch)
+export(sample_MCMC)
 export(write_sf_posterior)
 import(IDPmisc)
 import(ellipse)
diff --git a/modules/assim.batch/R/pda.emulator.R b/modules/assim.batch/R/pda.emulator.R
index 84eec0e80db..ecec05461d9 100644
--- a/modules/assim.batch/R/pda.emulator.R
+++ b/modules/assim.batch/R/pda.emulator.R
@@ -52,11 +52,6 @@ pda.emulator <- function(settings, external.data = NULL, external.priors = NULL,
     prior.id=prior.id, chain=chain, iter=iter, adapt=adapt, 
     adj.min=adj.min, ar.target=ar.target, jvar=jvar, n.knot=n.knot, run.round)
   
-  ## history restart
-  pda.restart.file <- file.path(settings$outdir,paste0("history.pda",
-                                                       settings$assim.batch$ensemble.id, ".Rdata"))
-  current.step <- "START" 
-  
   ## will be used to check if multiplicative Gaussian is requested
   any.mgauss <- sapply(settings$assim.batch$inputs, `[[`, "likelihood")
   isbias <- which(unlist(any.mgauss) == "multipGauss")
@@ -65,6 +60,9 @@ pda.emulator <- function(settings, external.data = NULL, external.priors = NULL,
   any.scaling <- sapply(settings$assim.batch$param.names, `[[`, "scaling")
   sf <- unique(unlist(any.scaling))
   
+  # used in rounds only
+  pass2bias <- NULL
+  
   ## Open database connection
   if (settings$database$bety$write) {
     con <- try(db.open(settings$database$bety), silent = TRUE)
@@ -138,6 +136,10 @@ pda.emulator <- function(settings, external.data = NULL, external.priors = NULL,
   ## Create an ensemble id
   settings$assim.batch$ensemble.id <- pda.create.ensemble(settings, con, workflow.id)
   
+  ## history restart
+  pda.restart.file <- file.path(settings$outdir,paste0("history.pda",
+                                                       settings$assim.batch$ensemble.id, ".Rdata"))
+  current.step <- "START" 
   
   ## Set up likelihood functions
   llik.fn <- pda.define.llik.fn(settings)
@@ -178,72 +180,29 @@ pda.emulator <- function(settings, external.data = NULL, external.priors = NULL,
   ## Run this block if this is a "round" extension
   if (run.round) {
     
-    # loads the posteriors of the the previous emulator run
-    temp.round <- pda.load.priors(settings, con, run.round)
-    prior.round.list <- temp.round$prior
-    
-    
-    prior.round.fn <- lapply(prior.round.list, pda.define.prior.fn)
-    
-    ## Propose a percentage (if not specified 80%) of the new parameter knots from the posterior of the previous run
+    ## Propose a percentage (if not specified 90%) of the new parameter knots from the posterior of the previous run
     knot.par        <- ifelse(!is.null(settings$assim.batch$knot.par),
                               as.numeric(settings$assim.batch$knot.par),
-                              0.8)
+                              0.9)
     
     n.post.knots    <- floor(knot.par * settings$assim.batch$n.knot)
     
-    if(!is.null(sf)){
-      load(settings$assim.batch$sf.path)
-      sf.round.post <- pda.define.prior.fn(sf.post.distns)
-      rm(sf.post.distns)
-      n.sf <- length(sf)
-      sf.round.list <- pda.generate.knots(n.post.knots,
-                                          sf = NULL, probs.sf = NULL,
-                                          n.param.all = n.sf,
-                                          prior.ind = seq_len(n.sf),
-                                          prior.fn = sf.round.post, 
-                                          pname = paste0(sf, "_SF"))
-      probs.round.sf     <- sf.round.list$params
-    }else {
-      probs.round.sf     <- NULL
-    }
-    
-    ## set prior distribution functions for posterior of the previous emulator run
-    ## need to do two things here: 
-    ## 1) for non-SF parameters, use the posterior of previous emulator
-    knots.list.nonsf <- lapply(seq_along(settings$pfts),
-                              function(x) pda.generate.knots(n.post.knots,
-                                                             sf, probs.round.sf,
-                                                             n.param.all[x],
-                                                             prior.ind.orig[[x]],
-                                                             prior.round.fn[[x]],
-                                                             pname[[x]]))
-    
-    knots.params.nonsf <- lapply(knots.list.nonsf, `[[`, "params")
-    
-    ## 2) for SF parameters use the posterior sf-values but on the prior of the actual params
-    knots.list.sf <- lapply(seq_along(settings$pfts),
-                               function(x) pda.generate.knots(n.post.knots,
-                                                              sf, probs.round.sf,
-                                                              n.param.all[x],
-                                                              prior.ind.orig[[x]],
-                                                              prior.fn[[x]], # note the difference
-                                                              pname[[x]]))
-    
-    knots.params.sf <- lapply(knots.list.sf, `[[`, "params")
-    
-    
-    knots.params.temp <- knots.params.nonsf
+    # trim down, as a placeholder
+    knots.params.temp <- lapply(knots.params, function(x) x[1:n.post.knots, ])
     
     if(!is.null(sf)){
-      # get new proposals for non-sf and sf together
-      for(i in seq_along(settings$pfts)){
-        if(!is.null(any.scaling[[i]])){
-          knots.params.temp[[i]] <- knots.params.sf[[i]]
-        }
-      }
+      load(settings$assim.batch$sf.samp)
+    }else{
+      sf.samp <- NULL
     }
-    
+    sampled_knots <- sample_MCMC(settings$assim.batch$mcmc.path, n.param.orig, prior.ind.orig, 
+                                     n.post.knots, knots.params.temp,
+                                     prior.list, prior.fn, sf, sf.samp)
+
+    knots.params.temp <- sampled_knots$knots.params.temp
+    probs.round.sf    <- sampled_knots$sf_knots
+    pass2bias         <- sampled_knots$pass2bias
+
     # mixture of knots
     mix.knots <- sample(settings$assim.batch$n.knot, (settings$assim.batch$n.knot - n.post.knots))
     for (i in seq_along(settings$pfts)) {
@@ -257,8 +216,6 @@ pda.emulator <- function(settings, external.data = NULL, external.priors = NULL,
     }
     
     knots.params <- lapply(knots.list, `[[`, "params")
-    # don't need anymore
-    # knots.probs  <- lapply(knots.list, `[[`, "probs")
     
     current.step <- "Generate Knots: round-if block"
     save(list = ls(all.names = TRUE),envir=environment(),file=pda.restart.file)
@@ -302,17 +259,16 @@ pda.emulator <- function(settings, external.data = NULL, external.priors = NULL,
     
     # handle bias parameters if multiplicative Gaussian is listed in the likelihoods
     if(any(unlist(any.mgauss) == "multipGauss")) {
-      # how many bias parameters per dataset requested
-      nbias <- ifelse(is.null(settings$assim.batch$inputs[[isbias]]$nbias), 1,
-                      as.numeric(settings$assim.batch$inputs[[isbias]]$nbias))
-      bias.list <- return.bias(isbias, model.out, inputs, prior.list, nbias, run.round, settings$assim.batch$bias.path)
+      bias.list  <- return.bias(settings, isbias, model.out, inputs, prior.list, run.round, pass2bias)
       bias.terms <- bias.list$bias.params
       prior.list <- bias.list$prior.list.bias
-      prior.fn <- lapply(prior.list, pda.define.prior.fn)
+      nbias      <- bias.list$nbias
+      prior.fn   <- lapply(prior.list, pda.define.prior.fn)
     } else {
       bias.terms <- NULL
     }
     
+    
     for (i in seq_len(settings$assim.batch$n.knot)) {
       if(!is.null(bias.terms)){
         all.bias <- lapply(bias.terms, function(n) n[i,])
@@ -379,12 +335,10 @@ pda.emulator <- function(settings, external.data = NULL, external.priors = NULL,
     for(inputi in seq_len(n.input)){
       error.statistics[[inputi]] <- sapply(pda.errors,`[[`, inputi)
       
-      if(unlist(any.mgauss)[inputi] == "multipGauss") {
+     if(unlist(any.mgauss)[inputi] == "multipGauss") {
         
         # if yes, then we need to include bias term in the emulator
-        #bias.probs <- bias.list$bias.probs
-        #biases <- c(t(bias.probs[[bc]]))
-        bias.params <- bias.list$bias.params
+        bias.params <- bias.terms
         biases <- c(t(bias.params[[bc]]))
         bc <- bc + 1
         
@@ -498,26 +452,31 @@ pda.emulator <- function(settings, external.data = NULL, external.priors = NULL,
   prior.fn.all <- pda.define.prior.fn(prior.all)
   
   # define range to make sure mcmc.GP doesn't propose new values outside
-  rng <- matrix(c(sapply(prior.fn.all$qprior[prior.ind.all], eval, list(p = 1e-05)),
-                  sapply(prior.fn.all$qprior[prior.ind.all], eval, list(p = 0.99999))),
-                nrow = sum(n.param))
+  
+  # NOTE: this will need to change when there is more than one bias parameter
+  # but then, there are other things that needs to change in the emulator workflow
+  # such as the way proposed parameters are used in estimation in get_ss function
+  # so punting this development until it is needed
+  rng <-  t(apply(SS[[isbias]][,-ncol(SS[[isbias]])], 2, range))
   
   if (run.normal | run.round) {
     
     resume.list <- list()
     
+    # start from knots
+    indx <- sample(seq_len(settings$assim.batch$n.knot), settings$assim.batch$chain)
+    
     for (c in seq_len(settings$assim.batch$chain)) {
       jmp.list[[c]] <- sapply(prior.fn.all$qprior, 
                               function(x) 0.1 * diff(eval(x, list(p = c(0.05, 0.95)))))[prior.ind.all]
       jmp.list[[c]] <- sqrt(jmp.list[[c]])
       
-      init.x <- lapply(prior.ind.all, function(v) eval(prior.fn.all$rprior[[v]], list(n = 1)))
-      names(init.x) <- rownames(prior.all)[prior.ind.all]
-      init.list[[c]] <- init.x
+      init.list[[c]] <- as.list(SS[[isbias]][indx[c], -ncol(SS[[isbias]])])
       resume.list[[c]] <- NA
     }
   }
   
+
   if (!is.null(settings$assim.batch$mix)) {
     mix <- settings$assim.batch$mix
   } else if (sum(n.param) > 1) {
@@ -682,12 +641,15 @@ pda.emulator <- function(settings, external.data = NULL, external.priors = NULL,
   
   # save sf posterior
   if(!is.null(sf)){
-    sf.filename <- file.path(settings$outdir, 
+    sf.post.filename <- file.path(settings$outdir, 
                              paste0("post.distns.pda.sf", "_", settings$assim.batch$ensemble.id, ".Rdata"))
+    sf.samp.filename <- file.path(settings$outdir, 
+                             paste0("samples.pda.sf", "_", settings$assim.batch$ensemble.id, ".Rdata"))
     sf.prior <- prior.list[[sf.ind]]
-    sf.post.distns <- write_sf_posterior(sf.samp.list, sf.prior, sf.filename)
-    save(sf.post.distns, file = sf.filename)
-    settings$assim.batch$sf.path <- sf.filename
+    sf.post.distns <- write_sf_posterior(sf.samp.list, sf.prior, sf.samp.filename)
+    save(sf.post.distns, file = sf.post.filename)
+    settings$assim.batch$sf.path <- sf.post.filename
+    settings$assim.batch$sf.samp <- sf.samp.filename
   }
   
   # Separate each PFT's parameter samples (and bias term) to their own list
diff --git a/modules/assim.batch/R/pda.get.model.output.R b/modules/assim.batch/R/pda.get.model.output.R
index 6848fa386cc..23dd3b2d8a7 100644
--- a/modules/assim.batch/R/pda.get.model.output.R
+++ b/modules/assim.batch/R/pda.get.model.output.R
@@ -112,7 +112,7 @@ pda.get.model.output <- function(settings, run.id, bety, inputs) {
     # seq.POSIXt returns class "POSIXct"
     # the model output is since the beginning of the year but 'settings$run$start.date' may not be the first day of the year, using lubridate::floor_date
     if(diff(model.secs)[1] != 0){
-      model$posix <- seq.POSIXt(from = as.POSIXlt(settings$run$start.date, tz="GMT"), by = diff(model.secs)[1], length.out = length(model$time))
+      model$posix <- seq.POSIXt(from = as.POSIXlt(settings$run$start.date, tz="GMT"), by = round(diff(model.secs)[1]), length.out = length(model$time))
     }else{
       # yearly output
       model$posix <- seq.POSIXt(from = as.POSIXlt(settings$run$start.date, tz="GMT"), by = "year", length.out = length(model$time))
diff --git a/modules/assim.batch/R/pda.postprocess.R b/modules/assim.batch/R/pda.postprocess.R
index 79da0a28d34..2f09caaa724 100644
--- a/modules/assim.batch/R/pda.postprocess.R
+++ b/modules/assim.batch/R/pda.postprocess.R
@@ -226,10 +226,13 @@ pda.plot.params <- function(settings, mcmc.param.list, prior.ind, par.file.name
 
 ##' Function to write posterior distributions of the scaling factors
 ##' @export
-write_sf_posterior <- function(sf.samp.list, sf.prior, sf.filename){
+write_sf_posterior <- function(sf.samp.list, sf.prior, sf.samp.filename){
   
   sf.samp <- as.mcmc.list(lapply(sf.samp.list, mcmc))
   
+  # saving this before discarding burnin, because in resampling we want to keep the samples together
+  save(sf.samp, file = sf.samp.filename)
+  
   burnin <- getBurnin(sf.samp, method = "gelman.plot")
   
   sf.samp <- window(sf.samp, start = max(burnin, na.rm = TRUE))
@@ -238,13 +241,12 @@ write_sf_posterior <- function(sf.samp.list, sf.prior, sf.filename){
   sf.subset.list <- list()
   sf.subset.list[[1]] <- as.data.frame(do.call("rbind", sf.samp))
 
-  filename.flag <- gsub(".*post.distns\\s*|.Rdata.*", "", basename(sf.filename))
+  filename.flag <- paste0("_", basename(sf.samp.filename))
   
   sf.post.distns <- PEcAn.MA::approx.posterior(trait.mcmc = sf.subset.list[[1]], priors = sf.prior,
-                                               outdir = dirname(sf.filename),
+                                               outdir = dirname(sf.samp.filename),
                                                filename.flag = filename.flag)
   
-  save(sf.subset.list, file = file.path(dirname(sf.filename), paste0("samples", filename.flag, ".Rdata")))
   
   return(sf.post.distns)
   
diff --git a/modules/assim.batch/R/pda.utils.R b/modules/assim.batch/R/pda.utils.R
index 99ce798cac6..94ad553f906 100644
--- a/modules/assim.batch/R/pda.utils.R
+++ b/modules/assim.batch/R/pda.utils.R
@@ -487,7 +487,7 @@ pda.init.run <- function(settings, con, my.write.config, workflow.id, params,
     ## write config
     do.call(my.write.config, args = list(defaults = settings$pfts, 
                                          trait.values = lapply(params, 
-                                                               function(x, n) { x[n, ] },
+                                                               function(x, n) { as.data.frame(x[n, , drop=FALSE]) },
                                                                n = i), 
                                          settings = settings, 
                                          run.id = run.ids[i]))
@@ -668,20 +668,50 @@ pda.generate.sf <- function(n.knot, sf, prior.list){
 
 
 ##' @title return.bias
+##' @param settings settings list
+##' @param isbias bias variable index
+##' @param model.out model output list
+##' @param inputs inputs list
+##' @param prior.list.bias prior list, bias prior to be added
+##' @param run.round extension flag
+##' @param pass2bias if this is another round, this is re-sampled MCMC samples, will go with the rest of model params
+##' 
 ##' @author Istem Fer
 ##' @export
-return.bias <- function(isbias, model.out, inputs, prior.list.bias, nbias, run.round = FALSE, prev.bias = NULL){
+return.bias <- function(settings, isbias, model.out, inputs, prior.list.bias, run.round = FALSE, pass2bias = NULL){
+  
+  # how many bias parameters per dataset requested
+  nbias <- ifelse(is.null(settings$assim.batch$inputs[[isbias]]$nbias), 1,
+                  as.numeric(settings$assim.batch$inputs[[isbias]]$nbias))
+
+  prev.bias <- settings$assim.batch$bias.path
+  
+  # to store priors
+  bprior <- data.frame(distn  = rep(NA,length(isbias)),
+                       parama = rep(NA,length(isbias)),
+                       paramb = rep(NA,length(isbias)),
+                       n      = rep(NA,length(isbias)))
+  for(b in seq_along(isbias)){
+    # any prior passed via settings?
+    if(!is.null(settings$assim.batch$inputs[[isbias]]$bprior)){
+      bprior$distn[b]  <- settings$assim.batch$inputs[[isbias[b]]]$bprior$distn
+      bprior$parama[b] <- settings$assim.batch$inputs[[isbias[b]]]$bprior$parama
+      bprior$paramb[b] <- settings$assim.batch$inputs[[isbias[b]]]$bprior$paramb
+    }else{ # assume log-normal(0,1)
+      PEcAn.logger::logger.info(paste0("No prior is defined for the bias parameter, assuming standard log-normal"))
+      bprior$distn[b]  <- "lnorm"
+      bprior$parama[b] <- 0
+      bprior$paramb[b] <- 1
+    }
+  }
+  bias.prior <- bprior
   
   # there can be more than one multiplicative Gaussian requested
   ibias <- length(isbias)
   
   # to store bias parameters and probabilitied
   bias.params <- bias.probs <- list()
-  # to store priors
-  bias.prior <- data.frame(distn = rep("unif", ibias), 
-                           parama = rep(NA, ibias), 
-                           paramb = rep(NA, ibias),  
-                           n =rep(NA, ibias), stringsAsFactors=FALSE)
+
   prior.names <- rep(NA, ibias)
   
   for(i in seq_along(isbias)){
@@ -702,39 +732,22 @@ return.bias <- function(isbias, model.out, inputs, prior.list.bias, nbias, run.r
       }
     }
     
-    bias.prior$parama[i] <- min(bias.params[[i]], na.rm = TRUE) - sd(bias.params[[i]], na.rm = TRUE)
-    bias.prior$paramb[i] <- max(bias.params[[i]], na.rm = TRUE) + sd(bias.params[[i]], na.rm = TRUE)
-    
     prior.names[i] <- paste0("bias.", sapply(model.out[[1]],names)[isbias[i]])
     names(bias.params)[i] <- paste0("bias.", sapply(model.out[[1]],names)[isbias[i]])
   }
   
   rownames(bias.prior) <- prior.names
   prior.list.bias[[(length(prior.list.bias)+1)]] <- bias.prior
-  
-  # convert params to probs for GPfit 
-  # note: there can be new parameters out of previous min/max if this is a round extension
-  bias.probs <- lapply(seq_along(isbias), 
-                       function(b) punif(bias.params[[b]], 
-                                         prior.list.bias[[length(prior.list.bias)]]$parama[b], 
-                                         prior.list.bias[[length(prior.list.bias)]]$paramb[b]))
-  
-  
+
   # if this is another round, use the first priors
   if(run.round){
     load(prev.bias)
     prior.list.bias <- prior.list
-    
-    # convert params to probs for GPfit 
-    # note: there can be new parameters out of previous min/max if this is a round extension
-    bias.probs <- lapply(seq_along(isbias), 
-                         function(b) punif(bias.params[[b]], 
-                                           prior.list.bias[[length(prior.list.bias)]]$parama[b], 
-                                           prior.list.bias[[length(prior.list.bias)]]$paramb[b]))
-    
+    # TODO: implementation for multiple bias params, this requires multiple changes int he PDA workflow
+    bias.params[[1]][(nrow(bias.params[[1]])-length(pass2bias)+1):nrow(bias.params[[1]]), 1] <- pass2bias
   }
   
-  return(list(bias.params = bias.params, bias.probs = bias.probs, prior.list.bias = prior.list.bias))
+  return(list(bias.params = bias.params, prior.list.bias = prior.list.bias, nbias = nbias))
   
 } # return.bias
 
@@ -754,7 +767,7 @@ return_hyperpars <- function(assim.settings, inputs){
     for(k in seq_along(assim.settings$inputs)){
       hyper.pars[[k]] <- list()
       hyper.pars[[k]]$parama <- 0.001
-      hyper.pars[[k]]$paramb <- 0.001 * mean(inputs[[k]]$data[,1], na.rm = TRUE) ^ 2
+      hyper.pars[[k]]$paramb <- 0.001 * var(inputs[[k]]$data[,1], na.rm = TRUE)
     }
     
   }else{
@@ -765,7 +778,7 @@ return_hyperpars <- function(assim.settings, inputs){
       if(is.null(check.hypers[[k]])){
         hyper.pars[[k]] <- list()
         hyper.pars[[k]]$parama <- 0.001
-        hyper.pars[[k]]$paramb <- 0.001 * mean(inputs[[k]]$data[,1], na.rm = TRUE) ^ 2
+        hyper.pars[[k]]$paramb <- 0.001 * var(inputs[[k]]$data[,1], na.rm = TRUE)
       }else{
         hyper.pars[[k]] <- list()
         hyper.pars[[k]]$parama <- as.numeric(assim.settings$inputs[[k]]$hyper.pars$parama)
@@ -778,3 +791,99 @@ return_hyperpars <- function(assim.settings, inputs){
   
   return(hyper.pars)
 } # return_hyperpars
+
+
+##' Helper function to sample from previous MCMC chain while proposing new knots
+##' 
+##' @param mcmc_path path to previous emulator mcmc samples object
+##' @param n.param.orig vector, number of parameters targeted in each (pft) sublist
+##' @param prior.ind.orig list, actual indices of parameters targeted in each (pft) sublist
+##' @param n.post.knots number of new samples requested
+##' @param knots.params.temp list of parameter samples proposed from the original PDA-prior
+##' @param prior.list PDA-prior list
+##' @param prior.fn list for parameter d/r/q/p functions
+##' @param sf SF parameter names
+##' @param sf.samp SF parameters MCMC samples
+##' 
+##' @author Istem Fer
+##' @export
+sample_MCMC <- function(mcmc_path, n.param.orig, prior.ind.orig, n.post.knots, knots.params.temp, 
+                        prior.list, prior.fn, sf, sf.samp){
+  
+  PEcAn.logger::logger.info("Sampling from previous round's MCMC")
+  
+  load(mcmc_path)
+  
+  mcmc.param.list <- params.subset <- list()
+  ind <- 0
+  for (i in seq_along(n.param.orig)) {
+    mcmc.param.list[[i]] <- lapply(mcmc.samp.list, function(x) x[, (ind + 1):(ind + n.param.orig[i]), drop = FALSE])
+    ind <- ind + n.param.orig[i]
+  }
+  
+  
+  burnins <- rep(NA, length(mcmc.param.list))
+  for (i in seq_along(mcmc.param.list)) {
+    params.subset[[i]] <- as.mcmc.list(lapply(mcmc.param.list[[i]], mcmc))
+    
+    burnin     <- getBurnin(params.subset[[i]], method = "gelman.plot")
+    burnins[i] <- max(burnin, na.rm = TRUE)
+  }
+  maxburn <- max(burnins)
+  
+  if(maxburn ==1){ # if no convergence focus last bit
+    maxburn <- 0.9*nrow(params.subset[[1]][[1]])
+  }
+  
+  collect_samples <- list()
+  for (i in seq_along(mcmc.samp.list)) {
+    collect_samples[[i]] <- window(mcmc.samp.list[[i]], start = maxburn)
+  }
+  
+  mcmc_samples <- do.call(rbind, collect_samples)
+  
+ 
+  get_samples <- sample(1:nrow(mcmc_samples), n.post.knots)
+  new_knots <- mcmc_samples[get_samples,]
+  pass2bias <- new_knots[, ncol(new_knots)] # if there is bias param, it will be the last col
+  # if there is no bias param this won't be used anyway
+  # the rest of the code is not ready for bias params for multiple variables
+    
+  # when using sf, need to sample from sf mcmc samples and calculate back actual parameter values
+  if(!is.null(sf.samp)){
+    
+    sf_samples <- list()
+    for (i in seq_along(sf.samp)) {
+      sf_samples[[i]] <- window(sf.samp[[i]], start = maxburn)
+    }
+    sf_samples <- do.call(rbind, sf_samples)
+    
+    sf_knots    <- sf_samples[get_samples,]
+    
+    ind <- 0
+    for(i in seq_along(n.param.orig)){
+      if(all(sf %in% rownames(prior.list[[i]]))){
+        temp.knots <- sapply(seq_along(prior.ind.orig[[i]]), function(z){
+          eval(prior.fn[[i]]$qprior[prior.ind.orig[[i]]][[z]], list(p = sf_knots[,z]))
+        })
+        new_knots[, (ind + 1):(ind + n.param.orig[i])] <- temp.knots
+      }
+      ind <- ind + n.param.orig[i]
+    }
+    
+  }else{
+    sf_knots <- NULL
+  }
+  
+  # now replace with new knots
+  ind <- 0
+  for(i in seq_along(n.param.orig)){
+    sub_knots <- new_knots[, (ind + 1):(ind + n.param.orig[i]), drop = FALSE]
+    knots.params.temp[[i]][, prior.ind.orig[[i]]] <- sub_knots
+
+    ind <- ind + n.param.orig[i]
+  }
+  
+  return(list(knots.params.temp = knots.params.temp, sf_knots = sf_knots, pass2bias = pass2bias))
+  
+}
diff --git a/modules/assim.batch/man/autoburnin.Rd b/modules/assim.batch/man/autoburnin.Rd
index 2f2773a41f9..e2a78b88653 100644
--- a/modules/assim.batch/man/autoburnin.Rd
+++ b/modules/assim.batch/man/autoburnin.Rd
@@ -15,6 +15,9 @@ samples (as list). Default = FALSE.}
 \item{...}{Additional arguments for \code{getBurnin}, \code{gelman_diag_mw}, 
 and \code{gelman.diag}.}
 }
+\description{
+Automatically calculate and apply burnin value
+}
 \examples{
      z1 <- coda::mcmc(c(rnorm(2500, 5), rnorm(2500, 0)))
      z2 <- coda::mcmc(c(rnorm(2500, -5), rnorm(2500, 0)))
diff --git a/modules/assim.batch/man/gelman_diag_mw.Rd b/modules/assim.batch/man/gelman_diag_mw.Rd
index 20fa695a186..c1ecc70342d 100644
--- a/modules/assim.batch/man/gelman_diag_mw.Rd
+++ b/modules/assim.batch/man/gelman_diag_mw.Rd
@@ -4,8 +4,8 @@
 \alias{gelman_diag_mw}
 \title{Calculate Gelman diagnostic on moving window}
 \usage{
-gelman_diag_mw(x, width_fraction = 0.1, width = ceiling(coda::niter(x) *
-  width_fraction), njump = 50, include.mpsrf = TRUE, ...)
+gelman_diag_mw(x, width_fraction = 0.1, width = ceiling(coda::niter(x)
+  * width_fraction), njump = 50, include.mpsrf = TRUE, ...)
 }
 \arguments{
 \item{x}{MCMC samples, of class \code{mcmc} or \code{mcmc.list}}
@@ -21,6 +21,9 @@ gelman_diag_mw(x, width_fraction = 0.1, width = ceiling(coda::niter(x) *
 \value{
 Gelman Diagnostic 3D array. First dim -- mean (1) and 95% confidence (2). Second dim -- iteration
 }
+\description{
+Calculate Gelman diagnostic on moving window
+}
 \author{
 Alexey Shiklomanov
 }
diff --git a/modules/assim.batch/man/load.pda.data.Rd b/modules/assim.batch/man/load.pda.data.Rd
index 17c012f9f11..6fabdd500ed 100644
--- a/modules/assim.batch/man/load.pda.data.Rd
+++ b/modules/assim.batch/man/load.pda.data.Rd
@@ -3,7 +3,6 @@
 \name{load.pda.data}
 \alias{load.pda.data}
 \alias{load.L2Ameriflux.cf}
-\alias{load.pda.data}
 \title{Load Ameriflux L2 Data From NetCDF}
 \usage{
 load.L2Ameriflux.cf(file.in)
diff --git a/modules/assim.batch/man/makeMCMCList.Rd b/modules/assim.batch/man/makeMCMCList.Rd
index c639407f214..23a791ee5b4 100644
--- a/modules/assim.batch/man/makeMCMCList.Rd
+++ b/modules/assim.batch/man/makeMCMCList.Rd
@@ -9,3 +9,6 @@ makeMCMCList(samps)
 \arguments{
 \item{samps}{samples list (output from invert.custom)}
 }
+\description{
+Make MCMC list from samples list
+}
diff --git a/modules/assim.batch/man/pda.autocorr.calc.Rd b/modules/assim.batch/man/pda.autocorr.calc.Rd
index e2c0d092093..4e77cf19d8b 100644
--- a/modules/assim.batch/man/pda.autocorr.calc.Rd
+++ b/modules/assim.batch/man/pda.autocorr.calc.Rd
@@ -14,6 +14,9 @@ pda.autocorr.calc(input, model = "heteroskedastic.laplacian")
 \value{
 rho AR(1)
 }
+\description{
+autocorrelation correction
+}
 \author{
 Istem Fer
 }
diff --git a/modules/assim.batch/man/pda.emulator.Rd b/modules/assim.batch/man/pda.emulator.Rd
index 178e8545504..ccf401c2c28 100644
--- a/modules/assim.batch/man/pda.emulator.Rd
+++ b/modules/assim.batch/man/pda.emulator.Rd
@@ -5,9 +5,9 @@
 \title{Paramater Data Assimilation using emulator}
 \usage{
 pda.emulator(settings, external.data = NULL, external.priors = NULL,
-  params.id = NULL, param.names = NULL, prior.id = NULL, chain = NULL,
-  iter = NULL, adapt = NULL, adj.min = NULL, ar.target = NULL,
-  jvar = NULL, n.knot = NULL)
+  params.id = NULL, param.names = NULL, prior.id = NULL,
+  chain = NULL, iter = NULL, adapt = NULL, adj.min = NULL,
+  ar.target = NULL, jvar = NULL, n.knot = NULL)
 }
 \arguments{
 \item{settings}{= a pecan settings list}
diff --git a/modules/assim.batch/man/pda.mcmc.Rd b/modules/assim.batch/man/pda.mcmc.Rd
index f284ee5d8a9..66cf1048bd6 100644
--- a/modules/assim.batch/man/pda.mcmc.Rd
+++ b/modules/assim.batch/man/pda.mcmc.Rd
@@ -4,9 +4,9 @@
 \alias{pda.mcmc}
 \title{Paramater Data Assimilation using MCMC}
 \usage{
-pda.mcmc(settings, params.id = NULL, param.names = NULL, prior.id = NULL,
-  chain = NULL, iter = NULL, adapt = NULL, adj.min = NULL,
-  ar.target = NULL, jvar = NULL, n.knot = NULL)
+pda.mcmc(settings, params.id = NULL, param.names = NULL,
+  prior.id = NULL, chain = NULL, iter = NULL, adapt = NULL,
+  adj.min = NULL, ar.target = NULL, jvar = NULL, n.knot = NULL)
 }
 \arguments{
 \item{settings}{= a pecan settings list}
diff --git a/modules/assim.batch/man/pda.plot.params.Rd b/modules/assim.batch/man/pda.plot.params.Rd
index ee9269c6522..5ba73614d04 100644
--- a/modules/assim.batch/man/pda.plot.params.Rd
+++ b/modules/assim.batch/man/pda.plot.params.Rd
@@ -4,7 +4,8 @@
 \alias{pda.plot.params}
 \title{Plot PDA Parameter Diagnostics}
 \usage{
-pda.plot.params(settings, mcmc.param.list, prior.ind, par.file.name = NULL)
+pda.plot.params(settings, mcmc.param.list, prior.ind,
+  par.file.name = NULL)
 }
 \arguments{
 \item{all}{params are the identically named variables in pda.mcmc / pda.emulator}
diff --git a/modules/assim.batch/man/return.bias.Rd b/modules/assim.batch/man/return.bias.Rd
index e220b5a890d..b5729b9515e 100644
--- a/modules/assim.batch/man/return.bias.Rd
+++ b/modules/assim.batch/man/return.bias.Rd
@@ -4,8 +4,26 @@
 \alias{return.bias}
 \title{return.bias}
 \usage{
-return.bias(isbias, model.out, inputs, prior.list.bias, nbias,
-  run.round = FALSE, prev.bias = NULL)
+return.bias(settings, isbias, model.out, inputs, prior.list.bias,
+  run.round = FALSE, pass2bias = NULL)
+}
+\arguments{
+\item{settings}{settings list}
+
+\item{isbias}{bias variable index}
+
+\item{model.out}{model output list}
+
+\item{inputs}{inputs list}
+
+\item{prior.list.bias}{prior list, bias prior to be added}
+
+\item{run.round}{extension flag}
+
+\item{pass2bias}{if this is another round, this is re-sampled MCMC samples, will go with the rest of model params}
+}
+\description{
+return.bias
 }
 \author{
 Istem Fer
diff --git a/modules/assim.batch/man/return_hyperpars.Rd b/modules/assim.batch/man/return_hyperpars.Rd
index 5ec107d66ca..5c7b9ae2442 100644
--- a/modules/assim.batch/man/return_hyperpars.Rd
+++ b/modules/assim.batch/man/return_hyperpars.Rd
@@ -6,6 +6,9 @@
 \usage{
 return_hyperpars(assim.settings, inputs)
 }
+\description{
+return_hyperpars
+}
 \author{
 Istem Fer
 }
diff --git a/modules/assim.batch/man/sample_MCMC.Rd b/modules/assim.batch/man/sample_MCMC.Rd
new file mode 100644
index 00000000000..389a18df78e
--- /dev/null
+++ b/modules/assim.batch/man/sample_MCMC.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pda.utils.R
+\name{sample_MCMC}
+\alias{sample_MCMC}
+\title{Helper function to sample from previous MCMC chain while proposing new knots}
+\usage{
+sample_MCMC(mcmc_path, n.param.orig, prior.ind.orig, n.post.knots,
+  knots.params.temp, prior.list, prior.fn, sf, sf.samp)
+}
+\arguments{
+\item{mcmc_path}{path to previous emulator mcmc samples object}
+
+\item{n.param.orig}{vector, number of parameters targeted in each (pft) sublist}
+
+\item{prior.ind.orig}{list, actual indices of parameters targeted in each (pft) sublist}
+
+\item{n.post.knots}{number of new samples requested}
+
+\item{knots.params.temp}{list of parameter samples proposed from the original PDA-prior}
+
+\item{prior.list}{PDA-prior list}
+
+\item{prior.fn}{list for parameter d/r/q/p functions}
+
+\item{sf}{SF parameter names}
+
+\item{sf.samp}{SF parameters MCMC samples}
+}
+\description{
+Helper function to sample from previous MCMC chain while proposing new knots
+}
+\author{
+Istem Fer
+}
diff --git a/modules/assim.batch/man/write_sf_posterior.Rd b/modules/assim.batch/man/write_sf_posterior.Rd
index 727ca550e93..8d7f96339f6 100644
--- a/modules/assim.batch/man/write_sf_posterior.Rd
+++ b/modules/assim.batch/man/write_sf_posterior.Rd
@@ -4,7 +4,7 @@
 \alias{write_sf_posterior}
 \title{Function to write posterior distributions of the scaling factors}
 \usage{
-write_sf_posterior(sf.samp.list, sf.prior, sf.filename)
+write_sf_posterior(sf.samp.list, sf.prior, sf.samp.filename)
 }
 \description{
 Function to write posterior distributions of the scaling factors
diff --git a/modules/assim.sequential/DESCRIPTION b/modules/assim.sequential/DESCRIPTION
index 25a155707f5..f366acdd838 100644
--- a/modules/assim.sequential/DESCRIPTION
+++ b/modules/assim.sequential/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.assim.sequential
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
@@ -18,8 +18,11 @@ Imports:
     lubridate (>= 1.6.0),
     reshape2 (>= 1.4.2),
     nimble
+Suggests:
+    testthat
 License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/assim.sequential/NAMESPACE b/modules/assim.sequential/NAMESPACE
index 261c65c105a..0518682f059 100644
--- a/modules/assim.sequential/NAMESPACE
+++ b/modules/assim.sequential/NAMESPACE
@@ -2,4 +2,5 @@
 
 export(assessParams)
 export(load_data_paleon_sda)
+export(sample_met)
 export(sda.enkf)
diff --git a/modules/assim.sequential/R/assess.params.R b/modules/assim.sequential/R/assess.params.R
index b52d3abcfa6..2d70c4e313a 100644
--- a/modules/assim.sequential/R/assess.params.R
+++ b/modules/assim.sequential/R/assess.params.R
@@ -13,21 +13,46 @@
 ##' @export
 ##' 
 
-assessParams <- function(dat, Xt, mu_f_TRUE, P_f_TRUE){  
+
+assessParams <- function(dat, Xt, mu_f_TRUE = NULL, P_f_TRUE = NULL){  
+  #mu_f_TRUE and P_f_TRUE used for simulation
+
+  
+  #* page 6 looks more like I expected, but I’m not sure how we’re getting negative variances
+  
+  #* In general, the first 3 pages of pairs plots doesn’t seem to be producing anything too absurd — there’s no estimates going off to large negative values and nothing TOO far from the sample mean. That said, I do find some of the estimates to be surprising (e.g. why is the posterior for mu12 at t=2 lower than the sample mean when the ensemble shouldn’t include any zeros)
   
   imuf   <- grep("muf", colnames(dat))
   muf <- colMeans(dat[, imuf])
   mufT <- apply(Xt,2,mean)
+  PfT <- cov(Xt)
+  
+  mufCI <- apply(dat[,imuf],2,quantile,c(0.025,0.975))
+  mufTCI <- apply(Xt,2,quantile,c(0.025,0.975))
+  
+  par(mfrow=c(1,1))
+  plot(mufT,muf,pch=19,ylim=range(mufCI),xlim=range(mufTCI))
+  abline(a=0,b=1,lty=2)
+  for(i in 1:length(muf)){
+    lines(mufTCI[,i],rep(as.vector(muf)[i],2),col=i,lwd=2)
+    lines(rep(as.vector(mufT)[i],2),mufCI[,i],col=i,lwd=2)
+  }
   
+  #muf mufT scatter plot
   par(mfrow=c(2,2))
   for(i in 1:(length(imuf)-1)){
-    plot(dat[,i],dat[,i+1])
-    points(mu_f_TRUE[i],mu_f_TRUE[i+1],cex=3,col=2,pch=18)
+    plot(dat[,i],dat[,i+1],xlab=paste('mu', i),ylab=paste('mu', i+1))
+    #points(mu_f_TRUE[i],mu_f_TRUE[i+1],cex=3,col=2,pch=18)
     points(muf[i],muf[i+1],cex=3,col=3,pch=19)
     points(mufT[i],mufT[i+1],cex=3,col=4,pch=20)
   }
   plot.new()
-  legend("topleft",legend=c("TRUE","post","sampT"),col=2:4,pch = 18:20)
+  legend("topleft",legend=c("post","sampT"),col=3:4,pch = 19:20)
+  #legend("topleft",legend=c("TRUE","post","sampT"),col=2:4,pch = 18:20)
+  
+  boxplot(Xt,xlab='State Variables',ylab='X')
+  points(muf,col='red',pch=19)
+  legend("topleft",legend=c("muf"),col='red',pch = 19)
   
   #cor(dat[,1:6])
   
@@ -35,12 +60,63 @@ assessParams <- function(dat, Xt, mu_f_TRUE, P_f_TRUE){
   Pf <- matrix(colMeans(dat[, iPf]),ncol(X),ncol(X))
   
   PfCI <- apply(dat[,iPf],2,quantile,c(0.025,0.975))
+
+  diag.stopper <- diag(length(muf))
+  
   par(mfrow=c(1,1))
-  plot(P_f_TRUE,Pf,ylim=range(PfCI))
+  plot(PfT,Pf,ylim=range(PfCI),pch=19,xlab='Pf Ensemble (True)',ylab='Pf Estimated (tobit2space)')
   abline(0,1,lty=2)
   for(i in 1:length(Pf)){
-    lines(rep(as.vector(P_f_TRUE)[i],2),PfCI[,i],col=i,lwd=2)
+    lines(rep(as.vector(PfT)[i],2),PfCI[,i],col=i,lwd=2)
+    if(diag.stopper[i]==1){
+      points(PfT[i],Pf[i],cex=2,pch = 7)
+    }
+  }
+  legend('topleft','variance',pch = 7,cex=2)
+  
+  diag.stopper2 <- diag.stopper+1
+  diag(diag.stopper2) <- 0
+  
+  plot(cov2cor(PfT)[which(diag.stopper2==1)],
+       cov2cor(Pf)[which(diag.stopper2==1)],pch=19,
+       ylab = 'Pf', xlab = 'Pft', main = 'Correlations')
+  abline(a=0,b=1,lty=2)
+  
+  corrCI <- apply(dat[,iPf[which(diag.stopper2!=0)]],2,quantile,c(0.025,0.975))
+  
+  par(mfrow=c(1,1))
+  plot(PfT[which(diag.stopper2!=0)],Pf[which(diag.stopper2!=0)],
+       ylim=range(corrCI),pch=19,xlab='Pf Ensemble (True)',
+       ylab='Pf Estimated (tobit2space)',
+       main='Non-Diagonal Covariance')
+  abline(a=0,b=1,lty=2)
+  for(i in 1:length(Pf)){
+    if(diag.stopper2[i]==1){
+      lines(rep(as.vector(PfT)[i],2),PfCI[,i],col=i,lwd=2)
+    }
   }
+  
+  par(mfrow=c(1,1))
+  plot(diag(PfT)-diag(Pf),xlab='State Variable',pch=19,
+       cex=2,main='Which variance changed the most?')
+  
+  
+  #var.change <- data.frame(mufT = signif(colMeans(Xt),digits=2),muf=signif(muf,digits=2),abs.change.var = abs(diag(PfT)-diag(Pf)))
+  #var.change[order(var.change$abs.change.var),]
+  
+  # sort(diag(Pf)-diag(PfT),decreasing = T)
+  # 
+  # par(mfrow=c(3,3))
+  # for(i in 1:length(Pf)) {
+  #   if(diag.stopper[i]==1){
+  #   plot(dat[,i+14],ylim=c(0,10)); abline(h=as.vector(PfT)[i],col='red',lwd=2)
+  #   }
+  # }
+  #scatterplots
+  #var 
+  #corr #pull diags out ==1 
+  #check mu v var to make sure variance is only changing near 0# shifts in Xt v X on same plot
+  
   #PfT <- cov(Xt)
   #points(P_f_TRUE,PfT,col=1:14,pch="-",cex=2)
-}
\ No newline at end of file
+}
diff --git a/modules/assim.sequential/R/load_data_paleon_sda.R b/modules/assim.sequential/R/load_data_paleon_sda.R
index d48a37a021b..9765caa44ac 100644
--- a/modules/assim.sequential/R/load_data_paleon_sda.R
+++ b/modules/assim.sequential/R/load_data_paleon_sda.R
@@ -12,7 +12,7 @@
 load_data_paleon_sda <- function(settings){
   
   #### Types of Data needed
-  ## STEPPS Fcomp
+  ## STEPPS Fcomp (Work in progress)
   ## ReFAB biomass
   ## HF Tree Rings (CHECK)
   ## Tree Rings from tree ring module
@@ -52,7 +52,7 @@ load_data_paleon_sda <- function(settings){
   obs.cov <- obs.cov.tmp <- list()
 
   obs.times <- seq(as.Date(start_date), as.Date(end_date), by = settings$state.data.assimilation$forecast.time.step)
-  obs.times <- lubridate::year(obs.times)
+  obs.times <- formatC(lubridate::year(obs.times), width = 4, format = "d", flag = "0")
   
   biomass2carbon <- 0.48
   
@@ -63,7 +63,9 @@ load_data_paleon_sda <- function(settings){
     data.path <- PEcAn.DB::query.file.path(input.id[[i]], settings$host$name, bety$con)
     format_full <- format <- PEcAn.DB::query.format.vars(input.id = input.id[[i]], bety, format.id = NA, var.ids=NA)
     
-    if(TRUE){
+
+    ### Tree Ring Data Product
+    if(format_id[[i]] == '1000000040'){
       # hack instead of changing the units in BETY format for now
       # I don't want load_data to convert anything
       # data itself is in Mg / ha 
@@ -78,14 +80,11 @@ load_data_paleon_sda <- function(settings){
     time.row <- format$time.row
     time.type <- format$vars$input_units[time.row] #THIS WONT WORK IF TIMESTEP ISNT ANNUAL
     
-    # ---- LOAD INPUT DATA ---- #
-    PEcAn.logger::logger.info(paste('Using PEcAn.benchmark::load_data.R on format_id',format_id[[i]],'-- may take a few minutes'))
-    obvs[[i]] <- PEcAn.benchmark::load_data(data.path, format, start_year = lubridate::year(start_date), end_year = lubridate::year(end_date), site)
-    
-    variable <- intersect(var.names,colnames(obvs[[i]]))
+      # ---- LOAD INPUT DATA ---- #
+      PEcAn.logger::logger.info(paste('Using PEcAn.benchmark::load_data.R on format_id',format_id[[i]],'-- may take a few minutes'))
+      obvs[[i]] <- PEcAn.benchmark::load_data(data.path, format, start_year = lubridate::year(start_date), end_year = lubridate::year(end_date), site)
     
-    kgms2Mghayr <- (10000/1)*(1/1000)*(365.25*24*60*60) ## kg m-2 s-1 -> Mg ha-1 yr-1
-    kgm2Mgha <- (10000/1)*(1/1000) ## kg m-2  -> Mg ha-1
+      variable <- intersect(var.names,colnames(obvs[[i]]))
     
     ### Tree Ring Data Product
     if(format_id[[i]] == '1000000040'){
@@ -95,64 +94,179 @@ load_data_paleon_sda <- function(settings){
       arguments <- list(.(year, MCMC_iteration, site_id), .(variable))
       arguments2 <- list(.(year), .(variable))
       arguments3 <- list(.(MCMC_iteration), .(variable), .(year))
-    }else{
-      PEcAn.logger::logger.severe('ERROR: This data format has not been added to this function (ツ)_/¯ ')
-    }
-    
-    dataset <- obvs[[i]]
-    
-    ### Map species to model specific PFTs
-    if(any(var.names == 'AGB.pft')){
-      spp_id <- match_species_id(unique(dataset$species_id),format_name = 'usda',bety)
-      pft_mat <- match_pft(spp_id$bety_species_id, settings$pfts,
-                           con = bety$con, allow_missing = TRUE)
-      
-      x <- paste0('AGB.pft.', pft_mat$pft)
-      names(x) <- spp_id$input_code
-      
-      PEcAn.logger::logger.info('Now, mapping data species to model PFTs')
-      dataset$pft.cat <- x[dataset$species_id]
-      dataset <- dataset[dataset$pft.cat!='AGB.pft.NA',]
-      
-      variable <- c('AbvGrndWood')
-      arguments <- list(.(year, MCMC_iteration, site_id, pft.cat), .(variable))
-      arguments2 <- list(.(year, pft.cat), .(variable))
-      arguments3 <- list(.(MCMC_iteration), .(pft.cat, variable), .(year))
-    } 
-    
-    PEcAn.logger::logger.info('Now, aggregating data and creating SDA input lists')
-    melt_id <- colnames(dataset)[-which(colnames(dataset) %in% variable)]
-    melt.test <- reshape2::melt(dataset, id = melt_id, na.rm = TRUE)
-    cast.test <- reshape2::dcast(melt.test, arguments, sum, margins = variable)
-    
-    melt_id_next <- colnames(cast.test)[-which(colnames(cast.test) %in% variable)]
-    melt.next <- reshape2::melt(cast.test, id = melt_id_next)
-    mean_mat <- reshape2::dcast(melt.next, arguments2, mean)
-    
-    iter_mat <- reshape2::acast(melt.next, arguments3, mean)
-    cov.test <- apply(iter_mat,3,function(x){cov(x)})
-   
-    for(t in seq_along(obs.times)){
-      obs.mean.tmp[[t]] <- mean_mat[mean_mat[,time.type]==obs.times[t], -c(1)] #THIS WONT WORK IF TIMESTEP ISNT ANNUAL
       
+      dataset <- obvs[[i]]
+      
+      ### Map species to model specific PFTs
       if(any(var.names == 'AGB.pft')){
-        obs.mean.tmp[[t]] <- rep(NA, length(unique(dataset$pft.cat)))
-        names(obs.mean.tmp[[t]]) <- sort(unique(dataset$pft.cat))
-        for(r in seq_along(unique(dataset$pft.cat))){
-          k <- mean_mat[mean_mat$year==obs.times[t] & mean_mat$pft.cat==names(obs.mean.tmp[[t]][r]), variable]
-          if(any(k)){
-            obs.mean.tmp[[t]][r] <- k
+        spp_id <- match_species_id(unique(dataset$species_id),format_name = 'usda',bety)
+        pft_mat <- match_pft(spp_id$bety_species_id, settings$pfts,
+                             con = bety$con, allow_missing = TRUE)
+        
+        x <- paste0('AGB.pft.', pft_mat$pft)
+        names(x) <- spp_id$input_code
+        
+        PEcAn.logger::logger.info('Now, mapping data species to model PFTs')
+        dataset$pft.cat <- x[dataset$species_id]
+        dataset <- dataset[dataset$pft.cat!='AGB.pft.NA',]
+        
+        variable <- c('AbvGrndWood')
+        arguments <- list(.(year, MCMC_iteration, site_id, pft.cat), .(variable))
+        arguments2 <- list(.(year, pft.cat), .(variable))
+        arguments3 <- list(.(MCMC_iteration), .(pft.cat, variable), .(year))
+      } 
+      
+      PEcAn.logger::logger.info('Now, aggregating data and creating SDA input lists')
+      melt_id <- colnames(dataset)[-which(colnames(dataset) %in% variable)]
+      melt.test <- reshape2::melt(dataset, id = melt_id, na.rm = TRUE)
+      cast.test <- reshape2::dcast(melt.test, arguments, sum, margins = variable)
+      
+      melt_id_next <- colnames(cast.test)[-which(colnames(cast.test) %in% variable)]
+      melt.next <- reshape2::melt(cast.test, id = melt_id_next)
+      mean_mat <- reshape2::dcast(melt.next, arguments2, mean)
+      
+      iter_mat <- reshape2::acast(melt.next, arguments3, mean)
+      cov.test <- apply(iter_mat,3,function(x){cov(x)})
+      
+      for(t in seq_along(obs.times)){
+        obs.mean.tmp[[t]] <- mean_mat[mean_mat[,time.type]==obs.times[t], -c(1)] #THIS WONT WORK IF TIMESTEP ISNT ANNUAL
+        
+        if(any(var.names == 'AGB.pft')){
+          obs.mean.tmp[[t]] <- rep(NA, length(unique(dataset$pft.cat)))
+          names(obs.mean.tmp[[t]]) <- sort(unique(dataset$pft.cat))
+          for(r in seq_along(unique(dataset$pft.cat))){
+            k <- mean_mat[mean_mat$year==obs.times[t] & mean_mat$pft.cat==names(obs.mean.tmp[[t]][r]), variable]
+            if(any(k)){
+              obs.mean.tmp[[t]][r] <- k
+            }
           }
         }
+        
+        obs.cov.tmp[[t]] <- matrix(cov.test[,which(colnames(cov.test) %in% obs.times[t])],
+                                   ncol = sqrt(dim(cov.test)[1]),
+                                   nrow = sqrt(dim(cov.test)[1]))
+        if(any(var.names == 'AGB.pft')){
+          colnames(obs.cov.tmp[[t]]) <- names(iter_mat[1,,t]) 
+        }
       }
+    }
+    
+    ### Pollen Data Product (STEPPS)
+    if(format_id[[i]] == '1000000058'){
+      ncin <- ncdf4::nc_open(data.path)
       
-      obs.cov.tmp[[t]] <- matrix(cov.test[,which(colnames(cov.test) %in% obs.times[t])],
-                             ncol = sqrt(dim(cov.test)[1]),
-                             nrow = sqrt(dim(cov.test)[1]))
-      if(any(var.names == 'AGB.pft')){
-        colnames(obs.cov.tmp[[t]]) <- names(iter_mat[1,,t]) 
+      coords <- data.frame(x=site$lon,y=site$lat)
+      sp::coordinates(coords) <- ~ x + y
+      sp::proj4string(coords) <- sp::CRS('+proj=longlat +ellps=WGS84')
+      
+      ### site utm coordinates
+      utm <- sp::spTransform(coords, CRS("+proj=utm +zone=18N ellps=WGS84"))
+      utm <- as.matrix(data.frame(utm))
+      
+      ### find grid cell
+      site.x <- which(min(abs(ncvar_get(ncin, 'x') - utm[1])) == abs(ncvar_get(ncin, 'x') - utm[1]))
+      site.y <- which(min(abs(ncvar_get(ncin, 'y') - utm[2])) == abs(ncvar_get(ncin, 'y') - utm[2]))
+      years <- formatC(ncvar_get(ncin, 'year'), width = 4, format = "d", flag = "0")
+      
+      taxa <- names(ncin$var)
+      if('other'%in%taxa) taxa <- taxa[-c(grep('other',taxa))]
+        
+      sims.keep <- array(NA,dim=c(length(taxa),length(ncin$dim$year$vals),length(ncin$dim$sample$vals)))
+      for(n in seq_along(taxa)){
+        taxa.start <- ncvar_get(ncin, taxa[n])
+        
+        # input is a matrix 'sims', with rows as time and columns as MCMC samples
+        sims.keep[n,,] <- taxa.start[site.x,site.y,,]
+      }
+      
+      #####
+      ##### Calculating Effective Sample Size #####
+      #####
+      
+      ESS_calc <- function(ntimes, sims){
+        row.means.sims <- sims - rowMeans(sims)  # center based on mean at each time to remove baseline temporal correlation 
+        # (we want to estimate effective sample size effect from correlation of the errors)
+        
+        # compute all pairwise covariances at different times
+        covars <- NULL
+        for(lag in 1:(ntimes-1)){
+          covars <- c(covars, rowMeans(row.means.sims[(lag+1):ntimes, , drop = FALSE] * row.means.sims[1:(ntimes-lag), , drop = FALSE])) 
+        }
+        vars <- apply(row.means.sims, 1, var) # pointwise post variances at each time, might not be homoscedastic
+        
+        # nominal sample size scaled by ratio of variance of an average
+        # under independence to variance of average of correlated values
+        neff <- ntimes * sum(vars) / (sum(vars) + 2 * sum(covars))
+        return(neff)
       }
-    } 
+      
+      neff.keep <- mean.keep <- list()
+      pecan.pfts <- as.character(lapply(settings$pfts, function(x) x[["name"]]))
+      
+      for(n in taxa){
+        sims.start <- ncvar_get(ncin,n)
+        
+        # input is a matrix 'sims', with rows as time and columns as MCMC samples
+        sims <- sims.start[site.x,site.y,,]
+        
+        ntimes <- 10
+      
+        neff.keep[[n]] <- ESS_calc(ntimes = ntimes, sims = sims)
+        mean.keep[[n]] <- rowMeans(sims)
+       
+      }
+      
+      var.inf <- 1000/mean(unlist(neff.keep))
+      
+      mean.mat <- as.data.frame(mean.keep)
+      
+      for(n in seq_len(ncol(mean.mat))){
+        new.name <- pecan.pfts[grep(taxa[n],pecan.pfts,ignore.case = T)]
+        if(any(nchar(new.name))){
+          colnames(mean.mat)[n] <- paste0('Fcomp.',new.name)
+        }
+      }
+      
+      #####
+      ##### Calculating Mean and Covariance
+      #####
+
+      obs.mean <- list()
+      for(n in 1:nrow(mean.mat)){
+        obs.mean[[n]]<- mean.mat[n,]
+      }
+      
+      names(obs.mean) <- paste0(years,'/12/31')
+
+      rownames(sims.keep) <- colnames(mean.mat)
+      obs.cov <- list()
+      for(n in 1:length(ncin$dim$year$vals)){
+        obs.cov[[n]] <- cov(t(sims.keep[,n,])) #* var.inf
+      }
+      
+      names(obs.cov) <- paste0(years,'/12/31')
+      
+      #### Interpolate over all years
+      which.keep <- list()
+      
+      for(n in obs.times){
+        min.vec <- na.omit(as.numeric(n) - year(as.Date(names(obs.mean))))
+        which.keep[[n]] <- which(min(abs(min.vec))==abs(min.vec))
+        obs.mean.tmp[[n]] <- obs.mean[[which.keep[[n]][1]]]
+        obs.cov.tmp[[n]] <- obs.cov[[which.keep[[n]][1]]]
+      }
+      
+      names(obs.mean.tmp)<-paste0(obs.times,'/12/31')
+      names(obs.cov.tmp)<-paste0(obs.times,'/12/31')
+      
+    }
+    
+    ### Error Message for no data product
+    if(format_id[[i]] != '1000000040' & format_id[[i]] != '1000000058'){
+      PEcAn.logger::logger.severe('ERROR: This data format has not been added to this function (ツ)_/¯ ')
+    }
+    
+  }
     
     ### Combine data if more than one type of data
     if(i > 1){
@@ -167,7 +281,6 @@ load_data_paleon_sda <- function(settings){
     
     names(obs.mean) <- paste0(obs.times,'/12/31')
     names(obs.cov) <- paste0(obs.times,'/12/31')
-  }
   
   obs.list <- list(obs.mean = obs.mean, obs.cov = obs.cov)
   save(obs.list,file=file.path(settings$outdir,'sda.obs.Rdata'))
diff --git a/modules/assim.sequential/R/met_filtering_helpers.R b/modules/assim.sequential/R/met_filtering_helpers.R
index f698e599b31..74bceefd3ad 100644
--- a/modules/assim.sequential/R/met_filtering_helpers.R
+++ b/modules/assim.sequential/R/met_filtering_helpers.R
@@ -1,11 +1,28 @@
+##' 
+##' @param settings PEcAn settings list
+##' @param nens number of ensemble members to be sampled
+##' 
+##' @export
+sample_met <- function(settings, nens=1){
 
-sample_met <- function(settings,nens=1){
+  # path where ensemble met folders are
+  if(length(settings$run$inputs$met[["path"]]) == 1){
+    path <- settings$run$inputs$met[["path"]]
+  }else if(!is.null(settings$run$inputs$met[["path"]])){ # this function will be deprecated soon anyway
+    path <- settings$run$inputs$met[["path"]][[1]]
+  }else{
+    PEcAn.logger::logger.error("Met path not found in settings.")
+  }
   
-  path <- settings$run$inputs$met[["path"]]
 
-  ens_members <- list.files(path, recursive = TRUE)
-  
+  if(settings$host$name == "localhost"){
+    ens_members <- list.files(path, recursive = TRUE)
+  }else{
+    # remote
+    ens_members <- PEcAn.remote::remote.execute.cmd(host, paste0('ls -d -1 ', path, "/*.*"))
+  }
   
+
   start_date <- as.POSIXlt(strptime(settings$run$site$met.start, "%Y/%m/%d"))
   end_date   <- as.POSIXlt(strptime(settings$run$site$met.end, "%Y/%m/%d"))
   start_date$zone <- end_date$zone <- NULL
@@ -15,8 +32,18 @@ sample_met <- function(settings,nens=1){
   tmp_members <- gsub(paste0(".", end_date),   "", tmp_members) 
   member_names <- unique(dirname(ens_members))
   
-  #this will change from model to model, generalize later
-  ens_ind <- unlist(sapply(paste0(member_names, ".clim"), grep, tmp_members))
+  # this will change from model to model, generalize later
+  # This function is temporary but if we will continue to use this approach for met ensembles (instead of met process workflow)
+  # it might not be a bad idea to have sample_met.model
+  if(settings$model$type == "ED2"){
+    # TODO : it doesn't have to be called ED_MET_DRIVER_HEADER
+    ens_members <- file.path(basename(ens_members), "ED_MET_DRIVER_HEADER") 
+    ens_ind     <- seq_along(ens_members)
+  }else if(settings$model$type == "SIPNET"){
+    ens_ind <- unlist(sapply(paste0(member_names, ".clim"), grep, tmp_members))
+  }
+  
+
   # ens_members[ens_ind]
   ens_input <- list()
   for(i in seq_len(nens)){
diff --git a/modules/assim.sequential/R/sda.enkf.R b/modules/assim.sequential/R/sda.enkf.R
index f917731b060..9a390926570 100644
--- a/modules/assim.sequential/R/sda.enkf.R
+++ b/modules/assim.sequential/R/sda.enkf.R
@@ -33,7 +33,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
   model      <- settings$model$type
   write      <- settings$database$bety$write
   defaults   <- settings$pfts
-  outdir     <- settings$host$outdir
+  outdir     <- settings$modeloutdir # currently model runs locally, this will change if remote is enabled
   rundir     <- settings$host$rundir
   host       <- settings$host
   forecast.time.step <- settings$state.data.assimilation$forecast.time.step  #idea for later generalizing
@@ -47,7 +47,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
                              USE.NAMES = FALSE), 
                       use.names = FALSE)
   names(var.names) <- NULL
-  dir.create(rundir,recursive=TRUE)
+  dir.create(rundir,recursive=TRUE) # remote will give warning
   
   ###-------------------------------------------------------------------###
   ### get model specific functions                                      ###
@@ -58,16 +58,19 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
   my.write_restart <- paste0("write_restart.", model)
   my.split_inputs  <- paste0("split_inputs.", model)
   
+  # models that don't need split_inputs, check register file for that
+  register.xml <- system.file(paste0("register.", model, ".xml"), package = paste0("PEcAn.", model))
+  register <- XML::xmlToList(XML::xmlParse(register.xml))
+  no_split <- !as.logical(register$exact.dates)
+  
   if (!exists(my.write.config)) {
-    print(paste(my.write.config, "does not exist"))
-    print(paste("please make sure that the PEcAn interface is loaded for", model))
-    stop()
+    PEcAn.logger::logger.warn(my.write.config, "does not exist")
+    PEcAn.logger::logger.severe("please make sure that the PEcAn interface is loaded for", model)
   }
   
-  if (!exists(my.split_inputs)) {
-    print(paste(my.split_inputs, "does not exist"))
-    print(paste("please make sure that the PEcAn interface is loaded for", model))
-    stop()
+  if (!exists(my.split_inputs)  &  !no_split) {
+    PEcAn.logger::logger.warn(my.split_inputs, "does not exist")
+    PEcAn.logger::logger.severe("please make sure that the PEcAn interface is loaded for", model)
   }
   
   ###-------------------------------------------------------------------###
@@ -80,25 +83,35 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
     sampleIDs <- c(1:n.inputs,sample.int(n.inputs, (nens - n.inputs), replace = TRUE))
   }
   
- 
+
   if(is.null(restart) & is.null(restart$ens.inputs)){
-    ens.inputs <- sample_met(settings,nens)
-  } else {
+    ens.inputs <- sample_met(settings, nens)
+  }else {
     ens.inputs <- restart$ens.inputs
   }
-  #ens.inputs <- list()
+
   inputs <- list()
   for(i in seq_len(nens)){
+    
+    if(no_split){ # currently this is only for ED2, ensemble generator + refactoring will change these soon anyway
+      # note that write configs accepts one "settings" for now, so I'll use the inputs arg to pass IC ensembles
+      inputs[[i]]  <- lapply(settings$run$inputs, function(x) {
+             return( x %>% purrr::map(function(inputs){return((inputs%>%unlist)[i])}))
+      })
+      inputs[[i]]$met <- ens.inputs[[i]]$met 
+    }else{
+      ### get only necessary ensemble inputs. Do not change in analysis
+      #ens.inputs[[i]] <- get.ensemble.inputs(settings = settings, ens = sampleIDs[i])
+      ### model specific split inputs
+      inputs[[i]] <- do.call(my.split_inputs, 
+                             args = list(settings = settings, 
+                                         start.time = settings$run$start.date, 
+                                         stop.time = as.Date(names(obs.mean)[1]),#settings$run$end.date,
+                                         inputs = ens.inputs[[i]]))#,
+      #                                       outpath = file.path(rundir,paste0("met",i))))
+    }
+
 
-    ### get only necessary ensemble inputs. Do not change in analysis
-    #ens.inputs[[i]] <- get.ensemble.inputs(settings = settings, ens = sampleIDs[i])
-    ### model specific split inputs
-    inputs[[i]] <- do.call(my.split_inputs, 
-                           args = list(settings = settings, 
-                                       start.time = settings$run$start.date, 
-                                       stop.time = as.Date(names(obs.mean)[1]),#settings$run$end.date,
-                                       inputs = ens.inputs[[i]]))#,
-#                                       outpath = file.path(rundir,paste0("met",i))))
   }
   
   ###-------------------------------------------------------------------###
@@ -216,6 +229,9 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
   
   for (i in seq_len(nens)) {
     
+    # is this gonna break other model runs? inputs is usually just the met path which is all they need anyway?
+    settings$run$inputs <- inputs[[i]]
+    
     ## set RUN.ID
     if (!is.null(con)) {
       now <- format(Sys.time(), "%Y-%m-%d %H:%M:%S")
@@ -278,7 +294,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
   }
   save(list = ls(envir = environment(), all.names = TRUE), 
        file = file.path(outdir, "sda.initial.runs.Rdata"), envir = environment())
-
+  
   
   
   ###-------------------------------------------------------------------###
@@ -301,6 +317,10 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         ### Adding 12:59:59PM assuming next time step starts one second later
         print("Pumpkin Warning: adding one minute before midnight time assumption to dates associated with data")
         obs.times.POSIX[i] <- ymd_hms(paste(obs.times[i], "23:59:59"))
+        # if(nchar(year(obs.times.POSIX[i]))==3){
+        #   #TODO: BROKEN: need to add leading zeros to years with less than 4 digits
+        #   obs.times.POSIX[i] <- paste0('0',ymd_hms(paste(obs.times[i], "23:59:59")))
+        # } 
       }
     }
   }
@@ -355,6 +375,29 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
     )
   )
   
+  if(var.names=="Fcomp"){
+    y_star_create <-  nimbleFunction(
+      run = function(X = double(1)) {
+        returnType(double(1))
+        
+        X_use <- X
+        X_use[X_use<0] <- 0
+        y_star <- X_use/sum(X_use)
+        
+        return(y_star)
+      })
+  }else{
+    y_star_create <-  nimbleFunction(
+      run = function(X = double(1)) {
+        returnType(double(1))
+        
+        y_star <- X
+        
+        return(y_star)
+      })
+  }
+  
+  
   tobit.model <- nimbleCode({ 
     
     q[1:N,1:N]  ~ dwish(R = aq[1:N,1:N], df = bq) ## aq and bq are estimated over time
@@ -364,20 +407,17 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
     ## add process error
     X[1:N]  ~ dmnorm(X.mod[1:N], prec = q[1:N,1:N])
     
-    #agb linear
-    #y_star[1:N,1:N] <- X[1:N,1:N] #[choose]
-    
-    #f.comp non linear
-    #y_star <- X[1:9] / sum(X[1:9])
+    #observation operator
+    y_star[1:YN] <- y_star_create(X[1:YN])
     
     ## Analysis
-    y.censored[1:YN] ~ dmnorm(X[1:YN], prec = r[1:YN,1:YN]) #is it an okay assumpution to just have X and Y in the same order?
+    y.censored[1:YN] ~ dmnorm(y_star[1:YN], prec = r[1:YN,1:YN]) #is it an okay assumpution to just have X and Y in the same order?
     
     #don't flag y.censored as data, y.censored in inits
     #remove y.censored samplers and only assign univariate samplers on NAs
     
     for(i in 1:YN){
-      y.ind[i] ~ dconstraint(y.censored[i] > 0)
+      y.ind[i] ~ dinterval(y.censored[i], 0)
     }
     
   })
@@ -386,7 +426,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
     for(i in 1:N){
       y.censored[i,1:J] ~ dmnorm(muf[1:J], cov = pf[1:J,1:J])
       for(j in 1:J){
-        y.ind[i,j] ~ dconstraint(y.censored[i,j] > 0)
+        y.ind[i,j] ~ dinterval(y.censored[i,j], 0)
       }
     }
     
@@ -414,9 +454,9 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
   
   ###-------------------------------------------------------------------###
   ### loop over time                                                    ###
-  ###-------------------------------------------------------------------###  
+  ###-------------------------------------------------------------------### 
+  
   for(t in seq_len(nt)) {
-    
     ###-------------------------------------------------------------------###
     ### read restart                                                      ###
     ###-------------------------------------------------------------------###  
@@ -424,6 +464,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
     X <- list()
     new.params <- params
     
+    # var.names <- c("AbvGrndWood", "GWBI", "TotLivBiom", "leaf_carbon_content") 
     for (i in seq_len(nens)) {
       X_tmp[[i]] <- do.call(my.read_restart, args = list(outdir = outdir, 
                                                      runid = run.id[[i]], 
@@ -535,7 +576,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         H <- matrix(0, length(Y), ncol(X)) #H maps true state to observed state
         #linear
         for (i in choose) {
-          H[i, i] <- 1 
+          H[i, i] <- 1
         }
         #non-linear fcomp
         # for (i in choose) {
@@ -558,6 +599,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         ### create matrix the describes the support for each observed state variable at time t
         intervalX <- matrix(NA, ncol(X), 2)
         rownames(intervalX) <- colnames(X)
+        #TO DO: Not working for fcomp
         for(i in 1:length(var.names)){
           intervalX[which(startsWith(rownames(intervalX),
                                      var.names[i])), ] <- matrix(c(as.numeric(settings$state.data.assimilation$state.variables[[i]]$min_value),
@@ -569,17 +611,17 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         #### These vectors are used to categorize data based on censoring from the interval matrix
         x.ind <- x.censored <- matrix(NA, ncol=ncol(X), nrow=nrow(X))
         for(j in seq_along(mu.f)){
-          for(n in seq_len(nens)){
+          for(n in seq_len(nrow(X))){
             x.ind[n,j] <- as.numeric(X[n,j] > 0)
-            x.censored[n,j] <- as.numeric(ifelse(X[n,j] > intervalX[j,2], 0, X[n,j]))
+            x.censored[n,j] <- as.numeric(ifelse(X[n,j] > intervalX[j,2], 0, X[n,j])) #
           }
         }
         
-        if(t == 1){
+        if(t == 1 | length(run.id) < nens){
           #The purpose of this step is to impute data for mu.f 
           #where there are zero values so that 
           #mu.f is in 'tobit space' in the full model
-          constants.tobit2space = list(N = nens,
+          constants.tobit2space = list(N = nrow(X),
                                        J = length(mu.f))
           
           data.tobit2space = list(y.ind = x.ind,
@@ -596,14 +638,14 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
                                           name = 'space')
           ## Adding X.mod,q,r as data for building model.
           conf_tobit2space <- configureMCMC(tobit2space_pred, thin = 10, print=TRUE)
-          conf_tobit2space$addMonitors(c("pf", "muf")) 
+          conf_tobit2space$addMonitors(c("pf", "muf","y.censored")) 
           ## [1] conjugate_dmnorm_dmnorm sampler: X[1:5]
           ## important!
           ## this is needed for correct indexing later
           samplerNumberOffset_tobit2space <- length(conf_tobit2space$getSamplers())
           
           for(j in seq_along(mu.f)){
-            for(n in seq_len(nens)){
+            for(n in seq_len(nrow(X))){
               node <- paste0('y.censored[',n,',',j,']')
               conf_tobit2space$addSampler(node, 'toggle', control=list(type='RW'))
               ## could instead use slice samplers, or any combination thereof, e.g.:
@@ -628,22 +670,26 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         }else{
           Cmodel_tobit2space$y.ind <- x.ind
           Cmodel_tobit2space$y.censored <- x.censored
-          Cmodel_tobit2space$lambda_0 <- diag(10,length(mu.f)) #enkf.params[[t-1]]$Pa
-          Cmodel_tobit2space$mu_0 <- rep(0,length(mu.f)) #enkf.params[[t-1]]$mu.a
+          
+          inits.tobit2space = list(pf = Pf, muf = colMeans(X))
+          Cmodel_tobit2space$setInits(inits.tobit2space)
           
           for(i in seq_along(X)) {
-              ## ironically, here we have to "toggle" the value of y.ind[i]
-              ## this specifies that when y.ind[i] = 1,
-              ## indicator variable is set to 0, which specifies *not* to sample
-              valueInCompiledNimbleFunction(Cmcmc_tobit2space$samplerFunctions[[samplerNumberOffset_tobit2space+i]], 'toggle', 1-x.ind[i])
+            ## ironically, here we have to "toggle" the value of y.ind[i]
+            ## this specifies that when y.ind[i] = 1,
+            ## indicator variable is set to 0, which specifies *not* to sample
+            valueInCompiledNimbleFunction(Cmcmc_tobit2space$samplerFunctions[[samplerNumberOffset_tobit2space+i]], 'toggle', 1-x.ind[i])
           }
           
         }
-         
+        
         set.seed(0)
         dat.tobit2space <- runMCMC(Cmcmc_tobit2space, niter = 50000, progressBar=TRUE)
         
-        assessParams(dat = dat.tobit2space[1000:5000,], Xt = X, mu_f_TRUE = colMeans(X), P_f_TRUE = Pf)
+        pdf(file.path(outdir,paste0('assessParams',t,'.pdf')))
+        
+        assessParams(dat = dat.tobit2space[1000:5000,], Xt = X)
+        dev.off()
         
         ## update parameters
         dat.tobit2space  <- dat.tobit2space[1000:5000, ]
@@ -652,11 +698,12 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         iPf   <- grep("pf", colnames(dat.tobit2space))
         Pf <- matrix(colMeans(dat.tobit2space[, iPf]),ncol(X),ncol(X))
         
-        #plot(dat.tobit2space[,16])
+        iycens <- grep("y.censored",colnames(dat.tobit2space))
         
+        X.new <- matrix(colMeans(dat.tobit2space[,iycens]),nrow(X),ncol(X))
         
         if(sum(diag(Pf)-diag(cov(X))) > 10 | sum(diag(Pf)-diag(cov(X))) < -10) logger.severe('Increase Sample Size')
-      
+        
         ###-------------------------------------------------------------------###
         ### Generalized Ensemble Filter                                       ###
         ###-------------------------------------------------------------------###
@@ -670,7 +717,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
             print('error: X has changed dimensions')
           }
         }
-        aqq[1, , ] <- diag(length(mu.f)) * bqq[1]
+        aqq[1, , ] <- diag(length(mu.f)) * bqq[1] #Q
         
         ### create matrix the describes the support for each observed state variable at time t
         interval <- matrix(NA, length(obs.mean[[t]]), 2)
@@ -687,18 +734,20 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         y.ind <- as.numeric(Y > interval[,1])
         y.censored <- as.numeric(ifelse(Y > interval[,1], Y, 0))
         
-        if(t==1){ #TO need to make something that works to pick weather to compile or not
-          #y.obs = Y.dat[1,]
-          constants.tobit = list(N = ncol(X), YN = length(y.ind)) #, nc = 1
-          dimensions.tobit = list(X = ncol(X), X.mod = ncol(X), Q = c(ncol(X),ncol(X))) #  b = dim(inits.pred$b),
+        if(t == 1){ #TO DO need to make something that works to pick weather to compile or not
+          constants.tobit = list(N = ncol(X), YN = length(y.ind))
+          dimensions.tobit = list(X = length(mu.f), X.mod = ncol(X),
+                                  Q = c(length(mu.f),length(mu.f)))
+          
+          data.tobit = list(muf = as.vector(mu.f),
+            pf = solve(Pf), 
+            aq = aqq[t,,], bq = bqq[t],
+            y.ind = y.ind,
+            y.censored = y.censored,
+            r = solve(R))
+          inits.pred = list(q = diag(length(mu.f)), X.mod = as.vector(mu.f),
+                            X = rnorm(length(mu.f),0,1)) #
           
-          data.tobit = list(muf = as.vector(mu.f), pf = Pf, aq = aqq[t,,], bq = bqq[t],
-                            y.ind = y.ind,
-                            y.censored = y.censored,
-                            r = solve(R))
-          inits.pred = list(q = diag(ncol(X)), X.mod = as.vector(mu.f), X = rnorm(ncol(X),0,1)) #
-          #set.seed(0)
-          #ptm <- proc.time()
           model_pred <- nimbleModel(tobit.model, data = data.tobit, dimensions = dimensions.tobit,
                                     constants = constants.tobit, inits = inits.pred,
                                     name = 'base')
@@ -740,9 +789,13 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
           Cmodel$aq <- aqq[t,,]
           Cmodel$bq <- bqq[t]
           Cmodel$muf <- mu.f
-          Cmodel$pf <- Pf
+          Cmodel$pf <- solve(Pf)
           Cmodel$r <- solve(R)
           
+          inits.pred = list(q = diag(length(mu.f)), X.mod = as.vector(mu.f),
+                            X = rnorm(ncol(X),0,1)) #
+          Cmodel$setInits(inits.pred)
+          
           for(i in 1:length(y.ind)) {
             ## ironically, here we have to "toggle" the value of y.ind[i]
             ## this specifies that when y.ind[i] = 1,
@@ -753,33 +806,8 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         }
         
         set.seed(0)
-        dat <- runMCMC(Cmcmc, niter = 50000, progressBar=FALSE)
-        
-        # #### JAGS update list
-        # update <- list(interval = interval,
-        #                N = length(y.ind),
-        #                y.ind = y.ind,
-        #                y.censored = y.censored, 
-        #                r = solve(R),
-        #                muf = mu.f, 
-        #                pf =  Pf, #check
-        #                aq = aqq[t,,], 
-        #                bq = bqq[t],
-        #                choose = choose)
-        # 
-        # #### Run JAGS Tobit Model
-        # mod <- jags.model(file = textConnection(tobit.model),
-        #                   data = update,
-        #                   n.adapt = 1000, 
-        #                   n.chains = 3)  #inits for q?
-        # 
-        # jdat <- coda.samples(mod, variable.names = c("X", "q"), 
-        #                      n.iter = 10000)
-        # 
-        # #gelman.diag(jdat[,1:10])
-        # #is it reasonable to expect convergence every year of every parameter?
-        # #should we put a stop in if params don't converge?
-        
+        dat <- runMCMC(Cmcmc, niter = 50000)
+      
         ## update parameters
         dat  <- dat[10000:50000, ]
         iq   <- grep("q", colnames(dat))
@@ -812,6 +840,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         bqq[t + 1]       <- n
         enkf.params[[t]] <- list(mu.f = mu.f, Pf = Pf, mu.a = mu.a, 
                                  Pa = Pa, q.bar = q.bar, n = n)
+        
       }
       
     } else {
@@ -844,8 +873,13 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
       
       ## normalize
       Z <- X*0
-      for(i in seq_len(nens)){
-        Z[i,] <- 1/sqrt(L_f) * t(V_f)%*%(X[i,]-mu.f)
+      
+      for(i in seq_len(nrow(X))){
+        if(processvar == TRUE) {
+          Z[i,] <- 1/sqrt(L_f) * t(V_f)%*%(X.new[i,]-mu.f)
+        }else{
+          Z[i,] <- 1/sqrt(L_f) * t(V_f)%*%(X[i,]-mu.f)
+        }
       }
       Z[is.na(Z)]<-0
       
@@ -856,7 +890,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
       
       ## analysis ensemble
       X_a <- X*0
-      for(i in seq_len(nens)){
+      for(i in seq_len(nrow(X))){
         X_a[i,] <- V_a %*%diag(sqrt(L_a))%*%Z[i,] + mu.a
       }
       
@@ -865,18 +899,16 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
 #        wt.mat[i,t]<-dmnorm_chol(FORECAST[[t]][i,], mu.a, solve(Pa), log = TRUE)
 #      }
       
-      
-      
       if(sum(mu.a - colMeans(X_a)) > 1 | sum(mu.a - colMeans(X_a)) < -1) logger.warn('Problem with ensemble adjustment (1)')
       if(sum(diag(Pa) - diag(cov(X_a))) > 5 | sum(diag(Pa) - diag(cov(X_a))) < -5) logger.warn('Problem with ensemble adjustment (2)')
       
       analysis <- as.data.frame(X_a)
     }else{
-      analysis <- as.data.frame(rmvnorm(as.numeric(nens), mu.a, Pa, method = "svd"))
+      analysis <- as.data.frame(rmvnorm(as.numeric(nrow(X)), mu.a, Pa, method = "svd"))
     }
     
     colnames(analysis) <- colnames(X)
-    
+
     ##### Mapping analysis vectors to be in bounds of state variables
     if(processvar==TRUE){
       for(i in 1:ncol(analysis)){
@@ -891,7 +923,6 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
     new.state  <- analysis
     
     ANALYSIS[[t]] <- analysis
-    
     if (interactive() & t > 1) { #
       t1 <- 1
       names.y <- unique(unlist(lapply(obs.mean[t1:t], function(x) { names(x) })))
@@ -916,17 +947,19 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         
         YCI <- YCI[,Y.order]
         YCI[is.na(YCI)] <- 0
+
       }else{
         YCI <- matrix(NA,nrow=length(t1:t), ncol=max(length(names.y),1))
       }
       
       par(mfrow = c(2, 1))
-      for (i in 1:ncol(FORECAST[[t]])) {
-        Xbar <- plyr::laply(FORECAST[t1:t], function(x) { mean(x[, i], na.rm = TRUE) })
-        Xci  <- plyr::laply(FORECAST[t1:t], function(x) { quantile(x[, i], c(0.025, 0.975)) })
+      for (i in 1:ncol(FORECAST[[t]])) { #
+        
+        Xbar <- plyr::laply(FORECAST[t1:t], function(x) { mean(x[, i]/rowSums(x[,1:9]), na.rm = TRUE) })
+        Xci  <- plyr::laply(FORECAST[t1:t], function(x) { quantile(x[, i]/rowSums(x[,1:9]), c(0.025, 0.975), na.rm = TRUE) })
         
-        Xa <- plyr::laply(ANALYSIS[t1:t], function(x) { mean(x[, i], na.rm = TRUE) })
-        XaCI <- plyr::laply(ANALYSIS[t1:t], function(x) { quantile(x[, i], c(0.025, 0.975)) })
+        Xa <- plyr::laply(ANALYSIS[t1:t], function(x) { mean(x[, i]/rowSums(x[,1:9]), na.rm = TRUE) })
+        XaCI <- plyr::laply(ANALYSIS[t1:t], function(x) { quantile(x[, i]/rowSums(x[,1:9]), c(0.025, 0.975), na.rm = TRUE) })
         
         ylab.names <- unlist(sapply(settings$state.data.assimilation$state.variable, 
                                     function(x) { x })[2, ], use.names = FALSE)
@@ -966,10 +999,10 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
         # analysis
         ciEnvelope(as.Date(obs.times[t1:t]), XaCI[, 1], XaCI[, 2], col = alphapink)
         lines(as.Date(obs.times[t1:t]), Xa, col = "black", lty = 2, lwd = 2)
-        legend('topright',c('Forecast','Data','Analysis'),col=c(alphablue,alphagreen,alphapink),lty=1,lwd=5)
+        #legend('topright',c('Forecast','Data','Analysis'),col=c(alphablue,alphagreen,alphapink),lty=1,lwd=5)
       }
     }
-    
+    #dev.off()
     ###-------------------------------------------------------------------###
     ### forecast step                                                     ###
     ###-------------------------------------------------------------------### 
@@ -980,13 +1013,17 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
       ### split model specific inputs for current runs                      ###
       ###-------------------------------------------------------------------### 
       
-      inputs <- list()
-      for(i in seq_len(nens)){
-        inputs[[i]] <- do.call(my.split_inputs, 
-                               args = list(settings = settings, 
-                                           start.time = (ymd_hms(obs.times[t],truncated = 3) + second(hms("00:00:01"))), 
-                                           stop.time = obs.times[t + 1],
-                                           inputs = ens.inputs[[i]])) 
+      if(!no_split){
+        
+        inputs <- list()
+        for(i in seq_len(nens)){
+          inputs[[i]] <- do.call(my.split_inputs, 
+                                 args = list(settings = settings, 
+                                             start.time = (ymd_hms(obs.times[t],truncated = 3) + second(hms("00:00:01"))), 
+                                             stop.time = obs.times[t + 1],
+                                             inputs = ens.inputs[[i]])) 
+          
+        }
       }
       
       
@@ -994,14 +1031,15 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
       ### write restart by ensemble                                         ###
       ###-------------------------------------------------------------------### 
       
-      
-      
       for (i in seq_len(nens)) {
+        
+        settings$run$inputs <- inputs[[i]]
+        
         do.call(my.write_restart, 
                 args = list(outdir = outdir, 
                             runid = run.id[[i]], 
-                            start.time = (ymd_hms(obs.times[t],truncated = 3) + second(hms("00:00:01"))),
-                            stop.time = ymd_hms(obs.times[t + 1],truncated = 3), 
+                            start.time = strptime(obs.times[t],format="%Y-%m-%d %H:%M:%S"),
+                            stop.time = strptime(obs.times[t + 1],format="%Y-%m-%d %H:%M:%S"), 
                             settings = settings,
                             new.state = new.state[i, ], 
                             new.params = new.params[[i]], 
@@ -1041,6 +1079,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
   ###-------------------------------------------------------------------###
   ### time series                                                       ###
   ###-------------------------------------------------------------------### 
+  
   pdf(file.path(settings$outdir, "sda.enkf.time-series.pdf"))
   
   names.y <- unique(unlist(lapply(obs.mean[t1:t], function(x) { names(x) })))
@@ -1051,7 +1090,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
     tmp[mch] <- x[mch]
     tmp
   }))
-  Y.order <- na.omit(pmatch(colnames(X), colnames(Ybar)))
+  Y.order <- na.omit(pmatch(colnames(FORECAST[[t]]), colnames(Ybar)))
   Ybar <- Ybar[,Y.order]
   YCI <- t(as.matrix(sapply(obs.cov[t1:t], function(x) {
     if (is.null(x)) {
@@ -1065,14 +1104,27 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
   
   YCI <- YCI[,Y.order]
   Xsum <- plyr::laply(FORECAST, function(x) { mean(rowSums(x[,1:length(names.y)], na.rm = TRUE)) })[t1:t]
+  Xasum <- plyr::laply(ANALYSIS, function(x) { mean(rowSums(x[,1:length(names.y)], na.rm = TRUE)) })[t1:t]
   
   for (i in seq_len(ncol(X))) {
-    Xbar <- plyr::laply(FORECAST[t1:t], function(x) { mean(x[, i], na.rm = TRUE) })
-    Xci <- plyr::laply(FORECAST[t1:t], function(x) { quantile(x[, i], c(0.025, 0.975)) })
+    Xbar <- plyr::laply(FORECAST[t1:t], function(x) {
+      mean(x[, i], na.rm = TRUE) }) #/rowSums(x[,1:9],na.rm = T)
+    Xci <- plyr::laply(FORECAST[t1:t], function(x) { 
+      quantile(x[, i], c(0.025, 0.975),na.rm = T) })
+    
     Xci[is.na(Xci)]<-0
     
-    Xa <- plyr::laply(ANALYSIS[t1:t], function(x) { mean(x[, i]) })
-    XaCI <- plyr::laply(ANALYSIS[t1:t], function(x) { quantile(x[, i], c(0.025, 0.975)) })
+    Xbar <- Xbar
+    Xci <- Xci
+    
+    Xa <- plyr::laply(ANALYSIS[t1:t], function(x) { 
+      
+      mean(x[, i],na.rm = T) })
+    XaCI <- plyr::laply(ANALYSIS[t1:t], function(x) { 
+      quantile(x[, i], c(0.025, 0.975),na.rm = T )})
+    
+    Xa <- Xa
+    XaCI <- XaCI
     
     plot(as.Date(obs.times[t1:t]),
          Xbar, 
@@ -1083,7 +1135,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
          main = colnames(X)[i])
     
     # observation / data
-    if (i <= ncol(Ybar)) {
+    if (i<ncol(X)) { #
       ciEnvelope(as.Date(obs.times[t1:t]), 
                  as.numeric(Ybar[, i]) - as.numeric(YCI[, i]) * 1.96, 
                  as.numeric(Ybar[, i]) + as.numeric(YCI[, i]) * 1.96, 
@@ -1094,16 +1146,17 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
     }
     
     # forecast
-    ciEnvelope(as.Date(obs.times[t1:t]), Xci[, 1], Xci[, 2], col = alphablue)  #col='lightblue')
-    lines(as.Date(obs.times[t1:t]), Xbar, col = "darkblue", type = "l", lwd = 2)
+    ciEnvelope(as.Date(obs.times[t1:t]), Xci[, 1], Xci[, 2], col = alphablue)  #col='lightblue') #alphablue
+    lines(as.Date(obs.times[t1:t]), Xbar, col = "darkblue", type = "l", lwd = 2) #"darkblue"
     
     # analysis
-    ciEnvelope(as.Date(obs.times[t1:t]), XaCI[, 1], XaCI[, 2], col = alphapink)
-    lines(as.Date(obs.times[t1:t]), Xa, col = "black", lty = 2, lwd = 2)
+    ciEnvelope(as.Date(obs.times[t1:t]), XaCI[, 1], XaCI[, 2], col = alphapink) #alphapink
+    lines(as.Date(obs.times[t1:t]), Xa, col = "black", lty = 2, lwd = 2) #"black"
     
     legend('topright',c('Forecast','Data','Analysis'),col=c(alphablue,alphagreen,alphapink),lty=1,lwd=5)
     
   }
+  
   dev.off()
   ###-------------------------------------------------------------------###
   ### bias diagnostics                                                  ###
@@ -1165,7 +1218,7 @@ sda.enkf <- function(settings, obs.mean, obs.cov, IC = NULL, Q = NULL, adjustmen
     library(corrplot)
     pdf('process.var.plots.pdf')
     
-    cor.mat <- cov2cor(aqq[t, , ] / bqq[t])
+    cor.mat <- cov2cor(aqq[t,,] / bqq[t])
     colnames(cor.mat) <- colnames(X)
     rownames(cor.mat) <- colnames(X)
     par(mfrow = c(1, 1), mai = c(1, 1, 4, 1))
diff --git a/modules/assim.sequential/inst/NEFI/README.txt b/modules/assim.sequential/inst/NEFI/README.txt
new file mode 100644
index 00000000000..73bade4ee66
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/README.txt
@@ -0,0 +1,72 @@
+Author: Luke Dramko
+
+This collection of R scripts utilizes the PEcAn workflow to iteratively run forecasts.
+
+run.gefs.sipnet.sh, generate.gefs.xml.R, and gefs.sipnet.source.xml work in tandem
+to run PEcAn's SIPNET model with current NOAA GEFS data.  This system can be put
+on a cron job with minimal effort; simply put the target of the cron job as 
+run.gefs.sipnet.sh
+
+-- run.gefs.sipnet.sh --
+This master bash script is intended to be called as a cron job, but it can be run
+manually as well.  It first runs generate.gefs.xml.R, then runs PEcAn based on the
+resulting xml.  If being used to manually run a PEcAn workflow, run.gefs.sipnet.sh's
+first command line argument can be a date.  That date will be used as the start 
+date for the run.  Several variables, declared at the top of the script, control
+critical file paths, such as the location of the desired copy of workflow.R and 
+the location of gefs.sipnet.source.xml and generate.gefs.xml
+
+Note that the current version of run.gefs.sipnet.sh actually has EXAMPLE in the title.
+This is because the script requires absolute paths to work properly, which will be different for every user.
+These paths are listed as variables at the top of the file; simply change them to the appropriate paths on your machine.
+
+-- gefs.sipnet.source.xml --
+This is the basis xml file from which all workflows are based.  generate.gefs.xml.R
+uses this as its basis.  Aside from the fields which generate.gefs.xml.R changes,
+all changes to the xml file are conserved between runs.  This xml contains settings
+for state data assimilation; change remove these if SDA is not to be used.
+
+-- generate.gefs.xml.R --
+This script overwrites gefs.sipnet.source xml with fresh values for any given run.
+It updates the following fields:
+* start and end date for <run>
+* workflow id
+* time of the run (<pecan><info><date>)
+* met.start and met.end
+* start.year and end.year for <ensemble>
+* output directory (but not the dbfile directory)
+Additionally, this script does some important work usually done by the web interface.
+In particular, it generates a unique workflow id based on the ids in the database
+and insert the workflow ID.
+It also generates the output folder.
+
+Several other scripts are included to make gathering and interpeting data easier
+
+-- graphs.R --
+Generates a graph of NEE and LE calculated via a run with a 95% confidence interval
+vs. observed data.  Can be called with either a date or a workflow ID as a command line argument.
+By default, this script places all graphs in ./graphs/.  If you want a different directory, change the graphs_dir
+file path at the start of the file.
+
+graphs.R is not intended to be a part of the PEcAn workflow; it is an independent script.
+
+-- graphs_timeframe.R --
+graphs_timeframe.R is intended to be used to make frames for a gif or other video format.  It locks the x and y axes,
+leading to consistent axes values between runs.  (graphs.R uses ggplot2's default x and y axes, which fit themselves to the
+data).  graphs_timeframe.R will graph only NEE or LE; this is because when both are graphed, the pdf device puts
+them into a single file.  graphs_timeframe.R accepts a second command line argument telling it which to run for.
+graphs_timeframe.R pads the data with NA's in order to properly place the data in the appropriate
+time span in the graph.  Otherwise, it works like graphs.R.
+
+Like graphs.R, graphs_timeframe.R is not intended to be part of the PEcAn workflow; it is an independent script.
+
+-- last12days.R --
+This is a simple and very specific script that runs NOAA GEFS for the last 12
+days.  This is useful because that's the range of time that NOAA_GEFS data is
+avaliable.
+
+* Database scripts *
+These scripts are useful for modifying the database.  Because everything NOAA_GEFS 
+does is repeated 21 times (1 for each ensemble member) it is impractical to 
+clean the database via the web interface, where only one file can be removed at
+a time. 
diff --git a/modules/assim.sequential/inst/NEFI/dbscripts/README.txt b/modules/assim.sequential/inst/NEFI/dbscripts/README.txt
new file mode 100644
index 00000000000..80e1a3f436b
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/dbscripts/README.txt
@@ -0,0 +1,22 @@
+These database scripts help identify and modify the state of the BETY database.
+Working with NOAA_GEFS data produces a lot of database files and IDs, so 
+this is a nicer way to interact with them all at once, rather than through
+the web interface.
+
+-- dbsetup.R --
+Sets up the connection to the database for running interactively in the consonle
+sourcing this script produces a PostgreSQL connection object named con, which
+can be passed to any of the PEcAn.DB functions.  Remember to close the connection
+when you're done with it.
+
+-- dbclean.R --
+Completely wipes the database of all NOAA_GEFS data at site 676 (Willow Creek)
+The script will print out all of the files it wants to wipe first, and exit.
+Run with the command line argument TRUE in order to clear files.
+
+-- dbSelectRemove.R --
+dbSelectRemove is a more conservative version of dbclean.  It removes only dbfiles
+and input files from a given day, provided as a command line argument.  By default,
+it will then print each file and exit; run with TRUE as a second command line a
+rgument to delete the files.  dbSelectRemove.R doesn NOT remove input/dbfiles
+for raw data, only for gapfilled and model-converted data.
diff --git a/modules/assim.sequential/inst/NEFI/dbscripts/dbSelectRemove.R b/modules/assim.sequential/inst/NEFI/dbscripts/dbSelectRemove.R
new file mode 100644
index 00000000000..57c68a9acf4
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/dbscripts/dbSelectRemove.R
@@ -0,0 +1,83 @@
+# Removes all references of the given date from the database
+
+library("dplyr")
+
+args <- commandArgs(trailingOnly = TRUE)
+
+len = length(args)
+args_idx = 1
+
+# Defaults
+pattern <- "NOAA_GEFS"
+delete <- FALSE
+
+if (len > 0) {
+  start_date <- args[1]
+} else {
+  print("Please enter a date to search for.")
+  quit("no")
+}
+
+if (len > 1 && args[2] == "TRUE") {
+  delete <- TRUE
+}
+
+## Open Connection
+bety <- dplyr::src_postgres(dbname   = 'bety', 
+                            host     = 'psql-pecan.bu.edu', 
+                            user     = 'bety', 
+                            password = 'bety')
+
+con <- bety$con
+##List All tables
+# src_tbls(bety)
+
+inputs = PEcAn.DB::db.query(paste0("SELECT * FROM inputs WHERE site_id=676 AND start_date='", start_date,
+                                   "' AND name='NOAA_GEFS_SIPNET_site_0-676'"), con = con)
+inputs = rbind(inputs, PEcAn.DB::db.query(paste0("SELECT * FROM inputs WHERE site_id=676 AND start_date='",start_date,
+                                                 "' AND name LIKE 'NOAA_GEFS__'"), con))
+
+inputs = rbind(inputs, PEcAn.DB::db.query(paste0("SELECT * FROM inputs WHERE site_id=676 AND start_date='",start_date,
+                                                 "' AND name LIKE 'NOAA_GEFS___'"), con))
+
+print("-------------- All matching files ----------------")
+print(inputs)
+print("--------------------------------------------------")
+
+inputs <- inputs[grepl(pattern, inputs$name),]
+print("@@@---------- Files to be Deleted -----------@@@")
+print(inputs)
+print("@@@------------------------------------------@@@")
+
+if (!delete) {
+  print("Run with TRUE as the second command line argument to delete files.")
+  quit("no")
+}
+
+for (i in 1:nrow(inputs)) {
+  print(paste0("i = ", i))
+  print(inputs[i,])
+  print("id")
+  print(inputs[i,]$id)
+  
+  hostname = PEcAn.remote::fqdn()
+  print(paste0("hostname = ", hostname))
+  
+  dbfile <- PEcAn.DB::dbfile.check(type = 'Input', container.id = inputs[i,]$id, con = con, hostname = hostname, machine.check = TRUE)
+  
+  print("dbfile")
+  print(dbfile)
+  
+  if (!is.null(dbfile$id)) {
+    PEcAn.DB::db.query(query =paste0("DELETE FROM dbfiles where id =", dbfile$id),
+                       con)
+    
+    print(paste0("dbfile ", dbfile$id ," removed."))
+  }
+  
+  PEcAn.DB::db.query(query =paste0("DELETE FROM inputs where id =", inputs[i,]$id),
+                     con)
+  print(paste0("inputfile ", inputs[i,]$id ," removed."))
+}
+
+PEcAn.DB::db.close(con)
\ No newline at end of file
diff --git a/modules/assim.sequential/inst/NEFI/dbscripts/dbclean.R b/modules/assim.sequential/inst/NEFI/dbscripts/dbclean.R
new file mode 100644
index 00000000000..81466350be7
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/dbscripts/dbclean.R
@@ -0,0 +1,79 @@
+# Database scrubbing script.  Destroys all input and associated dbfile entries with NOAA_GEFS in the file name.
+# @author Luke Dramko
+
+library("dplyr")
+
+args <- commandArgs(trailingOnly = TRUE)
+
+len = length(args)
+args_idx = 1
+
+# Defaults
+pattern <- "NOAA_GEFS"
+delete <- FALSE
+
+# Process command line arguments
+if (len >= 3 && args[args_idx] == "-P") {
+  args_idx = args_idx + 1
+  pattern = args[args_idx]
+  args_idx = args_idx + 1
+}
+if (len >= 1 && args[args_idx] == "TRUE") {
+  delete <- TRUE
+}
+
+## Open Connection
+bety <- dplyr::src_postgres(dbname   = 'bety', 
+                            host     = 'psql-pecan.bu.edu', 
+                            user     = 'bety', 
+                            password = 'bety')
+
+con <- bety$con
+##List All tables
+src_tbls(bety)
+
+inputs = PEcAn.DB::db.query("SELECT * FROM inputs WHERE site_id=676", con = con)
+
+print("-------------- All matching files ----------------")
+print(inputs)
+print("--------------------------------------------------")
+
+inputs <- inputs[grepl(pattern, inputs$name),]
+print("@@@---------- Files to be Deleted -----------@@@")
+print(inputs)
+print("@@@------------------------------------------@@@")
+
+if (delete) {
+  print("Moving on to delete files.")
+} else {
+  print("Quitting (default behavior).  Run with 'TRUE' as a command line argument to delete files.")
+  quit("no")  ### Remove to run.  This is a safety feature.
+}
+
+for (i in 1:nrow(inputs)) {
+  print(paste0("i = ", i))
+  print(inputs[i,])
+  print("id")
+  print(inputs[i,]$id)
+  
+  hostname = PEcAn.remote::fqdn()
+  print(paste0("hostname = ", hostname))
+  
+  dbfile <- PEcAn.DB::dbfile.check(type = 'Input', container.id = inputs[i,]$id, con = con, hostname = hostname, machine.check = TRUE)
+  
+  print("dbfile")
+  print(dbfile)
+  
+  if (!is.null(dbfile$id)) {
+    PEcAn.DB::db.query(query =paste0("DELETE FROM dbfiles where id =", dbfile$id),
+                      con)
+    
+    print(paste0("dbfile ", dbfile$id ," removed."))
+  }
+  
+   PEcAn.DB::db.query(query =paste0("DELETE FROM inputs where id =", inputs[i,]$id),
+           con)
+   print(paste0("inputfile ", inputs[i,]$id ," removed."))
+}
+
+PEcAn.DB::db.close(con)
\ No newline at end of file
diff --git a/modules/assim.sequential/inst/NEFI/dbscripts/dbsetup.R b/modules/assim.sequential/inst/NEFI/dbscripts/dbsetup.R
new file mode 100644
index 00000000000..1ae7590355e
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/dbscripts/dbsetup.R
@@ -0,0 +1,17 @@
+# Creates a database connection to BETY.  Useful for working in the console.
+
+dbparms = list()
+dbparms$dbname = "bety"
+dbparms$host = "128.197.168.114"
+dbparms$user = "bety"
+dbparms$password = "bety"
+
+
+#--------------------------------------------------
+#Connection code copied and pasted from met.process
+bety <- dplyr::src_postgres(dbname   = dbparms$dbname, 
+                            host     = dbparms$host, 
+                            user     = dbparms$user, 
+                            password = dbparms$password)
+
+con <- bety$con #Connection to the database.  dplyr returns a list.
diff --git a/modules/assim.sequential/inst/NEFI/gefs.sipnet.source.xml b/modules/assim.sequential/inst/NEFI/gefs.sipnet.source.xml
new file mode 100644
index 00000000000..79ec5c88184
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/gefs.sipnet.source.xml
@@ -0,0 +1,140 @@
+<?xml version="1.0"?>
+<pecan>
+ <state.data.assimilation>
+  <n.ensemble>35</n.ensemble>
+  <process.variance>FALSE</process.variance>
+  <sample.parameters>TRUE</sample.parameters>
+  <data>
+   <format_id>1000000040</format_id>
+   <input.id>1000013298</input.id>
+  </data>
+  <state.variables>
+   <variable>
+    <variable.name>NEE</variable.name>
+    <unit>MgC/ha/yr</unit>
+    <min_value>-9999</min_value>
+    <max_value>9999</max_value>
+   </variable>
+   <variable>
+    <variable.name>LE</variable.name>
+    <unit>MgC/ha/yr</unit>
+    <min_value>-9999</min_value>
+    <max_value>9999</max_value>
+   </variable>
+   <variable>
+    <variable.name>AbvGrndWood</variable.name>
+    <unit>KgC/m^2</unit>
+    <min_value>0</min_value>
+    <max_value>9999</max_value>
+   </variable>
+   <variable>
+    <variable.name>TotSoilCarb</variable.name>
+    <unit>KgC/m^2</unit>
+    <min_value>0</min_value>
+    <max_value>9999</max_value>
+   </variable>
+   <variable>
+    <variable.name>LeafC</variable.name>
+    <unit>m^2/m^2</unit>
+    <min_value>0</min_value>
+    <max_value>9999</max_value>
+   </variable>
+   <variable>
+    <variable.name>SoilMoistFrac</variable.name>
+    <unit></unit>
+    <min_value>0</min_value>
+    <max_value>9999</max_value>
+   </variable>
+   <variable>
+    <variable.name>SWE</variable.name>
+    <unit>cm</unit>
+    <min_value>0</min_value>
+    <max_value>9999</max_value>
+   </variable>
+   <variable>
+    <variable.name>Litter</variable.name>
+    <unit>gC/m^2</unit>
+    <min_value>0</min_value>
+    <max_value>9999</max_value>
+   </variable>
+  </state.variables>
+  <forecast.time.step>year</forecast.time.step>
+  <start.date>1980/01/01</start.date>
+  <end.date>2015/12/31</end.date>
+ </state.data.assimilation>
+ <info>
+  <notes></notes>
+  <userid>-1</userid>
+  <username></username>
+  <date>2018/08/02 09:04:39 +0000</date>
+ </info>
+ <outdir>/fs/data3/ldramko/output/PEcAn_1000009609/</outdir>
+ <database>
+  <bety>
+   <user>bety</user>
+   <password>bety</password>
+   <host>psql-pecan.bu.edu</host>
+   <dbname>bety</dbname>
+   <driver>PostgreSQL</driver>
+   <write>false</write>
+  </bety>
+  <dbfiles>/fs/data3/ldramko/pecan.data/dbfiles/</dbfiles>
+ </database>
+ <pfts>
+  <pft>
+   <name>temperate.coniferous</name>
+   <constants>
+    <num>1</num>
+   </constants>
+  </pft>
+ </pfts>
+ <meta.analysis>
+  <iter>3000</iter>
+  <random.effects>FALSE</random.effects>
+ </meta.analysis>
+ <ensemble>
+  <size>100</size>
+  <variable>NEE</variable>
+  <start.year>2018</start.year>
+  <end.year>2018</end.year>
+  <samplingspace>
+   <parameters>
+    <method>uniform</method>
+   </parameters>
+   <met>
+    <method>sampling</method>
+   </met>
+   <soil>
+    <parent>parameters</parent>
+   </soil>
+   <vegetation>
+    <parent>soil</parent>
+   </vegetation>
+  </samplingspace>
+ </ensemble>
+ <model>
+  <id>10</id>
+  <default.param>/fs/data3/ldramko/US_WCr/data/WillowCreek.param</default.param>
+ </model>
+ <workflow>
+  <id>1000009609</id>
+ </workflow>
+ <run>
+  <site>
+   <id>676</id>
+   <met.start>2018-07-21</met.start>
+   <met.end>2018-08-18</met.end>
+  </site>
+  <inputs>
+   <met>
+    <source>NOAA_GEFS</source>
+    <output>SIPNET</output>
+   </met>
+  </inputs>
+  <start.date>2018-07-20</start.date>
+  <end.date>2018-08-05</end.date>
+ </run>
+ <host>
+  <name>localhost</name>
+ </host>
+</pecan>
diff --git a/modules/assim.sequential/inst/NEFI/generate.gefs.xml.R b/modules/assim.sequential/inst/NEFI/generate.gefs.xml.R
new file mode 100644
index 00000000000..a110ba1f148
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/generate.gefs.xml.R
@@ -0,0 +1,133 @@
+## Some global environment variables
+.wd <- getwd() # Set this to whatever you want the working directory to be.  If this is run off a cron job, 
+               # you probably do not want the working directory to be cron's working directory, which is what getwd will return.
+
+
+##'
+##' Rounds a date to the previous 6 hours (0:00, 6:00, 12:00, or 18:00).
+##' 
+##' @author Luke Dramko
+round.to.six.hours <- function(date = Sys.time() - lubridate::hours(2)) {
+  if (is.character(date)) {
+    date <- as.POSIXct(date, tz="UTC")
+  }
+  forecast_hour = (lubridate::hour(date) %/% 6) * 6 #Integer division by 6 followed by re-multiplication acts like a "floor function" for multiples of 6
+  forecast_hour = sprintf("%04d", forecast_hour * 100)
+  date = as.POSIXct(paste0(lubridate::year(date), "-", lubridate::month(date), "-", lubridate::day(date), " ", 
+                                 substring(forecast_hour, 1,2), ":00:00"), tz="UTC")
+  
+  return(date)
+}
+
+
+##'
+##'This script sets up the xml for, and runs PEcAn for the following settings:
+##'
+##'NOAA_GEFS data
+##'Start date: current date/time
+##'End date: 16 days in the future
+##'model: SIPNET
+##'
+##'@author Luke Dramko
+
+# Settings file (including path) is passed in on the command line.
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) < 1) {
+  print("Please include an xml file as a command line argument.")
+  quit("no", status = 10)
+}
+if (!file.exists(args[1])) {
+  print(paste0("File ", args[1], " does not exist."))
+  quit("no", status = 11)
+}
+if (!is.na(args[2])) {
+  source_date <- args[2]
+}
+
+# These lines from the PEcAn workflow load the settings object.
+settings <- PEcAn.settings::read.settings(args[1])
+
+xmloutdir <- regmatches(args[1], regexpr("(~|\\./)?(/)?([^/]*/)*", args[1])) # extract xmloutdir from args[1]
+filename <- basename(args[1]) # Extract file name from args[1]
+
+if(xmloutdir == "") {xmloutdir <- "."}
+
+dbparms = list()
+dbparms$dbname = "bety"
+dbparms$host = "128.197.168.114"
+dbparms$user = "bety"
+dbparms$password = "bety"
+
+#Connection code copied and pasted from met.process
+bety <- dplyr::src_postgres(dbname   = dbparms$dbname, 
+                            host     = dbparms$host, 
+                            user     = dbparms$user, 
+                            password = dbparms$password)
+
+con <- bety$con #Connection to the database.  dplyr returns a list.
+if (is.null(con)) {
+  print("Database connection failed.")
+  quit("no", status=12)
+}
+
+# Set the run dates
+if (exists("source_date")) {
+  start_date <- round.to.six.hours(source_date)
+} else {
+  start_date <- round.to.six.hours()
+}
+
+end_date <- start_date + lubridate::days(16)
+settings$run$start.date <- as.character(start_date)
+settings$run$end.date <- as.character(end_date)
+
+#settings$ensemble$start.year <- start_date
+#settings$ensemble$end.year <- end_date
+
+# Update the time of the run
+settings$info$date <- paste0(format(Sys.time(), "%Y/%m/%d %H:%M:%S"), " +0000")
+
+# Update met.start and met.end for the xml (shouldn't make a difference,
+# but good practice anyway).
+settings$run$site$met.start <- format(Sys.time() - lubridate::days(12), "%Y-%m-%d")
+settings$run$site$met.end <- format(Sys.time() + lubridate::days(16), "%Y-%m-%d")
+
+settings$ensemble$start.year <- format(start_date, "%Y")
+settings$ensemble$end.year <- as.character(end_date, "%Y")
+
+# Create new workflow ID and register it with the database
+hostname <- PEcAn.remote::fqdn()
+query <- paste0("INSERT INTO workflows (site_id, model_id, notes, folder, hostname, start_date,", 
+                "end_date, params, advanced_edit) ", 
+                "values (", settings$run$site$id, ", ", settings$model$id, ", ", "''", ", '', '", hostname, "', '",
+                format(start_date, "%Y/%m/%d %H:%M:%S"), "', '", format(end_date, "%Y/%m/%d %H:%M:%S"), "', ", "''", ", ", "true) RETURNING id")
+workflowid <- PEcAn.DB::db.query(query, con = con)
+workflowid <- as.character(unlist(workflowid))
+
+settings$workflow$id <- workflowid
+
+#The outdirectory is specific to a particular workflow
+outdir <- settings$outdir
+if (substr(outdir, nchar(outdir), nchar(outdir)) == "/") {
+  outdir <- substr(outdir, 1, nchar(outdir) -1 )
+}
+
+basedir <- regmatches(outdir, regexpr("(~|\\./)?(/)?([^/]*/)*", outdir))
+outdir <- paste0(basedir, "PEcAn_", workflowid, "/")
+settings$outdir <- outdir
+
+# Create the output directory.  PEcAn does not do this for you.  It's normally the job of the
+# web interface's php code.
+if (!dir.exists(outdir)) {
+  dir.create(outdir, recursive=TRUE, showWarnings = FALSE)
+}
+
+
+# Log workflow ids generated by this system
+write(workflowid, append = TRUE, file = file.path(.wd, "workflow_id_log.txt"))
+
+PEcAn.DB::db.close(con)
+
+# Write out the file with updated settings
+PEcAn.settings::write.settings(settings, outputfile = filename, outputdir = xmloutdir)
+
diff --git a/modules/assim.sequential/inst/NEFI/graphs.R b/modules/assim.sequential/inst/NEFI/graphs.R
new file mode 100644
index 00000000000..fd398557b67
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/graphs.R
@@ -0,0 +1,160 @@
+# Creates a plot of the nc files generated by the workflow
+# @author Luke Dramko
+library("tidyverse")
+
+graph_dir = "./graphs/"
+args = commandArgs(trailingOnly = TRUE)
+if (is.na(args[1])) {
+  print("Please include a start date or workflow id.")
+  exit("Missing input parameter")
+}
+# Validate date
+start_date <- tryCatch(as.POSIXct(args[1]), error = function(e) {NULL} )
+if (is.null(start_date)) {
+  in_wid <- as.integer(args[1])
+}
+# Set up database connection
+dbparms = list()
+dbparms$dbname = "bety"
+dbparms$host = "128.197.168.114"
+dbparms$user = "bety"
+dbparms$password = "bety"
+#Connection code copied and pasted from met.process
+bety <- dplyr::src_postgres(dbname   = dbparms$dbname, 
+                            host     = dbparms$host, 
+                            user     = dbparms$user, 
+                            password = dbparms$password)
+con <- bety$con #Connection to the database.  dplyr returns a list.
+# Identify the workflow with the proper information
+if (!is.null(start_date)) {
+  workflows <- PEcAn.DB::db.query(paste0("SELECT * FROM workflows WHERE start_date='", format(start_date, "%Y-%m-%d %H:%M:%S"), 
+                                         "' ORDER BY id"), con)
+} else {
+  workflows <- PEcAn.DB::db.query(paste0("SELECT * FROM workflows WHERE id='", in_wid, "'"), con)
+}
+print(workflows)
+if (nrow(workflows) == 0) {
+  print("No workflow found.")
+  quit("no")
+}
+if (nrow(workflows) > 1) {
+  print("Multiple workflows found: Using the latest")
+  workflow <- workflows[nrow(workflows),]
+} else {
+  workflow <- workflows
+}
+print(paste0("Using workflow ", workflow$id))
+wid <- workflow$id
+pecan_out_dir <- paste0("/fs/data3/ldramko/output/PEcAn_", wid, "/out/");
+pecan_out_dirs <- list.dirs(path = pecan_out_dir)
+if (is.na(pecan_out_dirs[1])) {
+  print(paste0(pecan_out_dirs, " does not exist."))
+  quit("no")
+}
+neemat <- matrix(1:64, nrow=1, ncol=64) # Proxy row, will be deleted later.
+qlemat <- matrix(1:64, nrow=1, ncol=64) # Proxy row, will be deleted later.
+num_results <- 0;
+for (i in 1:length(pecan_out_dirs)) {
+  datafile <- file.path(pecan_out_dirs[i], format(workflow$start_date, "%Y.nc"))
+  if (!file.exists(datafile)) {
+    print(paste0("File ", datafile, " does not exist."))
+    next
+  }
+  
+  num_results <- num_results + 1
+  
+  #open netcdf file
+  ncptr <- ncdf4::nc_open(datafile);
+  
+  # Attach data to matricies
+  nee <- ncdf4::ncvar_get(ncptr, "NEE")
+  neemat <- rbind(neemat, nee)
+  
+  qle <- ncdf4::ncvar_get(ncptr, "Qle")
+  qlemat <- rbind(qlemat, qle)
+  
+  # Close netcdf file
+  ncdf4::nc_close(ncptr)
+}
+if (num_results == 0) {
+  print("No results found.")
+  quit("no")
+} else {
+  print(paste0(num_results, " results found."))
+}
+# Strip away proxy rows
+neemat <- neemat[-1,]
+qlemat <- qlemat[-1,]
+# Time
+time <- seq(6, 6 * ncol(neemat), by=6)
+# Caluclate means
+neemins <- NULL
+neemaxes <- NULL
+quantiles <- apply(neemat,2,quantile,c(0.025,0.5,0.975), na.rm=TRUE)
+neelower95 <- quantiles[1,]
+neemeans <- quantiles[2,]
+neeupper95 <- quantiles[3,]
+# Determines outliers... not requested anymore
+# for (i in 1:ncol(neemat)) {
+#  without_outliers <- neemat[,i]
+#  without_outliers <- without_outliers[!without_outliers %in% boxplot.stats(without_outliers)$out]
+#  neemins <- c(neemins, min(without_outliers))
+#  neemaxes <- c(neemaxes, max(without_outliers))
+#}
+needf <- data.frame(time = time, lower = neelower95, means = neemeans, upper = neeupper95)
+quantiles <- apply(qlemat,2,quantile,c(0.025,0.5,0.975), na.rm=TRUE)
+qlelower95 <- quantiles[1,]
+qlemeans <- quantiles[2,]
+qleupper95 <- quantiles[3,]
+qledf <- data.frame(time = time, lower = qlelower95, means = qlemeans, upper = qleupper95)
+# Reshape data for data frame
+#time <- factor(rep(seq(6, 6 * 64, by=6), each=num_results))
+#nee = NULL; # An empty vector
+#for (i in 1:ncol(neemat)) {
+#  nee <- c(nee, neemat[,i])
+#}
+#qle = NULL;
+#for (i in 1:ncol(qlemat)) {
+#  qle <- c(qle, qlemat[,i])
+#}
+#
+# Put data into data frame for ggplot
+#needf <- data.frame(time = time,
+#                    nee = nee)
+#qledf <- data.frame(time = time,
+#                     qle = qle)
+
+# Grab real data
+real_data <- PEcAn.data.atmosphere::download.US_WCr(workflow$start_date, workflow$end_date, timestep=6)
+needf$real_nee <- real_data$nee
+qledf$real_qle <- real_data$qle
+
+# Create plots
+neeplot <- ggplot(needf) + 
+  # geom_ribbon(aes(x=time, ymin=neemins, ymax=neemaxes, fill="Spread of data (excluding outliers)"), alpha = 0.7) +
+  geom_ribbon(aes(x = time, ymin=neelower95, ymax=neeupper95, fill="95% confidence interval"), alpha = 0.4) + 
+  geom_line(aes(x=time, y=neemeans, color="predicted mean")) +
+  geom_point(aes(x=time, y=real_data$nee, color="actual data")) +
+  ggtitle(paste0("Net Ecosystem Exchange for ", workflow$start_date, " to ", workflow$end_date, "")) +
+  scale_x_continuous(name="Time (hours)") + scale_y_continuous(name="NEE (kg C m-2 s-1)") + 
+  scale_colour_manual(name='Legend', values=c("predicted mean"="lightskyblue1", "actual data"="darkorange3")) +
+  scale_fill_manual(name='Legend', values=c("95% confidence interval" = "blue3", "mean"="lightskyblue1"))
+  qleplot <- ggplot(qledf) +
+ # geom_ribbon(aes(x=time, ymin=qlemins, ymax=qlemax, fill="Spread of data (excluding outliers)"), alpha=0.7) +
+  geom_ribbon(aes(x=time, ymin=qlelower95, ymax=qleupper95, fill="95% confidence interval"), alpha = 0.4) +
+  geom_line(aes(x=time, y=qlemeans, color="mean")) +
+  geom_point(aes(x=time, y=real_data$qle, color="actual data")) +
+  ggtitle(paste0("LE for ", workflow$start_date, " to ", workflow$end_date, ", \nSummary of All Ensembles")) +
+  scale_x_continuous(name="Time (hours)") + scale_y_continuous(name="LE (W m-2 s-1)") +
+  scale_color_manual(name='Legend', values=c("mean"="lightskyblue1", "actual data"="darkorange3")) + 
+  scale_fill_manual(name='Legend', values=c("95% confidence interval" = "blue3"))
+  
+if (!dir.exists(graph_dir)) {
+  dir.create(graph_dir, recursive = TRUE)
+}
+print("Saving plots")
+# save(neeplot, file="plot.Rdata")
+pdf(file.path(graph_dir, paste0(format(workflow$start_date, "%Y-%m-%dT%H:%M:%SNEE"), ".pdf")), width = 6, height = 3)
+plot(neeplot)
+plot(qleplot)
+dev.off()
diff --git a/modules/assim.sequential/inst/NEFI/graphs_timeframe.R b/modules/assim.sequential/inst/NEFI/graphs_timeframe.R
new file mode 100644
index 00000000000..a6c5939cde3
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/graphs_timeframe.R
@@ -0,0 +1,238 @@
+# Creates a plot of the nc files generated by the workflow.
+# This version of graphs.R, graphs_timeframe.R, generates the graphs inside a consistent frame (a consistent x
+# axis and y axis).
+# This makes them easier to make into a gif.
+# @author Luke Dramko
+
+library("ggplot2")
+
+args = commandArgs(trailingOnly = TRUE)
+outfolder = "./graphs"  # Where output graphs are put
+
+# These variables control the start and end dates of the x axis.
+frame_start <- as.POSIXct('2018-07-13 00:00')
+frame_end <- as.POSIXct('2018-08-18 00:00')
+
+# These variables control the start and end dates of the y axis
+nee_upper = 1e-06
+nee_lower = -1e-06
+qle_upper = 350
+qle_lower = -50
+
+
+if (is.na(args[1])) {
+  print("Please include a start date or workflow id.")
+  exit("Missing input parameter")
+}
+
+# Validate date
+start_date <- tryCatch(as.POSIXct(args[1]), error = function(e) {NULL} )
+
+in_wid = 0
+if (is.null(start_date)) {
+  in_wid <- as.integer(args[1])
+}
+
+if (is.na(in_wid)) {
+  print("First argument must be a date or workflow id")
+  quit("no")
+}
+
+graph_for = "NEE"
+if (!is.na(args[2]) && args[2] == "LE") {
+  graph_for = "LE"
+} else if (!is.na(args[2]) && args[2] == "NEE") {
+  graph_for = "NEE"
+} else {
+  print("Invalid second argument, must be NEE or LE.  Defaulting to NEE.")
+}
+
+# Set up database connection
+dbparms = list()
+dbparms$dbname = "bety"
+dbparms$host = "128.197.168.114"
+dbparms$user = "bety"
+dbparms$password = "bety"
+
+#Connection code copied and pasted from met.process
+bety <- dplyr::src_postgres(dbname   = dbparms$dbname, 
+                            host     = dbparms$host, 
+                            user     = dbparms$user, 
+                            password = dbparms$password)
+
+con <- bety$con #Connection to the database.  dplyr returns a list.
+
+# Identify the workflow with the proper information
+if (!is.null(start_date)) {
+  workflows <- PEcAn.DB::db.query(paste0("SELECT * FROM workflows WHERE start_date='", format(start_date, "%Y-%m-%d %H:%M:%S"), 
+                                         "' ORDER BY id"), con)
+} else {
+  workflows <- PEcAn.DB::db.query(paste0("SELECT * FROM workflows WHERE id='", in_wid, "'"), con)
+}
+
+print(workflows)
+
+if (nrow(workflows) == 0) {
+  print("No workflow found.")
+  quit("no")
+}
+
+if (nrow(workflows) > 1) {
+  print("Multiple workflows found: Using the latest")
+  workflow <- workflows[nrow(workflows),]
+} else {
+  workflow <- workflows
+}
+
+print(paste0("Using workflow ", workflow$id))
+
+wid <- workflow$id
+pecan_out_dir <- paste0("/fs/data3/ldramko/output/PEcAn_", wid, "/out/");
+pecan_out_dirs <- list.dirs(path = pecan_out_dir)
+
+if (is.na(pecan_out_dirs[1])) {
+  print(paste0(pecan_out_dirs, " does not exist."))
+  quit("no")
+}
+
+neemat <- matrix(1:64, nrow=1, ncol=64) # Proxy row, will be deleted later.
+qlemat <- matrix(1:64, nrow=1, ncol=64) # Proxy row, will be deleted later.
+
+num_results <- 0;
+
+for (i in 1:length(pecan_out_dirs)) {
+  datafile <- file.path(pecan_out_dirs[i], format(workflow$start_date, "%Y.nc"))
+  if (!file.exists(datafile)) {
+    print(paste0("File ", datafile, " does not exist."))
+    next
+  }
+  
+  num_results <- num_results + 1
+  
+  #open netcdf file
+  ncptr <- ncdf4::nc_open(datafile);
+  
+  # Attach data to matricies
+  nee <- ncdf4::ncvar_get(ncptr, "NEE")
+  neemat <- rbind(neemat, nee)
+  
+  qle <- ncdf4::ncvar_get(ncptr, "Qle")
+  qlemat <- rbind(qlemat, qle)
+  
+  # Close netcdf file
+  ncdf4::nc_close(ncptr)
+}
+
+if (num_results == 0) {
+  print("No results found.")
+  quit("no")
+} else {
+  print(paste0(num_results, " results found."))
+}
+
+# Strip away proxy rows
+neemat <- neemat[-1,]
+qlemat <- qlemat[-1,]
+
+# Time
+Time <- seq(frame_start, frame_end, by="6 hours")
+Time <- Time[-1] # The start date is not included in the forecast
+
+# Caluclate means
+neemins <- NULL
+neemaxes <- NULL
+
+quantiles <- apply(neemat,2,quantile,c(0.025,0.5,0.975), na.rm=TRUE)
+neelower95 <- quantiles[1,]
+neemeans <- quantiles[2,]
+neeupper95 <- quantiles[3,]
+
+quantiles <- apply(qlemat,2,quantile,c(0.025,0.5,0.975), na.rm=TRUE)
+qlelower95 <- quantiles[1,]
+qlemeans <- quantiles[2,]
+qleupper95 <- quantiles[3,]
+
+# Grab real data as.POSIXct(workflow$end_date)
+real_data <- PEcAn.data.atmosphere::download.US_WCr(frame_start, as.POSIXct(workflow$end_date), timestep = 6)
+
+real_nee <- real_data$nee
+real_qle <- real_data$qle
+
+# Pad data with NA's to appropriately position the forecast in the graph. (For the forecast data)
+# Pad NA's at the front
+numNAs = lubridate::as.duration(lubridate::interval(frame_start, as.POSIXct(workflow$start_date)))
+numNAs <- udunits2::ud.convert(numNAs, "s", "h") / 6
+if (floor(numNAs) != numNAs) {
+  print("Time scale incorrect.")
+  quit("no")
+}
+
+for (i in seq_len(numNAs)) {
+  neelower95 <- c(NA, neelower95)
+  neemeans <- c(NA, neemeans)
+  neeupper95 <- c(NA, neeupper95)
+  qlelower95 <- c(NA, qlelower95)
+  qlemeans <- c(NA, qlemeans)
+  qleupper95 <- c(NA, qleupper95)
+}
+
+# Pad NA's at the end
+numNAs = lubridate::as.duration(lubridate::interval(as.POSIXct(workflow$end_date), frame_end))
+numNAs <- udunits2::ud.convert(numNAs, "s", "h") / 6
+
+if (floor(numNAs) != numNAs) {
+  print("Time scale incorrect.")
+  quit("no")
+}
+
+for (i in seq_len(numNAs)) {
+  neelower95 <- c(neelower95, NA)
+  neemeans <- c(neemeans, NA)
+  neeupper95 <- c(neeupper95, NA)
+  qlelower95 <- c(qlelower95, NA)
+  qlemeans <- c(qlemeans, NA)
+  qleupper95 <- c(qleupper95, NA)
+  real_nee <- c(real_nee, NA)
+  real_qle <- c(real_qle, NA)
+}
+
+needf <- data.frame(Time = Time, lower = neelower95, means = neemeans, upper = neeupper95, real_nee = real_nee)
+qledf <- data.frame(Time = Time, lower = qlelower95, means = qlemeans, upper = qleupper95, real_qle = real_qle)
+
+# Create better plots
+neeplot <- ggplot(needf) + 
+  # geom_ribbon(aes(x=time, ymin=neemins, ymax=neemaxes, fill="Spread of data (excluding outliers)"), alpha = 0.7) +
+  geom_ribbon(aes(x = Time, ymin=neelower95, ymax=neeupper95, fill="95% confidence interval"), alpha = 0.4) + 
+  geom_line(aes(x=Time, y=neemeans, color="predicted mean")) +
+  geom_point(aes(x=Time, y=real_nee, color="observed data")) +
+  ggtitle(paste0("Net Ecosystem Exchange for ", workflow$start_date, " to ", workflow$end_date, ", Willow Creek, Wisconson")) +
+  xlim(frame_start, frame_end) +
+  theme(axis.text.x=element_text(angle=60, hjust=1)) +
+  scale_colour_manual(name='Legend', values=c("predicted mean"="lightskyblue1", "observed data"="orange1")) +
+  scale_fill_manual(name='Legend', values=c("Spread of data (excluding outliers)"="azure4", "95% confidence interval" = "blue3", "mean"="lightskyblue1")) +
+  scale_y_continuous(name="NEE (kg C m-2 s-1)", limits=c(nee_lower, nee_upper))
+
+  qleplot <- ggplot(qledf) +
+  geom_ribbon(aes(x=Time, ymin=qlelower95, ymax=qleupper95, fill="95% confidence interval"), alpha = 0.4) +
+  geom_line(aes(x=Time, y=qlemeans, color="mean")) +
+  geom_point(aes(x=Time, y=real_qle, color="observed data")) +
+  ggtitle(paste0("Latent Energy for ", workflow$start_date, " to ", workflow$end_date, ", Summary of All Ensembles")) + 
+  xlim(frame_start, frame_end) +
+  theme(axis.text.x=element_text(angle=60, hjust=1)) +
+  scale_color_manual(name='Legend', values=c("mean"="lightskyblue1", "observed data"="orange2")) + 
+  scale_fill_manual(name='Legend', values=c("95% confidence interval" = "blue3")) +
+  scale_y_continuous(name="LE (W m-2 s-1)", limits = c(qle_lower, qle_upper))
+  
+if (!dir.exists(outfolder)) {
+  dir.create(outfolder, recursive = TRUE)
+}
+
+print("Saving plots")
+if (graph_for == "LE") {
+  pdf(file.path(outfolder, format(workflow$start_date, "%Y-%m-%dT%H:%M:%SLE.pdf")), width = 12, height = 6)
+  plot(qleplot)
+} else {
+  pdf(file.path(outfolder, format(workflow$start_date, "%Y-%m-%dT%H:%M:%SNEE.pdf")), width = 12, height = 6)
+  plot(neeplot)
+}
+dev.off()
diff --git a/modules/assim.sequential/inst/NEFI/last12days.R b/modules/assim.sequential/inst/NEFI/last12days.R
new file mode 100644
index 00000000000..b8ab05269dc
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/last12days.R
@@ -0,0 +1,31 @@
+# Grab the last 12 days worth of data
+# Defaults to the midnight forecast.
+# @author Luke Dramko
+
+cur_date <- as.POSIXct(Sys.time(), tz = "UTC")
+print(cur_date)
+
+for (i in 1:1) {
+  cur_date_str <- paste0(format(cur_date, "%Y-%m-%d"), " 00:00");
+  print(paste("Running PEcAn for NOAA_GEFS for date", cur_date_str))
+  
+  #Generate the xml
+  system(paste0("Rscript generate.gefs.xml.R gefs.sipnet.source.xml ", cur_date_str))
+  
+  #Run PEcAn
+  cmd <- "Rscript"
+  args <- c("/home/ldramko/pecan/web/workflow.R", "/home/ldramko/NEFI_tools/pecan_scripts/gefs.sipnet.source.xml")
+  cmd_out <- system2(cmd, args, stdout=TRUE, stderr=TRUE)
+  # cmd_out <- "Redirected to shell."
+  
+  #Obtain information about the run
+  settings <- PEcAn.settings::read.settings("/home/ldramko/NEFI_tools/pecan_scripts/gefs.sipnet.source.xml")
+  workflowid <- settings$workflow$id
+  
+  #Write workflow output to a file
+  basefolder <- paste0("/fs/data3/ldramko/output/PEcAn_", workflowid);
+  write(cmd_out, append = TRUE, file = file.path(basefolder, "workflow.log.txt"))
+  
+  #Run for the previous day
+  cur_date <- cur_date - lubridate::days(1)
+}
\ No newline at end of file
diff --git a/modules/assim.sequential/inst/NEFI/run.gefs.sipnet.EXAMPLE.sh b/modules/assim.sequential/inst/NEFI/run.gefs.sipnet.EXAMPLE.sh
new file mode 100755
index 00000000000..ed1b0531e36
--- /dev/null
+++ b/modules/assim.sequential/inst/NEFI/run.gefs.sipnet.EXAMPLE.sh
@@ -0,0 +1,30 @@
+# This script first runs a program which sets up the xml file for a current
+# NOAA_GEFS PEcAn run, then runs PEcAn with that file.
+# @author Luke Dramko
+
+# REPLACE < username > WITH YOUR USERNAME
+# If running from a CRON job, these paths MUST be absolute paths.  This is because CRON assumes that the directory it is in is the working directory.
+xmlfile="./gefs.sipnet.source.xml" #Path to, and name of, the base xml file.
+workflow_path="./../../../../scripts/"                     #Path to workflow.R (in pecan/web for the standard version or pecan/scripts for the custom version).
+output_path="/fs/data3/< username >/output/"               #Path to the directory where all PEcAn output is put.
+xmlscript="./generate.gefs.xml.R"                          #Path to, and name of, the script that modifies the xml.
+# Could also be just workflow.R in pecan/web
+workflow_name="workflow.wcr.assim.R"                       #Name of the workflow.R version
+
+# Generates the xml file based on a given input file.  Overwrites the
+# input file.
+Rscript $xmlscript $xmlfile $1 &> /dev/null
+if [ $? -eq 11 ];
+then
+  echo "xml file not found."
+elif [ $? -eq 12 ]
+then
+  echo "Database connection failed."
+else
+  # Find the most recently created output directory.  This system is kind of hack-y, and is messed up if anything after
+  # "PEcAn", alphabetically, is put in the directory.  Fortunately, that is unlikely to happen.
+  output_dir=$(ls $output_path | sort -V | tail -n 1)
+  # Runs the PEcAn workflow.
+  Rscript ${workflow_path}${workflow_name} $xmlfile &> ${output_path}/${output_dir}/workflow.log.txt
+  echo "Workflow completed."
+fi
diff --git a/modules/assim.sequential/inst/ensemble_adj_visualization.R b/modules/assim.sequential/inst/ensemble_adj_visualization.R
new file mode 100644
index 00000000000..1bdb9c13d1b
--- /dev/null
+++ b/modules/assim.sequential/inst/ensemble_adj_visualization.R
@@ -0,0 +1,270 @@
+setwd('/fs/data2/output//PEcAn_1000008683/')
+load('/fs/data2/output//PEcAn_1000008683/sda.output.Rdata')
+load('/fs/data2/output//PEcAn_1000008683/out/sda.initial.runs.Rdata')
+library(nimble)
+
+time_step<-seq(950,1950,100)
+ntrees.save <- agb.pft.save <- array(NA,dim=c(9,length(run.id),
+                                              length(1:1950)))
+
+for(t in 1:(length(time_step)-1)){
+  for(i in 1:length(run.id)){
+    load(paste0('/fs/data2/output//PEcAn_1000008588/out/',run.id[[i]],'/',time_step[t],'-12-31 23:59:59','linkages.out.Rdata'))
+    ntrees.save[,i,time_step[t]:(time_step[t+1]-1)] <- ntrees.birth
+    agb.pft.save[,i,time_step[t]:(time_step[t+1]-1)] <- agb.pft
+    #dbh
+  }
+}
+
+library(colorspace)
+
+matplot(950:1949,apply(ntrees.save[,,950:1949]/(1/12),1,colMeans,na.rm=T),typ='l',lwd=3,col=rainbow(9),ylab='Stem Density (trees/ha)')
+matplot(950:1949,apply(agb.pft.save[,,950:1949],1,colMeans,na.rm=T),typ='l',lwd=3,col=rainbow(9),ylab='PFT Biomass (kgC/m^2)')
+
+sd.df <- apply(ntrees.save[,,950:1949]/(1/12),1,colMeans,na.rm=T)
+ag.df <- apply(agb.pft.save[,,950:1949],1,colMeans,na.rm=T)
+
+quant.keep<-quant.keep.a<-list()
+for(i in 1:9){
+  quant.keep[[i]]<-apply(ntrees.save[i,,950:1949]/(1/12),2,quantile,c(.025,.5,.975),na.rm=T)
+  quant.keep.a[[i]]<-apply(agb.pft.save[i,,950:1949],2,quantile,c(.025,.5,.975),na.rm=T)
+  }
+
+
+load("/fs/data2/output/PEcAn_1000008588/run/1001823086/linkages.input.Rdata")
+
+par(mfrow=c(3,2),mar=c(rep(3.8,4)))
+for(i in c(9,8,4)){
+  plot(950:1949,quant.keep[[i]][2,],typ='l',col=rainbow_hcl(9)[i],
+       ylab='Stem Density (trees/ha)',xlab='Year',
+       main=NA,lwd=2,ylim=c(0,max(quant.keep[[i]])))
+  ciEnvelope(x=950:1949,ylo=quant.keep[[i]][1,],yhi=quant.keep[[i]][3,],col=rainbow_hcl(9,alpha = .75)[i])
+  lines(950:1949,quant.keep[[i]][2,],col=rainbow_hcl(9)[i],lwd=4)
+  
+  plot(950:1949,quant.keep.a[[i]][2,],typ='l',col=rainbow_hcl(9)[i],
+       ylab='Spp. Biomass (kgC/m^2)',xlab='Year',
+       main=NA,lwd=2,ylim=c(0,max(quant.keep.a[[i]])))
+  ciEnvelope(x=950:1949,ylo=quant.keep.a[[i]][1,],yhi=quant.keep.a[[i]][3,],col=rainbow_hcl(9,alpha = .75)[i])
+  lines(950:1949,quant.keep.a[[i]][2,],col=rainbow_hcl(9)[i],lwd=4)
+}
+
+pf <- enkf.params[[10]]$Pf
+q.bar <- solve(enkf.params[[10]]$q.bar)
+
+rownames(pf) <- rownames(q.bar) <- colnames(pf) <- colnames(q.bar) <- c('Maple','Birch','Hickory',
+                                     'Chestnut','Beech','Spruce',
+                                     'Pine','Oak','Hemlock','SoilCarbon')
+
+par(mfrow=c(1,1))
+corrplot(cov2cor(pf), type = "upper", tl.srt = 25,
+         tl.cex = .8,col=c('#ca0020','#0571b0'),diag=FALSE,
+         order='original')
+corrplot(cov2cor(pf+q.bar), type = "upper", tl.srt = 25,
+         tl.cex = .8,col=c('#ca0020','#0571b0'),diag=FALSE)
+
+df <- round(apply(ntrees.save[,,950:1949]/(1/12),1,colMeans,na.rm=T))
+colnames(df) <- c('a','b','c','d','e','f','g','h','i')
+rownames(df) <- stringi::stri_rand_strings(1000, 5)
+barplot(t(as.data.frame(df)))
+
+list.trees <- list()
+for(i in 1:9){
+  list.trees[[i]] <- apply(ntrees.save[i,,950:1949],2,quantile,c(.025,.5,.975),na.rm=T)
+}
+
+plot(list.trees[[1]][2,],ylim=c(0,35),typ='l')
+for(i in 1:9){
+  lines(list.trees[[i]][2,])
+}
+
+par(mfrow=c(1,1))
+matplot(t(apply(agb.pft.save[,,,10],2,rowMeans,na.rm=TRUE)),typ='l')
+
+sum.list <- ntrees.list <- list()
+for(i in 1:10){
+  sum.list[[i]] <- t(apply(agb.pft.save[,,,i],2,rowMeans,na.rm=TRUE))
+  ntrees.list[[i]] <- t(apply(ntrees.save[,,,i],2,rowMeans,na.rm=TRUE))
+}
+
+sum.all <- do.call(rbind,sum.list)
+ntrees.all <- do.call(rbind,ntrees.list)
+par(mfrow=c(1,1))
+matplot(sum.all)
+matplot(ntrees.all)
+
+
+
+library(corrplot)
+par(mfrow=c(1,1))
+corrplot(cov2cor(enkf.params[[9]]$R))
+
+
+###-------------------------------------------------------------------###
+### ensemble adjustment plots                                         ###
+###-------------------------------------------------------------------### 
+
+#function for plotting matplot with ensemble number as label
+mattext = function(data, data_names, colors, ylab, xlab, type='b', na.fix = FALSE){
+  if(na.fix == TRUE){
+    data[is.na(data)] <- 0
+  }
+  
+  matplot(data, pch=NA, type=type, col=colors, ylab = ylab, xlab = xlab)
+  for (i in 1:ncol(data)){
+    text(x=1:nrow(data), y=data[,i], lab=data_names[i], col=colors[i])
+  }
+}
+
+#calculate the likelihood of the ensemble members given mu.a and Pa
+nens <- nrow(FORECAST[[1]])
+nt <- length(FORECAST)
+
+wt.mat <- matrix(NA,nrow=nens,ncol=nt)
+for(t in seq_len(nt-1)){
+  for(i in seq_len(nens)){
+    wt.mat[i,t]<-dmnorm_chol(FORECAST[[t]][i,],enkf.params[[t]]$mu.a,solve(enkf.params[[t]]$Pa))
+  }
+}
+#put into weights table  
+wt.props <- t(prop.table(wt.mat,2))
+
+pdf(file.path(settings$outdir,'ensemble.weights.time-series.pdf'))
+par(mfrow=c(1,1))
+mattext(data = wt.props,data_names = as.character(1:nens),colors=rainbow(nens),
+        ylab = c('Ensemble Weight'), xlab = c('Time'))
+dev.off()
+
+library(Hmisc)
+settings <- read.settings("pecan.SDA.xml")
+
+
+pft.names <- as.character(lapply(settings$pfts, function(x) x[["name"]]))
+param.names <- names(params[[1]][[1]])
+param.hist <- array(NA,dim=c(length(param.names),length(pft.names),nens))
+wt.df <- array(NA, dim = c(length(param.names),length(pft.names),nt,4))
+diff.mean.mat <- matrix(NA,19,9)
+
+pdf('weighted.param.time-series.pdf')
+par(mfrow=c(4,3))
+for(p in 1:19){
+  for(s in 1:4){
+    pft <- pft.names[s]
+    param.plot <- param.names[p]
+    
+    param.check <- unlist(lapply(lapply(params,'[[',pft),'[[',param.plot))
+    
+    if(!is.null(param.check)){
+      param.hist[p,s,] <- param.check
+      wt.mean <- wt.var <- numeric(nt)
+      
+      for(t in 2:(nt-1)){
+        wt.mean[t] <- wtd.mean(x=param.hist[p,s,], w = wt.props[t,])
+        wt.var[t] <- wtd.var(x=param.hist[p,s,], w = wt.props[t,])
+      }
+      
+      wt.df[p,s,,1] <- wt.mean
+      wt.df[p,s,,2] <- wt.mean - mean(param.hist[p,s,])
+      wt.df[p,s,,3] <- wt.var
+      wt.df[p,s,,4] <- wt.var - var(param.hist[p,s,])
+      
+      #plot weighted mean
+      plot(wt.mean[2:9],type='l',ylab='Weighted Mean',xlab='Time')
+      points(wt.mean[2:9], pch=19,cex=.4)
+      abline(h=mean(param.hist[p,s,]))
+      abline(h = param.hist[p,s,which.min(colMeans(wt.props,na.rm = TRUE))],col='red')
+      abline(h = param.hist[p,s,which.max(colMeans(wt.props,na.rm = TRUE))],col='green')
+      title(main = list(paste(pft,'\n',param.plot), cex = .5))
+      
+      #coloring by the difference in the mean relative to the scale of the parameter
+      diff.mean <- diff.mean.mat[p,s] <- abs(mean(wt.mean,na.rm=T) - mean(param.hist[p,s,],na.rm=T))
+      if(diff.mean > abs(.00001*mean(param.hist[p,s,]))){
+        mtext(text = paste(signif(diff.mean,digits = 3)), side = 3,col = 'red')
+      }else{
+        mtext(text = paste(signif(diff.mean,digits = 3)), side = 3)
+      }
+      
+      #Plot weighted variance
+      plot(wt.var,type='l',ylab='Weighted Variance',xlab='Time')
+      points(wt.var, pch=19,cex=.5)
+      abline(h=var(param.hist[p,s,]))
+      title(main = list(paste(pft,'\n',param.plot), cex = .5))
+      
+      hist(param.hist[p,s,], freq = FALSE, col= 'lightgrey', main = paste(pft,'\n',param.plot))
+      for(t in 2:(nt-1)){
+        lines(density(param.hist[p,s,], weights = wt.props[t,], na.rm = TRUE),
+              lwd = 2, col=cm.colors(10)[t])
+      }
+      
+    }else{
+      plot.new()
+    }
+    
+  }
+}
+dev.off()
+
+pdf('weighted.hists.pdf')
+par(mfrow = c(4,4))  
+plot.new()
+legend('center',c('Weighted Means','Prior Means'),pch = 19,col=c('lightgrey','black'))
+for(p in 1:length(param.names)){
+  hist(wt.df[p,,,1], main=param.names[p], freq = FALSE, col = 'lightgrey', xlab = 'Param Value')
+  lines(density(rowMeans(param.hist[p,,]),na.rm = TRUE), lwd = 2)
+  
+}
+dev.off()
+
+
+plot(param.hist[1,,],param.hist[5,,])
+par(mfrow=c(1,1))
+for(s in c(1,7,8,9)){
+  plot(param.hist[2,s,],param.hist[5,s,],col='black',pch=19,main=pft.names[s],xlab='MPLANT',ylab='AGEMX')
+  for(t in 1:nt){
+    points(param.hist[2,s,],param.hist[5,s,],col=terrain.colors(nt)[t],cex=wt.props[t,]*75)
+    
+  }
+  points(param.hist[2,s,order(colMeans(wt.props,na.rm=TRUE))],param.hist[5,s,order(colMeans(wt.props,na.rm=TRUE))],col=grey(seq(0,1,length.out = 50)),pch=19,cex=1)
+  #points(param.hist[2,s,which.min(colMeans(wt.props,na.rm = TRUE))],param.hist[5,s,which.min(colMeans(wt.props,na.rm = TRUE))],col='red',cex=1)
+} 
+
+
+
+
+
+
+which.min(colMeans(wt.props,na.rm = TRUE))
+which.max(colMeans(wt.props,na.rm = TRUE))
+
+
+
+par(mfrow=c(1,1))
+mattext(param.hist[1,,], data_names = as.character(1:nens), colors=rainbow(nens),
+        ylab = c('Parameter Value'), xlab = c('PFT'), type='p', na.fix = TRUE)
+
+library(weights)
+par(mfrow=c(1,2))
+weighted.hist(x = param.hist, w = wt.props[nt,],col = 'lightgrey')
+hist(param.hist,col = 'lightgrey',xlim = range(dd$x))
+plot(density(param.hist))
+plot(density(param.hist*wt.props[nt,]*10))
+
+## weighted quantile
+wtd.quantile <- function(x,wt,q){ 
+  ord <- order(x)
+  wstar <- cumsum(wt[ord])/sum(wt)
+  qi <- findInterval(q,wstar); qi[qi<1]=1;qi[qi>length(x)]=length(x)
+  return(x[ord[qi]])
+}
+
+param.quant <- matrix(NA, 3, nt)
+
+for(t in seq_len(nt)){
+  param.quant[,t] <- wtd.quantile(x = param.hist, wt=wt.mat[,t],q=c(.025,.5,.975))
+}
+
+plot(param.quant[2,], ylim = range(param.quant,na.rm = TRUE))
+ciEnvelope(x = 1:nt, ylo = param.quant[1,1:nt], yhi = param.quant[3,1:nt], col = 'lightblue')
+points(param.quant[2,], pch = 19, cex = 1)
+
+
+
diff --git a/modules/assim.sequential/inst/paleon_sda.R b/modules/assim.sequential/inst/paleon_sda.R
index 0e6c541ac7a..1b13f62f703 100644
--- a/modules/assim.sequential/inst/paleon_sda.R
+++ b/modules/assim.sequential/inst/paleon_sda.R
@@ -2,6 +2,8 @@
 library(PEcAn.all)
 library(PEcAn.SIPNET)
 library(PEcAn.LINKAGES)
+library(PEcAn.visualization)
+library(PEcAn.ED2)
 library(PEcAn.assim.sequential)
 library(nimble)
 library(lubridate)
@@ -14,6 +16,23 @@ setwd('/fs/data2/output//PEcAn_1000008008/')
 file.copy('/fs/data2/output//PEcAn_1000007999/sda.obs.Rdata',getwd())
 #TO DO: Having problem with running proc.var == TRUE because nimble isn't keeping the toggle sampler in the function environment.
 
+## linkages fcomp
+setwd('/fs/data2/output//PEcAn_1000008588/') #with variance inflation
+adjustment=TRUE
+
+setwd('/fs/data2/output//PEcAn_1000008683/') #without variance inflation
+adjustment=TRUE
+
+load("out/sda.initial.runs.Rdata")
+#run inter part
+load("sda.output.Rdata")
+nt <- length(obs.list$obs.mean)
+aqq <- array(NA,dim=c(nt,10,10))
+t <- length(FORECAST)+1
+aqq[t,,]<- solve(enkf.params[[t-1]]$q.bar)*enkf.params[[t-1]]$n
+bqq<-numeric(nt)
+bqq[t]<-enkf.params[[t-1]]$n
+
 
 #SIPNET
 #setwd('/fs/data2/output//PEcAn_1000003356')
@@ -26,7 +45,12 @@ file.copy('/fs/data2/output//PEcAn_1000007999/sda.obs.Rdata',getwd())
 # Open and read in settings file for PEcAn run.
 settings <- read.settings("pecan.SDA.xml")
 
-obs.list <- PEcAn.assim.sequential::load_data_paleon_sda(settings = settings)
+#PEcAn.assim.sequential::
+library(rgdal) # need to put in assim.sequential
+library(ncdf4) # need to put in assim.sequential
+
+obs.list <- load_data_paleon_sda(settings = settings) #add a way to get the correct time step in this function?
+
 
 IC <- NULL
 
@@ -37,19 +61,74 @@ colnames(state)<-c('AbvGrndWood','GWBI')
 IC <- sample.IC.SIPNET(ne, state = state)
 status.end()
 
+
 #develop/debug
 if(FALSE){
   obs.mean = obs.list$obs.mean
   obs.cov = obs.list$obs.cov
   Q = NULL
   adjustment = TRUE
+  restart=NULL
 }
 
 
 PEcAn.assim.sequential::sda.enkf(settings, obs.mean = obs.list$obs.mean, obs.cov = obs.list$obs.cov, IC = IC)
 
-for(i in 2:length(obs.mean)){
-  obs.mean[[i]]<-NA
-  obs.cov[[i]]<-NA
+obmn <- obvn <- list()
+times.keep <- seq(1,1100,100)
+
+for(i in 1:length(times.keep)){
+  obmn[[i]] <- obs.mean[[times.keep[i]]]
+  obvn[[i]] <- obs.cov[[times.keep[i]]]
+}
+
+names(obmn) <- names(obvn) <- names(obs.mean)[times.keep]
+
+obs.mean <- obmn
+obs.cov <- obvn
+
+##### 
+##### Plot Data #####
+##### 
+
+t1 <- 1
+t <- length(obs.list$obs.mean)
+names.y <- unique(unlist(lapply(obs.list$obs.mean[t1:t], function(x) { names(x) })))
+Ybar <- t(sapply(obs.list$obs.mean[t1:t], function(x) {
+  tmp <- rep(NA, length(names.y))
+  names(tmp) <- names.y
+  mch <- match(names(x), names.y)
+  tmp[mch] <- x[mch]
+  tmp
+}))
+
+YCI <- t(as.matrix(sapply(obs.list$obs.cov[t1:t], function(x) {
+  if (length(x)<2) {
+    rep(NA, length(names.y))
+  }
+  sqrt(diag(x))
+})))
+
+obs.dates <- rownames(Ybar)
+
+green      <- col2rgb("green")
+alphagreen <- rgb(green[1], green[2], green[3], 75, max = 255)
+
+
+for(i in 1:length(obs.list$obs.mean[[1]])){
+  plot(as.Date(obs.dates), 
+       as.numeric(Ybar[, i]), 
+       type = "l", 
+       col = "darkgreen", 
+       lwd = 2,ylim=c(0,1),main=colnames(Ybar)[i])
+  ciEnvelope(as.Date(obs.dates),
+             as.numeric(Ybar[, i]) - as.numeric(YCI[, i]) * 1.96, 
+             as.numeric(Ybar[, i]) + as.numeric(YCI[, i]) * 1.96, 
+             col = alphagreen)
+  lines(as.Date(obs.dates), 
+        as.numeric(Ybar[, i]), 
+        type = "l", 
+        col = "darkgreen", 
+        lwd = 2)
 }
 
diff --git a/modules/assim.sequential/inst/sda.rewind.R b/modules/assim.sequential/inst/sda.rewind.R
new file mode 100644
index 00000000000..dd96e910cd1
--- /dev/null
+++ b/modules/assim.sequential/inst/sda.rewind.R
@@ -0,0 +1,63 @@
+##' @title sda.rewind
+##' @name  sda.rewind
+##' @author Ann Raiho \email{araiho@nd.edu}
+##' 
+##' @param settings          SDA settings object
+##' @param run.id            list of current run.ids
+##' @param time_to_rewind    year that should be deleted last
+##' 
+##' @description Helper function for deleting SDA files to be able to run from a specified point
+##' 
+##' @return NA
+##' @export
+##' 
+
+
+sda_rewind <- function(settings,run.id,time_to_rewind){
+  if(nchar(time_to_rewind) == 4){
+    for(i in 1:length(run.id)){
+      file.rename(paste0(settings$outdir,
+                         '/out/',run.id[[i]],
+                         '/',time_to_rewind,'-12-31 23:59:59linkages.out.Rdata'),
+                  paste0(settings$outdir,
+                         '/out/',run.id[[i]],
+                         '/linkages.out.Rdata'))
+      for(t in time_to_rewind:year(settings$state.data.assimilation$end.date)){
+        file.remove(paste0(settings$outdir,
+                           '/out/',run.id[[i]],
+                           '/',t,'.nc'))
+        file.remove(paste0(settings$outdir,
+                           '/out/',run.id[[i]],
+                           '/',t,'.nc.var'))
+      }
+    }
+  }
+
+  if(nchar(time_to_rewind) == 3){
+    for(i in 1:length(run.id)){
+      file.rename(paste0(settings$outdir,
+                         '/out/',run.id[[i]],
+                         '/',time_to_rewind,'-12-31 23:59:59linkages.out.Rdata'),
+                  paste0(settings$outdir,
+                         '/out/',run.id[[i]],
+                         '/linkages.out.Rdata'))
+      for(t in time_to_rewind:year(settings$state.data.assimilation$end.date)){
+        file.remove(paste0(settings$outdir,
+                           '/out/',run.id[[i]],
+                           '/','0',t,'.nc'))
+        file.remove(paste0(settings$outdir,
+                           '/out/',run.id[[i]],
+                           '/','0',t,'.nc.var'))
+      }
+    }
+  }
+}
+
+sda_rewind(settings, run.id, time_to_rewind = as.character(951))
+
+# for example if you want to restart your sda run 
+# where t=1 and obs.times = 950 then you want time_to_rewind 
+# to be 951 because that is the last year of model 
+# run data you don't want
+
+
diff --git a/modules/assim.sequential/man/assess.params.Rd b/modules/assim.sequential/man/assess.params.Rd
index ca5b0c8c232..d741c5d0e34 100644
--- a/modules/assim.sequential/man/assess.params.Rd
+++ b/modules/assim.sequential/man/assess.params.Rd
@@ -5,7 +5,7 @@
 \alias{assessParams}
 \title{assess.params}
 \usage{
-assessParams(dat, Xt, mu_f_TRUE, P_f_TRUE)
+assessParams(dat, Xt, mu_f_TRUE = NULL, P_f_TRUE = NULL)
 }
 \arguments{
 \item{dat}{MCMC output}
diff --git a/modules/assim.sequential/man/sample.parameters.Rd b/modules/assim.sequential/man/sample.parameters.Rd
index f69bed7f65f..a9a33d487ac 100644
--- a/modules/assim.sequential/man/sample.parameters.Rd
+++ b/modules/assim.sequential/man/sample.parameters.Rd
@@ -16,6 +16,9 @@ sample.parameters(ne, settings, con)
 \value{
 data frame of sampled parameters from the posterior distribution
 }
+\description{
+sample parameters
+}
 \author{
 Michael Dietze \email{dietze@bu.edu}
 }
diff --git a/modules/benchmark/DESCRIPTION b/modules/benchmark/DESCRIPTION
index 7ff429a7380..41ccba3486d 100644
--- a/modules/benchmark/DESCRIPTION
+++ b/modules/benchmark/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.benchmark
 Type: Package
 Title: PEcAn functions used for benchmarking
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Michael Dietze, David LeBauer, Rob Kooper, Toni Viskari
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
@@ -28,4 +28,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/benchmark/NAMESPACE b/modules/benchmark/NAMESPACE
index 50eea9c0696..cc43c3d919b 100644
--- a/modules/benchmark/NAMESPACE
+++ b/modules/benchmark/NAMESPACE
@@ -15,6 +15,7 @@ export(define_benchmark)
 export(format_wide2long)
 export(load_csv)
 export(load_data)
+export(load_rds)
 export(load_tab_separated_values)
 export(load_x_netcdf)
 export(match_timestep)
@@ -34,8 +35,6 @@ export(metric_run)
 export(metric_scatter_plot)
 export(metric_timeseries_plot)
 export(read_settings_BRR)
-importFrom(PEcAn.utils,logger.info)
-importFrom(SimilarityMeasures,Frechet)
 importFrom(dplyr,collect)
 importFrom(dplyr,filter)
 importFrom(dplyr,rename)
diff --git a/modules/benchmark/R/align_by_first_observation.R b/modules/benchmark/R/align_by_first_observation.R
index 59fce7d81d7..38ee061c118 100644
--- a/modules/benchmark/R/align_by_first_observation.R
+++ b/modules/benchmark/R/align_by_first_observation.R
@@ -18,7 +18,7 @@
 #' table$plant_functional_type_two<- c('a','a','b', 'b') # PFT groupings
 #' table<-as.data.frame(table)
 #'
-#' aligned<-align_by_observation_one(observation_one = observation_one, observation_two = observation_two, 
+#' aligned<-align_by_first_observation(observation_one = observation_one, observation_two = observation_two,
 #' custom_table = table)
 #' 
 #' # aligned should be a vector '[1] "AMCA3" "ARHY"  "AMCA3" "AMCA3"'
diff --git a/modules/benchmark/R/align_data_to_data_pft.R b/modules/benchmark/R/align_data_to_data_pft.R
index d014d3b4963..7ce25ac53f9 100644
--- a/modules/benchmark/R/align_data_to_data_pft.R
+++ b/modules/benchmark/R/align_data_to_data_pft.R
@@ -41,13 +41,13 @@
 #' table<-as.data.frame(table)
 #'
 #' format_one<-"species_USDA_symbol"
-#' format_two<-"plant_funtional_type"
+#' format_two<-"plant_functional_type"
 #' 
 #' aligned<-align_data_to_data_pft(con = con, observation_one = observation_one, observation_two = observation_two, 
 #' format_one = format_one, format_two = format_two, custom_table = table)
 #' @export
 
-align_data_to_data_pft<-function(observation_one, observation_two, custom_table=NULL, format_one, format_two, subset_is_ok=FALSE){ 
+align_data_to_data_pft<-function(con, observation_one, observation_two, custom_table=NULL, format_one, format_two, subset_is_ok=FALSE){
 
   translation_table<-NULL
   bety_codes_one<-NA
@@ -139,12 +139,12 @@ align_data_to_data_pft<-function(observation_one, observation_two, custom_table=
         aligned_by_two<-align_by_first_observation(observation_two,observation_one, custom_table)
         
       }else{
-        logger.severe("custom_table provided does not correctly map plant_function_type_one to plant_functional_type_two. One or more rows are mapped to multiple plant funcitonal types.")
+        logger.severe("custom_table provided does not correctly map plant_functional_type_one to plant_functional_type_two. One or more rows are mapped to multiple plant functional types.")
       } 
     }
     
   }else{
-    PEcAn.logger::logger.severe("PFTs are not in the correct format. Observations must have variables compatible with check_if_species_list(), or use the 'plant_funtional_type' variable")
+    PEcAn.logger::logger.severe("PFTs are not in the correct format. Observations must have variables compatible with check_if_species_list(), or use the 'plant_functional_type' variable")
   }
   
   aligned_species_list<-list()
diff --git a/modules/benchmark/R/align_pft.R b/modules/benchmark/R/align_pft.R
index 4cb50603081..7c3b1bc1172 100644
--- a/modules/benchmark/R/align_pft.R
+++ b/modules/benchmark/R/align_pft.R
@@ -67,7 +67,7 @@ align_pft<-function(con, observation_one, observation_two, custom_table=NULL, fo
     
   }else if (comparison_type == "data_to_data"){
     
-    align_data_to_data_pft(observation_one, observation_two, custom_table=NULL, format_one, format_two, subset_are_ok=FALSE)
+    align_data_to_data_pft(con, observation_one, observation_two, custom_table=NULL, format_one, format_two, subset_are_ok=FALSE)
     
   }else if (comparison_type == "model_to_model"){
     
diff --git a/modules/benchmark/R/check_if_list_of_pfts.R b/modules/benchmark/R/check_if_list_of_pfts.R
index 4a5e4baf93d..0d2f8979db9 100644
--- a/modules/benchmark/R/check_if_list_of_pfts.R
+++ b/modules/benchmark/R/check_if_list_of_pfts.R
@@ -8,7 +8,7 @@
 #' @author Tempest McCabe
 check_if_list_of_pfts<-function(vars){
   
-  if( any(c("plant_functional_type","species_name")) %in% vars){
+  if( any(c("plant_functional_type","species_name") %in% vars)){
     return(TRUE)
   }else{
     return(FALSE)
diff --git a/modules/benchmark/R/check_if_species_list.R b/modules/benchmark/R/check_if_species_list.R
index db42cc8763a..620f281c7e8 100644
--- a/modules/benchmark/R/check_if_species_list.R
+++ b/modules/benchmark/R/check_if_species_list.R
@@ -10,7 +10,7 @@
 #' @author Tempest McCabe
 check_if_species_list<-function(vars,custom_table=NULL){
   
-  if(any(c("species_id", "species_name", "species_USDA_symbol", "species_FIA_symbol")) %in% vars){
+  if(any(c("species_id", "species_name", "species_USDA_symbol", "species_FIA_symbol") %in% vars)){
     return(TRUE)
   }else if(!is.null(custom_table)){
     if("bety_species_id" %in% names(custom_table)){
diff --git a/modules/benchmark/R/get_species_list_standard.R b/modules/benchmark/R/get_species_list_standard.R
index 2acb437d8e1..e1bae78078b 100644
--- a/modules/benchmark/R/get_species_list_standard.R
+++ b/modules/benchmark/R/get_species_list_standard.R
@@ -9,7 +9,7 @@
 #' @author Tempest McCabe
 get_species_list_standard<-function(vars){
   
-  if(any(c("species_id", "species_USDA_symbol")) %in% vars){
+  if(any(c("species_id", "species_USDA_symbol") %in% vars)){
     return("usda")
   }else if("species_name" %in% vars){
     return('latin_name')
diff --git a/modules/benchmark/R/load_netcdf.R b/modules/benchmark/R/load_netcdf.R
index ea85218ae05..9ffbbe01197 100644
--- a/modules/benchmark/R/load_netcdf.R
+++ b/modules/benchmark/R/load_netcdf.R
@@ -34,23 +34,43 @@ load_x_netcdf <- function(data.path, format, site, vars = NULL) {
     dims <- names(nc[[i]]$dim)
     time.var <- grep(pattern = "time", dims, ignore.case = TRUE)
     time.col[[i]] <- ncdf4::ncvar_get(nc[[i]], dims[time.var])
-
+    
+    t.units <- ncdf4::ncatt_get(nc[[i]], dims[time.var])$units
+    
+    # If the unit has if of the form * since YYYY-MM-DD * with "-hour" timezone offset
+    # This is a feature of the met produced by met2CF
+    if(str_detect(t.units, "ince\\s[0-9]{4}[.-][0-9]{2}[.-][0-9]{2}.*\\s-\\d+")){
+      unit2 <- str_split_fixed(t.units,"\\s-",2)[1]
+      offset <- str_split_fixed(t.units,"\\s-",2)[2] %>% as.numeric()
+      
+      date_time <- suppressWarnings(try(lubridate::ymd((unit2))))
+      if(is.na(date_time)){
+        date_time <- suppressWarnings(try(lubridate::ymd_hms(unit2)))
+      }
+      if(is.na(date_time)){
+        PEcAn.logger::logger.error("All time formats failed to parse. No formats found.")
+      }
+      
+      t.units <- paste(str_split_fixed(t.units," since",2)[1], "since",
+                       date_time - lubridate::hms(paste(offset,":00:00")))
+    }
+    
     # for heterogenous formats try parsing ymd_hms
-    date.origin <- suppressWarnings(try(lubridate::ymd_hms(ncdf4::ncatt_get(nc[[i]], dims[time.var])$units)))
+    date.origin <- suppressWarnings(try(lubridate::ymd_hms(t.units)))
     
     # parsing ymd
     if (is.na(date.origin)) {
-      date.origin <- lubridate::ymd(ncdf4::ncatt_get(nc[[i]], dims[time.var])$units)
+      date.origin <- lubridate::ymd(t.units)
     }
     # throw error if can't parse time format
     if (is.na(date.origin)) {
       PEcAn.logger::logger.error("All time formats failed to parse. No formats found.")
     }
     
-
+    
     time.stamp.match <- gsub("UTC", "", date.origin)
     t.units <- gsub(paste0(" since ", time.stamp.match, ".*"), "", 
-                    ncdf4::ncatt_get(nc[[i]], dims[time.var])$units)
+                    t.units)
     
     # need to change system TZ otherwise, lines below keeps writing in the current time zone
     Sys.setenv(TZ = 'UTC')
diff --git a/modules/benchmark/R/load_rds.R b/modules/benchmark/R/load_rds.R
new file mode 100644
index 00000000000..f7b81c49cda
--- /dev/null
+++ b/modules/benchmark/R/load_rds.R
@@ -0,0 +1,22 @@
+##' @name load_rds
+##' @title load_rds
+##' @export
+##' @param data.path character
+##' @param format list, not used, for compatibility
+##' @param site not used, for compatibility
+##' @param vars 
+##' 
+##' @author Istem Fer
+load_rds <- function(data.path, format, site, vars = NULL) {
+  
+  data.path <- sapply(data.path, function(x) dir(dirname(x), basename(x), full.names = TRUE))
+  
+  dat <- readRDS(data.path)
+
+  if(!is.null(vars)){
+    return(dplyr::select(dat, one_of(vars)))
+  }else{
+    return(dat)
+  }
+  
+} # load_rds
diff --git a/modules/benchmark/R/metric_Frechet.R b/modules/benchmark/R/metric_Frechet.R
index e2da618e78e..3a11cb96a77 100644
--- a/modules/benchmark/R/metric_Frechet.R
+++ b/modules/benchmark/R/metric_Frechet.R
@@ -2,14 +2,12 @@
 ##' @title Frechet Distance
 ##' @export
 ##' @param metric_dat dataframe
-##' @importFrom SimilarityMeasures Frechet
-##' @importFrom PEcAn.utils logger.info
 ##' 
 ##' @author Betsy Cowdery
 
 metric_Frechet <- function(metric_dat, ...) {
   logger.info("Metric: Frechet Distance")
   dat.no.na <- na.omit(metric_dat)
-  Fdist <- Frechet(as.matrix(dat.no.na$obvs), as.matrix(dat.no.na$model))
+  Fdist <- SimilarityMeasures::Frechet(as.matrix(dat.no.na$obvs), as.matrix(dat.no.na$model))
   return(Fdist)
 } # metric_Frechet
diff --git a/modules/benchmark/man/add_workflow_info.Rd b/modules/benchmark/man/add_workflow_info.Rd
index ff1fe34eea4..9ff67dfca18 100644
--- a/modules/benchmark/man/add_workflow_info.Rd
+++ b/modules/benchmark/man/add_workflow_info.Rd
@@ -11,6 +11,9 @@ add_workflow_info(settings, bety)
 
 \item{bety}{connection to the database}
 }
+\description{
+Add workflow specific info to settings list for benchmarking
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/align_by_first_observation.Rd b/modules/benchmark/man/align_by_first_observation.Rd
index 91559aeb106..dba4cf7e7f9 100644
--- a/modules/benchmark/man/align_by_first_observation.Rd
+++ b/modules/benchmark/man/align_by_first_observation.Rd
@@ -30,7 +30,7 @@ table$plant_functional_type_one<- c("AMCA3","AMCA3","ARHY", "ARHY")
 table$plant_functional_type_two<- c('a','a','b', 'b') # PFT groupings
 table<-as.data.frame(table)
 
-aligned<-align_by_observation_one(observation_one = observation_one, observation_two = observation_two, 
+aligned<-align_by_first_observation(observation_one = observation_one, observation_two = observation_two,
 custom_table = table)
 
 # aligned should be a vector '[1] "AMCA3" "ARHY"  "AMCA3" "AMCA3"'
diff --git a/modules/benchmark/man/align_data.Rd b/modules/benchmark/man/align_data.Rd
index a879383e4b4..5ab6125b9e2 100644
--- a/modules/benchmark/man/align_data.Rd
+++ b/modules/benchmark/man/align_data.Rd
@@ -16,6 +16,9 @@ align_data(model.calc, obvs.calc, var, align_method = "match_timestep")
 \value{
 dat
 }
+\description{
+Align timeseries data
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/align_data_to_data_pft.Rd b/modules/benchmark/man/align_data_to_data_pft.Rd
index 1e86bfe166c..dadff4daadf 100644
--- a/modules/benchmark/man/align_data_to_data_pft.Rd
+++ b/modules/benchmark/man/align_data_to_data_pft.Rd
@@ -4,10 +4,12 @@
 \alias{align_data_to_data_pft}
 \title{align_data_to_data_pft}
 \usage{
-align_data_to_data_pft(observation_one, observation_two, custom_table = NULL,
-  format_one, format_two, subset_is_ok = FALSE)
+align_data_to_data_pft(con, observation_one, observation_two,
+  custom_table = NULL, format_one, format_two, subset_is_ok = FALSE)
 }
 \arguments{
+\item{con}{database connection}
+
 \item{observation_one}{a vector of plant fucntional types, or species}
 
 \item{observation_two}{another vector of plant fucntional types, or species}
@@ -19,8 +21,6 @@ In the second case, must be passable to match_species_id.}
 
 \item{format_two}{The output of query.format.vars() of observation two of the form output$vars$bety_names}
 
-\item{con}{database connection}
-
 \item{subset_are_ok}{When aligning two species lists, this allows for alignement when species lists aren't identical. 
 set to FALSE by default.}
 }
@@ -59,7 +59,7 @@ table$plant_functional_type_two<- c('a','a','b', 'b') # PFT groupings
 table<-as.data.frame(table)
 
 format_one<-"species_USDA_symbol"
-format_two<-"plant_funtional_type"
+format_two<-"plant_functional_type"
 
 aligned<-align_data_to_data_pft(con = con, observation_one = observation_one, observation_two = observation_two, 
 format_one = format_one, format_two = format_two, custom_table = table)
diff --git a/modules/benchmark/man/bm_settings2pecan_settings.Rd b/modules/benchmark/man/bm_settings2pecan_settings.Rd
index 6d0ee62a598..e036504b3b5 100644
--- a/modules/benchmark/man/bm_settings2pecan_settings.Rd
+++ b/modules/benchmark/man/bm_settings2pecan_settings.Rd
@@ -9,6 +9,9 @@ bm_settings2pecan_settings(bm.settings)
 \arguments{
 \item{bm.settings}{settings or multisettings object}
 }
+\description{
+Move benchmarking settings back in to original pecan settings object
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/calc_metrics.Rd b/modules/benchmark/man/calc_metrics.Rd
index d68cd26c6e2..baca520e39a 100644
--- a/modules/benchmark/man/calc_metrics.Rd
+++ b/modules/benchmark/man/calc_metrics.Rd
@@ -19,6 +19,9 @@ calc_metrics(model.calc, obvs.calc, var, metrics, ensemble.id, bm_dir)
 
 \item{bm_dir}{directory where benchmarking outputs will be saved}
 }
+\description{
+calc_metrics
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/check_BRR.Rd b/modules/benchmark/man/check_BRR.Rd
index eb4be63aebe..525f75eee87 100644
--- a/modules/benchmark/man/check_BRR.Rd
+++ b/modules/benchmark/man/check_BRR.Rd
@@ -11,6 +11,9 @@ check_BRR(settings_xml, con)
 
 \item{con}{database connection}
 }
+\description{
+Check whether a run has been registered as a reference run in BETY
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/check_if_species_list.Rd b/modules/benchmark/man/check_if_species_list.Rd
index d1a356170be..02637b73657 100644
--- a/modules/benchmark/man/check_if_species_list.Rd
+++ b/modules/benchmark/man/check_if_species_list.Rd
@@ -17,6 +17,9 @@ In the second case, must be passable to match_species_id.}
 \value{
 \code{boolean}
 }
+\description{
+check_if_species_list
+}
 \details{
 Checks if format contains a species list in a known format, or a declared custom format.
 }
diff --git a/modules/benchmark/man/clean_settings_BRR.Rd b/modules/benchmark/man/clean_settings_BRR.Rd
index 78a30729fe0..bd79c07d163 100644
--- a/modules/benchmark/man/clean_settings_BRR.Rd
+++ b/modules/benchmark/man/clean_settings_BRR.Rd
@@ -9,6 +9,9 @@ clean_settings_BRR(inputfile)
 \arguments{
 \item{inputfile}{the PEcAn settings file to be used.}
 }
+\description{
+Cleans PEcAn settings file and prepares the settings to be saved in a reference run record in BETY
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/format_wide2long.Rd b/modules/benchmark/man/format_wide2long.Rd
index e8104ca97ff..ee1250fe320 100644
--- a/modules/benchmark/man/format_wide2long.Rd
+++ b/modules/benchmark/man/format_wide2long.Rd
@@ -16,6 +16,9 @@ format_wide2long(out, format, vars_used, time.row)
 \value{
 list of updated values
 }
+\description{
+format_wide2long
+}
 \author{
 Istem Fer
 Function to convert wide format to long format
diff --git a/modules/benchmark/man/load_csv.Rd b/modules/benchmark/man/load_csv.Rd
index e50d6bdbe59..1b9dcd7c089 100644
--- a/modules/benchmark/man/load_csv.Rd
+++ b/modules/benchmark/man/load_csv.Rd
@@ -17,6 +17,9 @@ load_csv(data.path, format, site, vars = NULL)
 
 \item{end_year}{numeric}
 }
+\description{
+load_csv
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/load_data.Rd b/modules/benchmark/man/load_data.Rd
index 051b5feb085..a3d17267db6 100644
--- a/modules/benchmark/man/load_data.Rd
+++ b/modules/benchmark/man/load_data.Rd
@@ -4,8 +4,8 @@
 \alias{load_data}
 \title{load_data}
 \usage{
-load_data(data.path, format, start_year = NA, end_year = NA, site = NA,
-  vars.used.index = NULL, ...)
+load_data(data.path, format, start_year = NA, end_year = NA,
+  site = NA, vars.used.index = NULL, ...)
 }
 \arguments{
 \item{data.path}{character}
@@ -18,6 +18,9 @@ load_data(data.path, format, start_year = NA, end_year = NA, site = NA,
 
 \item{site}{list}
 }
+\description{
+load_data
+}
 \author{
 Betsy Cowdery, Istem Fer, Joshua Mantooth
 Generic function to convert input files containing observational data to 
diff --git a/modules/benchmark/man/load_rds.Rd b/modules/benchmark/man/load_rds.Rd
new file mode 100644
index 00000000000..e684a796cf2
--- /dev/null
+++ b/modules/benchmark/man/load_rds.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/load_rds.R
+\name{load_rds}
+\alias{load_rds}
+\title{load_rds}
+\usage{
+load_rds(data.path, format, site, vars = NULL)
+}
+\arguments{
+\item{data.path}{character}
+
+\item{format}{list, not used, for compatibility}
+
+\item{site}{not used, for compatibility}
+
+\item{vars}{}
+}
+\description{
+load_rds
+}
+\author{
+Istem Fer
+}
diff --git a/modules/benchmark/man/load_tab_separated_values.Rd b/modules/benchmark/man/load_tab_separated_values.Rd
index 4badd474761..22a307047c8 100644
--- a/modules/benchmark/man/load_tab_separated_values.Rd
+++ b/modules/benchmark/man/load_tab_separated_values.Rd
@@ -17,6 +17,9 @@ load_tab_separated_values(data.path, format, site = NULL, vars = NULL)
 
 \item{end_year}{numeric}
 }
+\description{
+load_tab_separated_values
+}
 \author{
 Betsy Cowdery, Mike Dietze
 }
diff --git a/modules/benchmark/man/load_x_netcdf.Rd b/modules/benchmark/man/load_x_netcdf.Rd
index c5829ed19ce..7534f711a7d 100644
--- a/modules/benchmark/man/load_x_netcdf.Rd
+++ b/modules/benchmark/man/load_x_netcdf.Rd
@@ -19,6 +19,9 @@ load_x_netcdf(data.path, format, site, vars = NULL)
 
 \item{end_year}{numeric}
 }
+\description{
+load_x_netcdf
+}
 \author{
 Istem Fer
 }
diff --git a/modules/benchmark/man/match_timestep.Rd b/modules/benchmark/man/match_timestep.Rd
index eb23b3eb409..266f2c13ce9 100644
--- a/modules/benchmark/man/match_timestep.Rd
+++ b/modules/benchmark/man/match_timestep.Rd
@@ -13,6 +13,9 @@ match_timestep(date.coarse, date.fine, data.fine)
 
 \item{data.fine}{matrix}
 }
+\description{
+Match time step
+}
 \author{
 Istem Fer
 }
diff --git a/modules/benchmark/man/mean_over_larger_timestep.Rd b/modules/benchmark/man/mean_over_larger_timestep.Rd
index 61e286b112f..1821feac9c3 100644
--- a/modules/benchmark/man/mean_over_larger_timestep.Rd
+++ b/modules/benchmark/man/mean_over_larger_timestep.Rd
@@ -13,6 +13,9 @@ mean_over_larger_timestep(date.coarse, date.fine, data.fine)
 
 \item{data.fine}{data.frame}
 }
+\description{
+Calculate benchmarking statistics
+}
 \author{
 Betsy Cowdery, Michael Dietze
 }
diff --git a/modules/benchmark/man/metric_AME.Rd b/modules/benchmark/man/metric_AME.Rd
index 31fc05d6ff3..b7b8c539163 100644
--- a/modules/benchmark/man/metric_AME.Rd
+++ b/modules/benchmark/man/metric_AME.Rd
@@ -9,6 +9,9 @@ metric_AME(dat, ...)
 \arguments{
 \item{dat}{dataframe}
 }
+\description{
+Absolute Maximum Error
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_Frechet.Rd b/modules/benchmark/man/metric_Frechet.Rd
index 8e36050e112..ab81bcb5044 100644
--- a/modules/benchmark/man/metric_Frechet.Rd
+++ b/modules/benchmark/man/metric_Frechet.Rd
@@ -9,6 +9,9 @@ metric_Frechet(metric_dat, ...)
 \arguments{
 \item{metric_dat}{dataframe}
 }
+\description{
+Frechet Distance
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_MAE.Rd b/modules/benchmark/man/metric_MAE.Rd
index 76ce67de69d..8bcf95b9509 100644
--- a/modules/benchmark/man/metric_MAE.Rd
+++ b/modules/benchmark/man/metric_MAE.Rd
@@ -9,6 +9,9 @@ metric_MAE(dat, ...)
 \arguments{
 \item{dat}{dataframe}
 }
+\description{
+Mean Absolute Error
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_MSE.Rd b/modules/benchmark/man/metric_MSE.Rd
index 230a99da275..2c2ad1600e2 100644
--- a/modules/benchmark/man/metric_MSE.Rd
+++ b/modules/benchmark/man/metric_MSE.Rd
@@ -9,6 +9,9 @@ metric_MSE(dat, ...)
 \arguments{
 \item{dat}{dataframe}
 }
+\description{
+Mean Square Error
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_PPMC.Rd b/modules/benchmark/man/metric_PPMC.Rd
index cf9706b2bcd..413340bcd5c 100644
--- a/modules/benchmark/man/metric_PPMC.Rd
+++ b/modules/benchmark/man/metric_PPMC.Rd
@@ -9,6 +9,9 @@ metric_PPMC(metric_dat, ...)
 \arguments{
 \item{metric_dat}{dataframe}
 }
+\description{
+Pearson Product Moment Correlation
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_R2.Rd b/modules/benchmark/man/metric_R2.Rd
index 65733d53839..cd047b5183a 100644
--- a/modules/benchmark/man/metric_R2.Rd
+++ b/modules/benchmark/man/metric_R2.Rd
@@ -9,6 +9,9 @@ metric_R2(metric_dat, ...)
 \arguments{
 \item{metric_dat}{dataframe}
 }
+\description{
+Coefficient of Determination (R2)
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_RAE.Rd b/modules/benchmark/man/metric_RAE.Rd
index 6d52beb1723..69195ce87c6 100644
--- a/modules/benchmark/man/metric_RAE.Rd
+++ b/modules/benchmark/man/metric_RAE.Rd
@@ -9,6 +9,9 @@ metric_RAE(metric_dat, ...)
 \arguments{
 \item{metric_dat}{dataframe}
 }
+\description{
+Relative Absolute Error
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_RMSE.Rd b/modules/benchmark/man/metric_RMSE.Rd
index 1ae97ab221c..e6b0b608aee 100644
--- a/modules/benchmark/man/metric_RMSE.Rd
+++ b/modules/benchmark/man/metric_RMSE.Rd
@@ -9,6 +9,9 @@ metric_RMSE(dat, ...)
 \arguments{
 \item{dat}{dataframe}
 }
+\description{
+Root Mean Square Error
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_cor.Rd b/modules/benchmark/man/metric_cor.Rd
index 8a8e0bb7864..b2ea61b01d0 100644
--- a/modules/benchmark/man/metric_cor.Rd
+++ b/modules/benchmark/man/metric_cor.Rd
@@ -9,6 +9,9 @@ metric_cor(dat, ...)
 \arguments{
 \item{dat}{dataframe}
 }
+\description{
+Correlation Coefficient
+}
 \author{
 Mike Dietze
 }
diff --git a/modules/benchmark/man/metric_lmDiag_plot.Rd b/modules/benchmark/man/metric_lmDiag_plot.Rd
index 1244e4aa202..56628c76ad2 100644
--- a/modules/benchmark/man/metric_lmDiag_plot.Rd
+++ b/modules/benchmark/man/metric_lmDiag_plot.Rd
@@ -9,6 +9,9 @@ metric_lmDiag_plot(metric_dat, var, filename = NA, draw.plot = FALSE)
 \arguments{
 \item{metric_dat}{data.frame}
 }
+\description{
+Linear Regression Diagnostic Plot
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_residual_plot.Rd b/modules/benchmark/man/metric_residual_plot.Rd
index 9a80024df17..8ab1404c172 100644
--- a/modules/benchmark/man/metric_residual_plot.Rd
+++ b/modules/benchmark/man/metric_residual_plot.Rd
@@ -10,6 +10,9 @@ metric_residual_plot(metric_dat, var, filename = NA,
 \arguments{
 \item{draw.plot}{}
 }
+\description{
+Residual Plot
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_run.Rd b/modules/benchmark/man/metric_run.Rd
index ccc6f140a61..757cda2bda3 100644
--- a/modules/benchmark/man/metric_run.Rd
+++ b/modules/benchmark/man/metric_run.Rd
@@ -9,6 +9,9 @@ metric_run(settings)
 \arguments{
 \item{settings}{list}
 }
+\description{
+Model Run Check
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_scatter_plot.Rd b/modules/benchmark/man/metric_scatter_plot.Rd
index 32af95bad1c..ea0d94046f1 100644
--- a/modules/benchmark/man/metric_scatter_plot.Rd
+++ b/modules/benchmark/man/metric_scatter_plot.Rd
@@ -10,6 +10,9 @@ metric_scatter_plot(metric_dat, var, filename = NA,
 \arguments{
 \item{draw.plot}{}
 }
+\description{
+Scatter Plot
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/benchmark/man/metric_timeseries_plot.Rd b/modules/benchmark/man/metric_timeseries_plot.Rd
index ac027081fc4..3159de25b6d 100644
--- a/modules/benchmark/man/metric_timeseries_plot.Rd
+++ b/modules/benchmark/man/metric_timeseries_plot.Rd
@@ -7,6 +7,9 @@
 metric_timeseries_plot(metric_dat, var, filename = NA,
   draw.plot = is.na(filename))
 }
+\description{
+Timeseries Plot
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION
index b999cca1fcf..7344e140f24 100644
--- a/modules/data.atmosphere/DESCRIPTION
+++ b/modules/data.atmosphere/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.data.atmosphere
 Type: Package
 Title: PEcAn functions used for managing climate driver data
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Carl Davidson, Mike Dietze, Rob Kooper, Deepak Jaiswal, David LeBauer
 Maintainer: David LeBauer <dlebauer@illinois.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
@@ -11,35 +11,57 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     package converts climate driver data into a standard format for models
     integrated into PEcAn. As a standalone package, it provides an interface to
     access diverse climate data sets.
-Additional Repositories: http://r-forge.r-project.org/
 Depends:
     methods
 Imports:
-    PEcAn.logger,
-    PEcAn.remote,
-    PEcAn.utils,
-    PEcAn.DB,
-    ggplot2,
+    abind (>= 1.4.5),
+    car,
     data.table,
-    REddyProc,
-    dplyr,
     dbplyr,
+    dplyr,
     geonames,
-    abind (>= 1.4.5),
+    ggplot2,
+    glue,
+    httr,
+    jsonlite,
     lubridate (>= 1.6.0),
+    magrittr,
+    maptools,
+    MASS,
+    mgcv,
     ncdf4 (>= 1.15),
+    nneo,
+    PEcAn.DB,
+    PEcAn.logger,
+    PEcAn.remote,
+    PEcAn.utils,
+    purrr (>= 0.2.3),
+    RCurl,
+    REddyProc,
+    reshape2,
+    rgdal,
+    rnoaa,
+    sp,
     stringr (>= 1.1.0),
+    testthat (>= 2.0.0),
+    tibble,
+    tidyr,
+    truncnorm,
     udunits2 (>= 0.11),
     XML (>= 3.98-1.4),
-    nneo,
-    httr
+    zoo
 Suggests:
-    testthat
+    doParallel,
+    foreach,
+    parallel,
+    progress,
+    rlang (>= 0.2.0)
 Remotes:
-    github::ropenscilabs/nneo,
-    github::rforge/reddyproc/pkg/REddyProc
+    github::ropensci/geonames,
+    github::ropenscilabs/nneo
 License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/data.atmosphere/NAMESPACE b/modules/data.atmosphere/NAMESPACE
index 7be41d6844d..2206bae47f4 100644
--- a/modules/data.atmosphere/NAMESPACE
+++ b/modules/data.atmosphere/NAMESPACE
@@ -5,9 +5,11 @@ export(.met2model.module)
 export(AirDens)
 export(align.met)
 export(browndog.met)
+export(build_cf_variables_table_url)
 export(cfmet.downscale.daily)
 export(cfmet.downscale.subdaily)
 export(cfmet.downscale.time)
+export(check_met_input_file)
 export(closest_xy)
 export(cos_solar_zenith_angle)
 export(db.site.lat.lon)
@@ -25,10 +27,13 @@ export(download.Geostreams)
 export(download.MACA)
 export(download.MsTMIP_NARR)
 export(download.NARR)
+export(download.NARR_site)
 export(download.NEONmet)
 export(download.NLDAS)
+export(download.NOAA_GEFS)
 export(download.PalEON)
 export(download.PalEON_ENS)
+export(download.US_WCr)
 export(equation_of_time)
 export(exner)
 export(extract.local.CMIP5)
@@ -40,6 +45,9 @@ export(get.lv)
 export(get.ncvector)
 export(get.rh)
 export(get.vpd)
+export(get_NARR_thredds)
+export(get_cf_variables_table)
+export(latlon2lcc)
 export(lightME)
 export(lm_ensemble_sims)
 export(load.cfmet)
@@ -57,14 +65,17 @@ export(met2CF.PalEONregional)
 export(met2CF.csv)
 export(met_temporal_downscale.Gaussian_ensemble)
 export(metgapfill)
+export(metgapfill.NOAA_GEFS)
 export(model.train)
 export(nc.merge)
 export(par2ppfd)
+export(pecan_standard_met_table)
 export(permute.nc)
 export(predict_subdaily_met)
 export(qair2rh)
 export(read.register)
 export(rh2qair)
+export(robustly)
 export(save.betas)
 export(save.model)
 export(site.lst)
@@ -78,15 +89,4 @@ export(sw2ppfd)
 export(temporal.downscale.functions)
 export(upscale_met)
 export(wide2long)
-importFrom(PEcAn.DB,db.close)
-importFrom(PEcAn.DB,db.query)
-importFrom(PEcAn.DB,dbfile.input.insert)
-importFrom(ncdf4,nc_close)
-importFrom(ncdf4,nc_create)
-importFrom(ncdf4,nc_open)
-importFrom(ncdf4,ncatt_get)
-importFrom(ncdf4,ncdim_def)
-importFrom(ncdf4,ncvar_add)
-importFrom(ncdf4,ncvar_def)
-importFrom(ncdf4,ncvar_get)
-importFrom(ncdf4,ncvar_put)
+importFrom(magrittr,"%>%")
diff --git a/modules/data.atmosphere/R/align_met.R b/modules/data.atmosphere/R/align_met.R
index 4b1e40aa00f..af9749bc7a3 100644
--- a/modules/data.atmosphere/R/align_met.R
+++ b/modules/data.atmosphere/R/align_met.R
@@ -78,9 +78,6 @@
 # Begin Function
 #----------------------------------------------------------------------
 align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL, n.ens=NULL, pair.mems = FALSE, mems.train=NULL, seed=Sys.Date(), print.progress = FALSE) {
-  # Load required libraries
-  library(ncdf4)
-  library(lubridate)
   
   met.out <- list() # where the aligned data will be stored
 
@@ -106,7 +103,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
     # Loop through the .nc files putting everything into a list
     if(print.progress==TRUE){
       print("Processing Training Data")
-      pb <- txtProgressBar(min=0, max=length(files.train), style=3)
+      pb <- utils::txtProgressBar(min=0, max=length(files.train), style=3)
     } 
     for(i in 1:length(files.train)){
       yr.now <- yrs.file[i]
@@ -135,7 +132,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
       
       ncdf4::nc_close(ncT)
 
-      if(print.progress==TRUE) setTxtProgressBar(pb, i)
+      if(print.progress==TRUE) utils::setTxtProgressBar(pb, i)
     } # End looping through training data files
   } else { # we have an ensemble we need to deal with
     # Figure out how many ensemble members we're working with
@@ -163,7 +160,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
     
     if(print.progress==TRUE){
       print("Processing Training Data")
-      pb <- txtProgressBar(min=0, max=length(ens.train)*n.files, style=3)
+      pb <- utils::txtProgressBar(min=0, max=length(ens.train)*n.files, style=3)
       pb.ind=1
     }
     
@@ -210,7 +207,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
         ncdf4::nc_close(ncT)
 
         if(print.progress==TRUE){
-          setTxtProgressBar(pb, pb.ind)
+          utils::setTxtProgressBar(pb, pb.ind)
           pb.ind <- pb.ind+1
         }
       } # End looping through training data files
@@ -258,7 +255,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
     # Loop through the .nc files putting everything into a list
     if(print.progress==TRUE){
       print("Processing Source Data")
-      pb <- txtProgressBar(min=0, max=length(files.source), style=3)
+      pb <- utils::txtProgressBar(min=0, max=length(files.source), style=3)
     }
     
     for(i in 1:length(files.source)){
@@ -267,7 +264,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
       ncT <- ncdf4::nc_open(file.path(source.path, files.source[i]))
 
       # Set up the time data frame to help index
-      nday <- ifelse(leap_year(yr.now), 366, 365)
+      nday <- ifelse(lubridate::leap_year(yr.now), 366, 365)
       ntime <- length(ncT$dim$time$vals)
       step.day <- nday/ntime
       step.hr  <- step.day*24
@@ -301,7 +298,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
       
       # Extract the met info, making matrices with the appropriate number of ensemble members
       for(v in names(ncT$var)){
-        dat.tem <- ncvar_get(ncT, v)
+        dat.tem <- ncdf4::ncvar_get(ncT, v)
         
         if(align=="repeat"){ # if we need to coerce the time step to be repeated to match temporal resolution, do it here
           dat.tem <- rep(dat.tem, each=length(stamps.hr))
@@ -312,13 +309,13 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
         if(align == "aggregate"){
           df.tem <- cbind(src.time, data.frame(df.tem))
   
-          df.agg <- aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=mean)
+          df.agg <- stats::aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=mean)
           met.out$dat.source[[v]] <- rbind(met.out$dat.source[[v]], as.matrix(df.agg[,(3+1:n.src)]))
           
           # if workign wiht air temp, also find the max & min
           if(v=="air_temperature"){
-            tmin <- aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=min)
-            tmax <- aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=max)
+            tmin <- stats::aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=min)
+            tmax <- stats::aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=max)
             
             met.out$dat.source[["air_temperature_minimum"]] <- rbind(met.out$dat.source[["air_temperature_minimum"]], as.matrix(tmin[,(3+1:n.src)]))
             met.out$dat.source[["air_temperature_maximum"]] <- rbind(met.out$dat.source[["air_temperature_maximum"]], as.matrix(tmax[,(3+1:n.src)]))
@@ -329,7 +326,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
         
       }
       ncdf4::nc_close(ncT)
-      if(print.progress==TRUE) setTxtProgressBar(pb, i)
+      if(print.progress==TRUE) utils::setTxtProgressBar(pb, i)
     } # End looping through source met files
     if(print.progress==TRUE) print("")
   } else { # we have an ensemble we need to deal with
@@ -357,7 +354,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
     
     if(print.progress==TRUE){
       print("Processing Source Data")
-      pb <- txtProgressBar(min=0, max=length(ens.source)*n.files, style=3)
+      pb <- utils::txtProgressBar(min=0, max=length(ens.source)*n.files, style=3)
       pb.ind=1
     }
     for(j in 1:length(ens.source)){
@@ -384,10 +381,10 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
       for(i in 1:length(files.source)){
         yr.now <- yrs.file[i]
         
-        ncT <- nc_open(file.path(source.path, ens.source[j], files.source[i]))
+        ncT <- ncdf4::nc_open(file.path(source.path, ens.source[j], files.source[i]))
         
         # Set up the time data frame to help index
-        nday <- ifelse(leap_year(yr.now), 366, 365)
+        nday <- ifelse(lubridate::leap_year(yr.now), 366, 365)
         ntime <- length(ncT$dim$time$vals)
         step.day <- nday/ntime
         step.hr  <- step.day*24
@@ -428,7 +425,7 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
         
         # Extract the met info, making matrices with the appropriate number of ensemble members
         for(v in names(ncT$var)){
-          dat.tem <- ncvar_get(ncT, v)
+          dat.tem <- ncdf4::ncvar_get(ncT, v)
           
           if(align=="repeat"){ # if we need to coerce the time step to be repeated to match temporal resolution, do it here
             dat.tem <- rep(dat.tem, each=stamps.hr)
@@ -439,13 +436,13 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
           if(align == "aggregate"){
             df.tem <- cbind(src.time, data.frame(df.tem))
             
-            df.agg <- aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=mean)
+            df.agg <- stats::aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=mean)
             dat.ens[[v]] <- rbind(dat.ens[[v]], as.matrix(df.agg[,(3+1:n.src)]))
             
             # if working with air temp, also find the max & min
             if(v=="air_temperature"){
-              tmin <- aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=min)
-              tmax <- aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=max)
+              tmin <- stats::aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=min)
+              tmax <- stats::aggregate(df.tem[,(4+1:n.src)], by=df.tem[,c("Year", "DOY", "Hour")], FUN=max)
               
               dat.ens[["air_temperature_minimum"]] <- rbind(dat.ens[["air_temperature_minimum"]], as.matrix(tmin[,(3+1:n.src)]))
               dat.ens[["air_temperature_maximum"]] <- rbind(dat.ens[["air_temperature_maximum"]], as.matrix(tmax[,(3+1:n.src)]))
@@ -455,9 +452,9 @@ align.met <- function(train.path, source.path, yrs.train=NULL, yrs.source=NULL,
           }
           
         } #End variable loop
-        nc_close(ncT)
+        ncdf4::nc_close(ncT)
         if(print.progress==TRUE){
-          setTxtProgressBar(pb, pb.ind)
+          utils::setTxtProgressBar(pb, pb.ind)
           pb.ind <- pb.ind+1
         }
       } # End looping through source met files
diff --git a/modules/data.atmosphere/R/call_MODIS.R b/modules/data.atmosphere/R/call_MODIS.R
deleted file mode 100644
index 3c1f75bbc70..00000000000
--- a/modules/data.atmosphere/R/call_MODIS.R
+++ /dev/null
@@ -1,47 +0,0 @@
-
-call_MODIS <- function(start, end, lat, lon) {
-  # start = start date in year and day-of-year. For example May 1 2010 would be 2010121
-  # end = end date in year and day-of-year. For example May 1 2010 would be 2010121
-  # lat = Latitude of the pixel
-  # lon = Longitude of the pixel
-  
-  library(rPython)
-  
-  # The name of the netCDF file. I've here given a constant name, but it can easily be changed to be
-  # an input
-  fname <- "m_data.nc"
-  
-  # Distance of the are both east-west and north-south from the center of the pixel. Similarly to
-  # the file name, I've left it also easily inputtable.
-  kmNS <- 0
-  kmWE <- 0
-  
-  # Here it assigns the run directory and given variables values within python
-  python.assign("cwd", getwd())
-  python.assign("start", start)
-  python.assign("end", end)
-  python.assign("lat", lat)
-  python.assign("lon", lon)
-  python.assign("kmNS", kmNS)
-  python.assign("kmWE", kmWE)
-  python.assign("fn", fname)
-  
-  # Here we import the MODIS python script as a module for the python. That way we can run the
-  # routines within the script as independent commands.
-  python.exec("import sys; sys.path.append(cwd)")
-  python.exec("import modisWSDL")
-  
-  # This is overkill if you are not editting modisWSDL, but if you are developing this will refresh
-  # the definition of the module
-  python.exec("reload(modisWSDL)")
-  
-  # And here we execute the main MODIS run. Although it should be noted that while we get values of
-  # the run here, the script also does write a netCDF output file.
-  python.exec("m, k, date = modisWSDL.run_main(start_date=start, end_date=end,la=lat,lo=lon,kmAB=kmNS,kmLR=kmWE,fname=fn)")
-  
-  # m = The MODIS observed LAI for the given pixel k = The standard deviation of the MODIS LAI. Be
-  # careful with this as it is at times very low date = Year and day-of-year of the observation
-  m <- python.get("[ map(float, x) for x in m.data ]")
-  k <- python.get("[ map(float, x) for x in k.data ]")
-  date <- python.get("date")
-} # call_MODIS
diff --git a/modules/data.atmosphere/R/check_met_input.R b/modules/data.atmosphere/R/check_met_input.R
new file mode 100644
index 00000000000..fde275f760b
--- /dev/null
+++ b/modules/data.atmosphere/R/check_met_input.R
@@ -0,0 +1,125 @@
+#' Check a meteorology data file for compliance with the PEcAn standard
+#'
+#' @param metfile Path of met file to check, as a scalar character.
+#' @param variable_table `data.frame` linking standard names to their
+#'   units. Must contain columns "cf_standard_name" and "units".
+#'   Default is [pecan_standard_met_table].
+#' @param required_vars Character vector of required variables.
+#'   Defaults to variables marked as required in `variable_table`.
+#' @param warn_unknown Logical. If `TRUE` (default), throw a warning
+#'   for variables not in `variable_table`. Otherwise, ignore unknown
+#'   variables.
+#' @return `data.frame` summarizing the results of the tests.
+#' @author Alexey Shiklomanov
+#' @export
+check_met_input_file <- function(metfile,
+                                 variable_table = pecan_standard_met_table,
+                                 required_vars = variable_table %>%
+                                   dplyr::filter(is_required) %>%
+                                   dplyr::pull(cf_standard_name),
+                                 warn_unknown = TRUE
+                                 ) {
+
+  metfile <- normalizePath(metfile, mustWork = FALSE)
+
+  PEcAn.logger::severeifnot(
+    file.exists(metfile),
+    msg = glue::glue("File '{metfile}' does not exist.")
+  )
+
+  nc <- ncdf4::nc_open(metfile)
+
+  dimensions <- nc[["dim"]]
+  time_regex <- paste0(
+    "^(seconds|minutes|hours|hours|days) since ",
+    "[[:digit:]]{4}-[[:digit:]]{2}-[[:digit:]]{2}",
+    "T[[:digit:]]{2}:[[:digit:]]{2}:[[:digit:]]{2}Z$"
+  )
+
+  try2 <- purrr::partial(try, silent = TRUE)
+
+  dimensions <- nc[["dim"]]
+  time_regex <- paste0(
+    "^(seconds|minutes|hours|hours|days) since ",
+    "[[:digit:]]{4}-[[:digit:]]{2}-[[:digit:]]{2}",
+    "T[[:digit:]]{2}:[[:digit:]]{2}:[[:digit:]]{2}Z$"
+  )
+  test_dims <- list(
+    try2(testthat::expect_type(dimensions, "list")),
+    try2(testthat::expect_equal(length(dimensions), 3)),
+    try2(testthat::expect_true("time" %in% names(dimensions))),
+    try2(testthat::expect_match(
+      ncdf4::ncatt_get(nc, "time", "units")[["value"]],
+      time_regex
+    )),
+    try2(testthat::expect_true("latitude" %in% names(dimensions))),
+    try2(testthat::expect_equal(
+      ncdf4::ncatt_get(nc, "latitude", "units")[["value"]],
+      "degrees_north"
+    )),
+    try2(testthat::expect_true("longitude" %in% names(dimensions))),
+    try2(testthat::expect_equal(
+      ncdf4::ncatt_get(nc, "longitude", "units")[["value"]],
+      "degrees_east"
+    ))
+  )
+
+  dim_errors_lgl <- purrr::map_lgl(test_dims, inherits, "try-error")
+  dim_errors <- test_dims[dim_errors_lgl] %>%
+    purrr::map_chr(as.character) %>%
+    paste(collapse = "\n\n")
+
+  test_dims_summary <- tibble::tibble(
+    target_variable = "dimensions",
+    test_type = "correct dimensions",
+    test_passed = all(!dim_errors_lgl),
+    test_error_message = dim_errors
+  )
+
+  nc_vars <- names(nc[["var"]])
+  test_required_vars <- tibble::tibble(
+    test_type = "required variable present",
+    target_variable = required_vars,
+    test_passed = required_vars %in% nc_vars,
+    test_error_message = dplyr::if_else(
+      test_passed,
+      NA_character_,
+      as.character(glue::glue("Missing variable '{target_variable}'."))
+    )
+  )
+
+  test_var_units <- tibble::tibble(
+    test_type = "variable has correct units",
+    target_variable = nc_vars,
+    test_raw = purrr::map(nc_vars, check_unit, nc = nc, variable_table = variable_table),
+    test_passed = !purrr::map_lgl(test_raw, inherits, "try-error"),
+    test_error_message = purrr::map_chr(test_raw, purrr::possibly(as.character, NA_character_))
+  ) %>% dplyr::select(-test_raw)
+
+  results_df <- dplyr::bind_rows(test_dims_summary, test_required_vars, test_var_units)
+
+  return(results_df)
+}
+
+#' Check that the unit of a variable in a NetCDF file is equivalent to
+#' the expected unit.
+#'
+#' @param variable Name of target variable, as a length 1 character
+#' @param nc NetCDF object containing target variable
+#' @inheritParams check_met_input_file
+#' @return `TRUE` if unit is correct, or `try-error` object if there is a mismatch.
+#' @author Alexey Shiklomanov
+check_unit <- function(variable, nc, variable_table, warn_unknown = TRUE) {
+  if (!(variable %in% variable_table[["cf_standard_name"]]) && warn_unknown) {
+    PEcAn.logger::logger.warn(glue::glue("Variable '{variable}' not in known variables"))
+    return(TRUE)
+  }
+  var_correct_unit <- variable_table %>%
+    dplyr::filter(cf_standard_name == variable) %>%
+    dplyr::pull(units)
+  ncvar_unit <- ncdf4::ncatt_get(nc, variable, "units")[["value"]]
+  try(testthat::expect_true(
+    PEcAn.utils::units_are_equivalent(ncvar_unit, var_correct_unit),
+    glue::glue("NetCDF unit '{ncvar_unit}' not equivalent to expected unit '{var_correct_unit}'.")
+  ))
+}
diff --git a/modules/data.atmosphere/R/debias.met.R b/modules/data.atmosphere/R/debias.met.R
index 61b9eb049f0..ea05ad0609f 100644
--- a/modules/data.atmosphere/R/debias.met.R
+++ b/modules/data.atmosphere/R/debias.met.R
@@ -11,8 +11,9 @@ substrRight <- function(x, n) {
 ##' @param train_met - the observed dataset that will be used to train the modeled dataset in NC format
 ##' @param de_method - select which debias method you would like to use, options are 'normal', 'linear regression'
 ##' @param site.id
-##' @param overwrite
-##' @param verbose
+##' @param overwrite logical: replace output file if it already exists? Currently ignored.
+##' @param verbose logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}}
+##'   functions print debugging information as they run?
 ##' @author James Simkins
 debias.met <- function(outfolder, input_met, train_met, site_id, de_method = "linear", 
                        overwrite = FALSE, verbose = FALSE, ...) {
@@ -119,8 +120,8 @@ debias.met <- function(outfolder, input_met, train_met, site_id, de_method = "li
     if (de_method == "median") {
       for (u in add_var){
         if (all(is.na(source[[u]])) == FALSE) {
-          med_source <- median(source[[u]])
-          med_train <- median(train[[u]])
+          med_source <- stats::median(source[[u]])
+          med_train <- stats::median(train[[u]])
           med_diff <- med_train - med_source
           debi[1:reso_len, u] <- source[[u]] + med_diff
         } else {
@@ -129,8 +130,8 @@ debias.met <- function(outfolder, input_met, train_met, site_id, de_method = "li
       }
       for (u in mult_var){
         if (all(is.na(source[[u]])) == FALSE) {
-          med_source <- median(source[[u]][source[[u]]>0])
-          med_train <- median(train[[u]][train[[u]]>0])
+          med_source <- stats::median(source[[u]][source[[u]]>0])
+          med_train <- stats::median(train[[u]][train[[u]]>0])
           med_ratio <- med_train/med_source
           debi[1:reso_len, u] <- source[[u]] * med_ratio
         } else {
@@ -143,7 +144,7 @@ debias.met <- function(outfolder, input_met, train_met, site_id, de_method = "li
         for (i in add_var) {
           if (all(is.na(source[[i]])) == FALSE & all(is.na(lin_train[[i]])) == 
               FALSE) {
-            lin <- lm(lin_train[[i]] ~ source[[i]])
+            lin <- stats::lm(lin_train[[i]] ~ source[[i]])
             x <- as.numeric(lin$coefficients[2])
             b <- as.numeric(lin$coefficients[1])
             debi[1:reso_len,i] <- (source[[i]] * x + b)
@@ -157,7 +158,7 @@ debias.met <- function(outfolder, input_met, train_met, site_id, de_method = "li
         for (i in mult_var) {
           if (all(is.na(source[[i]])) == FALSE & all(is.na(lin_train[[i]])) == 
               FALSE) {
-            lin <- lm(lin_train[[i]] ~ source[[i]])
+            lin <- stats::lm(lin_train[[i]] ~ source[[i]])
             x <- as.numeric(lin$coefficients[2])
             b <- 0
             debi[1:reso_len,i] <- (source[[i]] * x + b)
diff --git a/modules/data.atmosphere/R/debias_met_regression.R b/modules/data.atmosphere/R/debias_met_regression.R
index 5213a8973ad..4c5ceead22d 100644
--- a/modules/data.atmosphere/R/debias_met_regression.R
+++ b/modules/data.atmosphere/R/debias_met_regression.R
@@ -38,8 +38,9 @@
 ##' @param path.diagnostics - path to where the diagnostic graphs should be saved
 ##' @param parallel - (experimental) logical stating whether to run temporal_downscale_functions.R in parallel *Not Implemented yet
 ##' @param n.cores - (experimental) how many cores to use in parallelization *Not implemented yet
-##' @param overwrite - overwrite existing files?
-##' @param verbose
+##' @param overwrite - overwrite existing files? Currently ignored
+##' @param verbose logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}}
+##'   functions print debugging information as they run?
 ##' @export
 # -----------------------------------
 # Workflow
@@ -66,10 +67,6 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
                                   parallel = FALSE, n.cores = NULL, overwrite = TRUE, verbose = FALSE) {
   library(MASS)
   library(mgcv)
-  library(ggplot2)
-  library(stringr)
-  library(lubridate)
-  library(ncdf4)
   
   set.seed(seed)
   
@@ -149,7 +146,7 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
   # -------------------------------------------
   print("")
   print("Debiasing Meteorology")
-  pb <- txtProgressBar(min=0, max=length(vars.debias)*n.ens, style=3)
+  pb <- utils::txtProgressBar(min=0, max=length(vars.debias)*n.ens, style=3)
   pb.ind=1
   for(v in vars.debias){
     # -------------
@@ -162,7 +159,7 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
       # rain.train <- met.bias[met.bias$dataset==dat.train.orig,]
       rainless <- vector()
       cons.wet <- vector()
-      for(y in min(train.data$time$Year):max(train.data$time$Year)){
+      for(y in unique(train.data$time$Year)){
         for(i in 1:ncol(train.data$precipitation_flux)){
           rain.now <- train.data$precipitation_flux[train.data$time$Year==y, i]
           
@@ -188,6 +185,8 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
       
       # Hard-coding in some sort of max for precipitaiton
       rain.max <- max(train.data$precipitation_flux) + sd(train.data$precipitation_flux)
+      rainless.min <- ifelse(min(rainless)-sd(rainless)>=0, min(rainless)-sd(rainless), max(min(rainless)-sd(rainless)/2, 0))
+      rainless.max <- ifelse(max(rainless)+sd(rainless)<=365, max(rainless)+sd(rainless), min(max(rainless)+sd(rainless)/2, 365))
     }
     # -------------
     
@@ -202,7 +201,7 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
     # -----
     met.train <- data.frame(year=train.data$time$Year,
                             doy=train.data$time$DOY,
-                            Y=stack(data.frame(train.data[[v]][,ens.train]))[,1],
+                            Y=utils::stack(data.frame(train.data[[v]][,ens.train]))[,1],
                             ind=rep(paste0("X", 1:n.ens), each=nrow(train.data[[v]]))
                             )
     met.train[,v] <- 0
@@ -230,7 +229,7 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
     # -----
     met.src <- data.frame(year=source.data$time$Year,
                           doy=source.data$time$DOY,
-                          X=stack(data.frame(source.data[[v]][,ens.src]))[,1],
+                          X=utils::stack(data.frame(source.data[[v]][,ens.src]))[,1],
                           ind.src=rep(paste0("X", 1:length(ens.src)), each=nrow(source.data[[v]]))
                           )
     # met.src[,v] <- 
@@ -258,12 +257,12 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
     
     # Adding in the covariates from what's been done:
     for(v.pred in vars.debias[!vars.debias==v]){
-      met.train[,v.pred] <- stack(data.frame(train.data[[v.pred]][,ens.train]))[,1]
+      met.train[,v.pred] <- utils::stack(data.frame(train.data[[v.pred]][,ens.train]))[,1]
       
       if(v.pred %in% names(dat.out)){
-        met.src[,v.pred] <- stack(data.frame(dat.out[[v.pred]]))[,1]
+        met.src[,v.pred] <- utils::stack(data.frame(dat.out[[v.pred]]))[,1]
       } else {
-        met.src[,v.pred] <- stack(data.frame(source.data[[v.pred]][,ens.src]))[,1]
+        met.src[,v.pred] <- utils::stack(data.frame(source.data[[v.pred]][,ens.src]))[,1]
       }
     }
     
@@ -853,19 +852,22 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
               dry <- rows.yr[which(sim1[rows.yr,j] < 0)] # update our dry days
             }
             
+            # n.now = number of rainless days for this sim
             n.now <- round(rnorm(1, mean(rainless, na.rm=T), sd(rainless, na.rm=T)), 0) 
-        
+            if(n.now < rainless.min) n.now <- rainless.min # Make sure we don't have negative or no rainless days
+            if(n.now > rainless.max) n.now <- rainless.max # Make sure we have at least one day with rain
+            
             # We're having major seasonality issues, so lets randomly redistribute our precip
-            # Pull twice what we need and randomly select from that so that we don't have such clean cuttoffs
+            # Pull ~twice what we need and randomly select from that so that we don't have such clean cuttoffs
             # set.seed(12)
             cutoff <- quantile(sim1[rows.yr, j], min(n.now/366*2.5, max(0.75, n.now/366)), na.rm=T)
             if(length(which(sim1[rows.yr,j]>0)) < n.now){
-              # if we need to re-distribute our rain, use the inverse of the cutoff
+              # if we need to re-distribute our rain (make more rainy days), use the inverse of the cutoff
               # cutoff <- 1-cutoff
               dry1 <- rows.yr[which(sim1[rows.yr,j] > cutoff)]
               dry <- sample(dry1, 365-n.now, replace=T)
               
-              wet <- sample(rows.yr[!rows.yr %in% dry], length(dry), replace=F)
+              wet <- sample(rows.yr[!rows.yr %in% dry], length(dry), replace=T)
               
               # Go through and randomly redistribute the precipitation to days we're not designating as rainless
               # Note, if we don't loop through, we might lose some of our precip
@@ -882,7 +884,7 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
               # too few rainless days because of only slight redistribution (r+1) or buildup 
               # towards the end of the year (random day that hasn't happened)
               dry1 <- rows.yr[which(sim1[rows.yr,j] < cutoff)]
-              dry <- sample(dry1, n.now, replace=F)
+              dry <- sample(dry1, min(n.now, length(dry1)), replace=F)
 
               dry1 <- dry1[!dry1 %in% dry]
               # dry <- dry[order(dry)]
@@ -957,7 +959,7 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
         sim.final[,ens] <- apply(sim1, 1, mean)
       }
       
-      setTxtProgressBar(pb, pb.ind)
+      utils::setTxtProgressBar(pb, pb.ind)
       pb.ind <- pb.ind+1
       
       rm(mod.bias, anom.train, anom.src, mod.anom, Xp, Xp.anom, sim1, sim1a, sim1b)
@@ -994,29 +996,29 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
       dat.pred$upr  <- apply(dat.out[[v]], 1, quantile, 0.975, na.rm=T)
       
       # Plotting the observed and the bias-corrected 95% CI
-      png(file.path(path.diagnostics, paste(ens.name, v, "day.png", sep="_")))
+      grDevices::png(file.path(path.diagnostics, paste(ens.name, v, "day.png", sep="_")))
       print(
-        ggplot(data=dat.pred[dat.pred$Year>=mean(dat.pred$Year)-1 & dat.pred$Year<=mean(dat.pred$Year)+1,]) +
-          geom_ribbon(aes(x=Date, ymin=lwr, ymax=upr), fill="red", alpha=0.5) +
-          geom_line(aes(x=Date, y=mean), color="red", size=0.5) +
-          geom_line(aes(x=Date, y=obs), color='black', size=0.5) +
-          ggtitle(paste0(v, " - ensemble mean & 95% CI (daily slice)")) +
-          theme_bw()
+        ggplot2::ggplot(data=dat.pred[dat.pred$Year>=mean(dat.pred$Year)-1 & dat.pred$Year<=mean(dat.pred$Year)+1,]) +
+          ggplot2::geom_ribbon(ggplot2::aes(x=Date, ymin=lwr, ymax=upr), fill="red", alpha=0.5) +
+          ggplot2::geom_line(ggplot2::aes(x=Date, y=mean), color="red", size=0.5) +
+          ggplot2::geom_line(ggplot2::aes(x=Date, y=obs), color='black', size=0.5) +
+          ggplot2::ggtitle(paste0(v, " - ensemble mean & 95% CI (daily slice)")) +
+          ggplot2::theme_bw()
       )
-      dev.off()
+      grDevices::dev.off()
       
       # Plotting a few random series to get an idea for what an individual pattern looks liek
-      stack.sims <- stack(data.frame(dat.out[[v]][,sample(1:n.ens, min(3, n.ens))]))
+      stack.sims <- utils::stack(data.frame(dat.out[[v]][,sample(1:n.ens, min(3, n.ens))]))
       stack.sims[,c("Year", "DOY", "Date")] <- dat.pred[,c("Year", "DOY", "Date")]
       
-      png(file.path(path.diagnostics, paste(ens.name, v, "day2.png", sep="_")))
+      grDevices::png(file.path(path.diagnostics, paste(ens.name, v, "day2.png", sep="_")))
       print(
-        ggplot(data=stack.sims[stack.sims$Year>=mean(stack.sims$Year)-2 & stack.sims$Year<=mean(stack.sims$Year)+2,]) +
-          geom_line(aes(x=Date, y=values, color=ind), size=0.2, alpha=0.8) +
-          ggtitle(paste0(v, " - example ensemble members (daily slice)")) +
-          theme_bw()
+        ggplot2::ggplot(data=stack.sims[stack.sims$Year>=mean(stack.sims$Year)-2 & stack.sims$Year<=mean(stack.sims$Year)+2,]) +
+          ggplot2::geom_line(ggplot2::aes(x=Date, y=values, color=ind), size=0.2, alpha=0.8) +
+          ggplot2::ggtitle(paste0(v, " - example ensemble members (daily slice)")) +
+          ggplot2::theme_bw()
       )
-      dev.off()
+      grDevices::dev.off()
       
       # Looking tat the annual means over the whole time series to make sure we're getting decent interannual variability
       dat.yr <- aggregate(dat.pred[,c("obs", "mean", "lwr", "upr")],
@@ -1024,16 +1026,16 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
                           FUN=mean)
       names(dat.yr)[1] <- "Year"
       
-      png(file.path(path.diagnostics, paste(ens.name, v, "annual.png", sep="_")))
+      grDevices::png(file.path(path.diagnostics, paste(ens.name, v, "annual.png", sep="_")))
       print(
-        ggplot(data=dat.yr[,]) +
-          geom_ribbon(aes(x=Year, ymin=lwr, ymax=upr), fill="red", alpha=0.5) +
-          geom_line(aes(x=Year, y=mean), color="red", size=0.5) +
-          geom_line(aes(x=Year, y=obs), color='black', size=0.5) +
-          ggtitle(paste0(v, " - annual mean time series")) +
-          theme_bw()
+        ggplot2::ggplot(data=dat.yr[,]) +
+          ggplot2::geom_ribbon(ggplot2::aes(x=Year, ymin=lwr, ymax=upr), fill="red", alpha=0.5) +
+          ggplot2::geom_line(ggplot2::aes(x=Year, y=mean), color="red", size=0.5) +
+          ggplot2::geom_line(ggplot2::aes(x=Year, y=obs), color='black', size=0.5) +
+          ggplot2::ggtitle(paste0(v, " - annual mean time series")) +
+          ggplot2::theme_bw()
       )
-      dev.off()
+      grDevices::dev.off()
       
     }
     # -------------
@@ -1060,12 +1062,12 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
 
   print("")
   print("Saving Ensemble")
-  pb <- txtProgressBar(min=0, max=length(yrs.save)*n.ens, style=3)
+  pb <- utils::txtProgressBar(min=0, max=length(yrs.save)*n.ens, style=3)
   pb.ind=1
   for(yr in yrs.save){
     # Doing some row/time indexing
     rows.yr <- which(dat.out$time$Year==yr)
-    nday <- ifelse(leap_year(yr), 366, 365)
+    nday <- ifelse(lubridate::leap_year(yr), 366, 365)
     
     # Finish defining our time variables (same for all ensemble members)
     dim.time <- ncdf4::ncdim_def(name='time', units="sec", vals=seq(1*24*360, (nday+1-1/24)*24*360, length.out=length(rows.yr)), create_dimvar=TRUE, unlim=TRUE)
@@ -1102,7 +1104,7 @@ debias.met.regression <- function(train.data, source.data, n.ens, vars.debias=NU
       }
       ncdf4::nc_close(loc)
 
-      setTxtProgressBar(pb, pb.ind)
+      utils::setTxtProgressBar(pb, pb.ind)
       pb.ind <- pb.ind+1
     } # End ensemble member loop
   } # End year loop
diff --git a/modules/data.atmosphere/R/download.Ameriflux.R b/modules/data.atmosphere/R/download.Ameriflux.R
index bf053044535..83cfc76a0b0 100644
--- a/modules/data.atmosphere/R/download.Ameriflux.R
+++ b/modules/data.atmosphere/R/download.Ameriflux.R
@@ -1,6 +1,6 @@
 # lookup the site based on the site_id
 download.Ameriflux.site <- function(site_id) {
-  sites <- read.csv(system.file("data/FLUXNET.sitemap.csv", package = "PEcAn.data.atmosphere"), 
+  sites <- utils::read.csv(system.file("data/FLUXNET.sitemap.csv", package = "PEcAn.data.atmosphere"), 
                     stringsAsFactors = FALSE)
   sites$FLUX.id[which(sites$site.id == site_id)]
 } # download.Ameriflux.site
@@ -11,7 +11,7 @@ download.Ameriflux.site <- function(site_id) {
 ##' @name download.Ameriflux
 ##' @title download.Ameriflux
 ##' @export
-##' @param site the FLUXNET ID of the site to be downloaded, used as file name prefix. 
+##' @param sitename the FLUXNET ID of the site to be downloaded, used as file name prefix. 
 ##' The 'SITE_ID' field in \href{http://ameriflux.lbl.gov/sites/site-list-and-pages/}{list of Ameriflux sites}
 ##' @param outfolder location on disk where outputs will be stored
 ##' @param start_date the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)
@@ -24,9 +24,6 @@ download.Ameriflux <- function(sitename, outfolder, start_date, end_date,
                                overwrite = FALSE, verbose = FALSE, ...) {
   # get start/end year code works on whole years only
   
-  library(PEcAn.utils)
-  library(data.table)
-  
   site <- sub(".* \\((.*)\\)", "\\1", sitename)
   
   start_date <- as.POSIXlt(start_date, tz = "UTC")
@@ -50,7 +47,7 @@ download.Ameriflux <- function(sitename, outfolder, start_date, end_date,
   
   # fetch all links
   links <- tryCatch({
-    xpathSApply(htmlParse(baseurl), "//a/@href")
+    XML::xpathSApply(XML::htmlParse(baseurl), "//a/@href")
   }, error = function(e) {
     PEcAn.logger::logger.severe("Could not get information about", site, ".", "Is this an Ameriflux site?")
   })
@@ -83,11 +80,11 @@ download.Ameriflux <- function(sitename, outfolder, start_date, end_date,
       next
     }
     
-    file <- tail(as.character(links[grep(paste0("_", year, "_.*.nc"), links)]), n = 1)
+    file <- utils::tail(as.character(links[grep(paste0("_", year, "_.*.nc"), links)]), n = 1)
     if (length(file) == 0) {
       PEcAn.logger::logger.severe("Could not download data for", site, "for the year", year)
     }
-    download.file(paste0(baseurl, file), outputfile)
+    PEcAn.utils::download.file(paste0(baseurl, file), outputfile)
   }
   
   # return list of files downloaded
diff --git a/modules/data.atmosphere/R/download.AmerifluxLBL.R b/modules/data.atmosphere/R/download.AmerifluxLBL.R
index 06431009bf9..64cd4180a1c 100644
--- a/modules/data.atmosphere/R/download.AmerifluxLBL.R
+++ b/modules/data.atmosphere/R/download.AmerifluxLBL.R
@@ -5,7 +5,7 @@
 ##' Uses Ameirflux LBL JSON API to download met data from Ameriflux towers in CSV format
 ##' 
 ##' @export
-##' @param site the Ameriflux ID of the site to be downloaded, used as file name prefix. 
+##' @param sitename the Ameriflux ID of the site to be downloaded, used as file name prefix. 
 ##' The 'SITE_ID' field in \href{http://ameriflux.lbl.gov/sites/site-list-and-pages/}{list of Ameriflux sites}
 ##' @param outfolder location on disk where outputs will be stored
 ##' @param start_date the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)
@@ -16,7 +16,9 @@
 ##' @param method Optional. download.file() function option.  Use this to set custom programs such as ncftp
 ##'
 ##' @examples
+##' \dontrun{
 ##' result <- download.AmerifluxLBL("US-Akn","~/","2011-01-01","2011-12-31",overwrite=TRUE)
+##' }
 ##' 
 ##' @author Ankur Desai, based on download.Ameriflux.R by Josh Mantooth, Rob Kooper, Shawn Serbin
 download.AmerifluxLBL <- function(sitename, outfolder, start_date, end_date, 
@@ -99,7 +101,7 @@ download.AmerifluxLBL <- function(sitename, outfolder, start_date, end_date,
     }
   }
   if (extract_file_flag) {
-    avail_file <- unzip(output_zip_file, list = TRUE)
+    avail_file <- utils::unzip(output_zip_file, list = TRUE)
     if (length(grep("HH", avail_file)) > 0) {
       file_timestep <- "HH"
     } else {
@@ -111,7 +113,7 @@ download.AmerifluxLBL <- function(sitename, outfolder, start_date, end_date,
         PEcAn.logger::logger.severe("Half-hourly or Hourly data file was not found in ", output_zip_file)
       }
     }
-    unzip(output_zip_file, outcsvname, exdir = outfolder)
+    utils::unzip(output_zip_file, outcsvname, exdir = outfolder)
     if (!file.exists(output_csv_file)) {
       PEcAn.logger::logger.severe("ZIP file ", output_zip_file, " did not contain CSV file ", outcsvname)
     }
diff --git a/modules/data.atmosphere/R/download.FACE.R b/modules/data.atmosphere/R/download.FACE.R
index b441cb98411..88e00cb2d5b 100644
--- a/modules/data.atmosphere/R/download.FACE.R
+++ b/modules/data.atmosphere/R/download.FACE.R
@@ -15,9 +15,6 @@ download.FACE <- function(sitename, outfolder, start_date, end_date, overwrite =
   # download.FACE <-
   # function(data.set,outfolder,pkg,raw.host,start_year,end_year,site.id,dbparams,con){
   
-  library(PEcAn.utils)
-  library(data.table)
-  
   start_date <- as.POSIXlt(start_date, tz = "UTC")
   end_date   <- as.POSIXlt(end_date, tz = "UTC")
   
diff --git a/modules/data.atmosphere/R/download.Fluxnet2015.R b/modules/data.atmosphere/R/download.Fluxnet2015.R
index 3321ec21098..c36bc5b94e7 100644
--- a/modules/data.atmosphere/R/download.Fluxnet2015.R
+++ b/modules/data.atmosphere/R/download.Fluxnet2015.R
@@ -3,7 +3,7 @@
 ##' @name download.Fluxnet2015
 ##' @title download.Fluxnet2015
 ##' @export
-##' @param site the FLUXNET ID of the site to be downloaded, used as file name prefix. 
+##' @param sitename the FLUXNET ID of the site to be downloaded, used as file name prefix. 
 ##' The 'SITE_ID' field in \href{http://fluxnet.fluxdata.org//sites/site-list-and-pages/}{list of Ameriflux sites}
 ##' @param outfolder location on disk where outputs will be stored
 ##' @param start_date the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)
@@ -105,13 +105,13 @@ download.Fluxnet2015 <- function(sitename, outfolder, start_date, end_date,
   
   if (download_file_flag) {
     extract_file_flag <- TRUE
-    download.file(ftplink, output_zip_file)
+    PEcAn.utils::download.file(ftplink, output_zip_file)
     if (!file.exists(output_zip_file)) {
       PEcAn.logger::logger.severe("FTP did not download ", output_zip_file, " from ", ftplink)
     }
   }
   if (extract_file_flag) {
-    avail_file <- unzip(output_zip_file, list = TRUE)
+    avail_file <- utils::unzip(output_zip_file, list = TRUE)
     if (length(grep("HH", avail_file)) > 0) {
       file_timestep <- "HH"
     } else {
@@ -123,7 +123,7 @@ download.Fluxnet2015 <- function(sitename, outfolder, start_date, end_date,
         PEcAn.logger::logger.severe("Half-hourly or Hourly data file was not found in ", output_zip_file)
       }
     }
-    unzip(output_zip_file, outcsvname, exdir = outfolder)
+    utils::unzip(output_zip_file, outcsvname, exdir = outfolder)
     if (!file.exists(output_csv_file)) {
       PEcAn.logger::logger.severe("ZIP file ", output_zip_file, " did not contain CSV file ", outcsvname)
     }
diff --git a/modules/data.atmosphere/R/download.FluxnetLaThuile.R b/modules/data.atmosphere/R/download.FluxnetLaThuile.R
index 154b430c6d4..97a02de10e4 100644
--- a/modules/data.atmosphere/R/download.FluxnetLaThuile.R
+++ b/modules/data.atmosphere/R/download.FluxnetLaThuile.R
@@ -1,6 +1,6 @@
 # lookup the site based on the site_id
 download.FluxnetLaThuile.site <- function(site_id) {
-  sites <- read.csv(system.file("data/FLUXNET.sitemap.csv", package = "PEcAn.data.atmosphere"), 
+  sites <- utils::read.csv(system.file("data/FLUXNET.sitemap.csv", package = "PEcAn.data.atmosphere"), 
                     stringsAsFactors = FALSE)
   sites$FLUX.id[which(sites$site.id == site_id)]
 } # download.FluxnetLaThuile.site
@@ -10,7 +10,7 @@ download.FluxnetLaThuile.site <- function(site_id) {
 ##' @name download.FluxnetLaThuile
 ##' @title download.FluxnetLaThuile
 ##' @export
-##' @param site the FLUXNET ID of the site to be downloaded, used as file name prefix. 
+##' @param sitename the FLUXNET ID of the site to be downloaded, used as file name prefix. 
 ##' The 'SITE_ID' field in \href{http://www.fluxdata.org/DataInfo/Dataset%20Doc%20Lib/SynthDataSummary.aspx}{list of Fluxnet LaThuile sites}
 ##' @param outfolder location on disk where outputs will be stored
 ##' @param start_date the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)
@@ -76,7 +76,7 @@ download.FluxnetLaThuile <- function(sitename, outfolder, start_date, end_date,
     }
     
     file <- paste(baseurl, year, "synth.hourly.coreplusquality.csv", sep = ".")
-    download.file(file, outputfile)
+    PEcAn.utils::download.file(file, outputfile)
   }
   
   # return list of files downloaded
diff --git a/modules/data.atmosphere/R/download.GFDL.R b/modules/data.atmosphere/R/download.GFDL.R
index 898296c631c..23bd360698b 100644
--- a/modules/data.atmosphere/R/download.GFDL.R
+++ b/modules/data.atmosphere/R/download.GFDL.R
@@ -1,39 +1,37 @@
-##' Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CF 
-##' @name download.GFDL
-##' @title download.GFDL
-##' @export
-##' @param outfolder
-##' @param start_date
-##' @param end_date
-##' @param lat
-##' @param lon
-##' @param model , select which GFDL model to run (options are CM3, ESM2M, ESM2G)
-##' @param scenario , select which scenario to run (options are rcp26, rcp45, rcp60, rcp85)
-##' @param ensemble_member , select which ensemble_member to initialize the run (options are r1i1p1, r3i1p1, r5i1p1)
-##' @author James Simkins
-download.GFDL <- function(outfolder, start_date, end_date, site_id, lat.in, lon.in, 
-                          overwrite = FALSE, verbose = FALSE, 
+#' Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CF 
+#'
+#' @export
+#' @param outfolder Directory for storing output
+#' @param start_date Start date for met (will be converted via [base::as.POSIXlt])
+#' @param end_date End date for met (will be converted via [base::as.POSIXlt])
+#' @param lat.in Latitude coordinate for met
+#' @param lon.in Longitude coordinate for met
+#' @param overwrite Logical: Download a fresh version even if a local file with
+#'    the same name already exists?
+#' @param verbose Logical, passed on to \code{\link[ncdf4]{ncvar_def}} and
+#'    \code{\link[ncdf4]{nc_create}} to control printing of debug info
+#' @param model Which GFDL model to run (options are CM3, ESM2M, ESM2G)
+#' @param scenario Which scenario to run (options are rcp26, rcp45, rcp60, rcp85)
+#' @param ensemble_member Which ensemble_member to initialize the run (options are r1i1p1, r3i1p1, r5i1p1)
+#' @author James Simkins, Alexey Shiklomanov, Ankur Desai
+download.GFDL <- function(outfolder, start_date, end_date, lat.in, lon.in,
+                          overwrite = FALSE, verbose = FALSE,
                           model = "CM3", scenario = "rcp45", ensemble_member = "r1i1p1", ...) {
 
   if(is.null(model))           model <- "CM3"
   if(is.null(scenario))        scenario <- "rcp45"
   if(is.null(ensemble_member)) ensemble_member <- "r1i1p1"
-  
-  start_date <- as.POSIXlt(start_date, tz = "UTC")
-  end_date   <- as.POSIXlt(end_date, tz = "UTC")
+
   start_year <- lubridate::year(start_date)
   end_year   <- lubridate::year(end_date)
-  site_id    <- as.numeric(site_id)
-  model      <- paste0(model)
-  scenario   <- paste0(scenario)
-  ensemble_member <- paste0(ensemble_member)
-  
+  obs_per_year <- 365 * 24 /3 # 3-hr intervals, leap days ignored
+
   #Fix Outfolder to include model and scenario
-  folder_name <- paste0("GFDL_",model,"_",scenario,"_",ensemble_member)
+  folder_name <- paste0("GFDL_", model, "_", scenario, "_", ensemble_member)
   source_id_foldername <- basename(outfolder)
   source_all_foldername <- gsub("GFDL", folder_name, source_id_foldername)
-  outfolder <- file.path(paste0(outfolder,source_all_foldername))
-  
+  outfolder <- file.path(paste0(outfolder, source_all_foldername))
+
   lat.in     <- as.numeric(lat.in)
   lat_floor  <- floor(lat.in)
   lon.in     <- as.numeric(lon.in)
@@ -43,111 +41,154 @@ download.GFDL <- function(outfolder, start_date, end_date, site_id, lat.in, lon.
   }
   lat_GFDL <- lat_floor * (0.5) + 45
   lat_GFDL <- floor(lat_GFDL) + 1
-  lon_GFDL <- lon_floor/2.5
+  lon_GFDL <- lon_floor / 2.5
   lon_GFDL <- floor(lon_GFDL) + 1
-  
-  start    <- as.Date(start_date, format = "Y%m%d")
-  start    <- gsub("-", "", start)
-  end      <- as.Date(end_date, format = "Y%m%d")
-  end      <- gsub("-", "", end)
+
   dap_base <- "http://nomads.gfdl.noaa.gov:9192/opendap/CMIP5/output1/NOAA-GFDL/GFDL"
-  
+
   dir.create(outfolder, showWarnings = FALSE, recursive = TRUE)
-  
+
   ylist <- seq(start_year, end_year, by = 1)
   rows <- length(ylist)
-  results <- data.frame(file = character(rows), 
-                        host = character(rows), 
-                        mimetype = character(rows), 
-                        formatname = character(rows), 
-                        startdate = character(rows), 
-                        enddate = character(rows), 
-                        dbfile.name = paste("GFDL", model, scenario, ensemble_member, sep = "."),   #'GFDL',
-                        stringsAsFactors = FALSE)
-  var <- data.frame(DAP.name = c("tas", "rlds", "ps", "rsds", "uas", "vas", "huss", "pr"), 
-                    CF.name = c("air_temperature", "surface_downwelling_longwave_flux_in_air",
-                                "air_pressure", "surface_downwelling_shortwave_flux_in_air", 
-                                "eastward_wind", "northward_wind", "specific_humidity", "precipitation_flux"), 
-                    units = c("Kelvin", "W/m2", "Pascal", "W/m2", "m/s", "m/s", "g/g", "kg/m2/s"))
-  
+
+  results <- data.frame(
+    file = character(rows),
+    host = character(rows),
+    mimetype = character(rows),
+    formatname = character(rows),
+    startdate = character(rows),
+    enddate = character(rows),
+    dbfile.name = paste("GFDL", model, scenario, ensemble_member, sep = "."),   # 'GFDL',
+    stringsAsFactors = FALSE
+  )
+
+  var <- tibble::tribble(
+    ~DAP.name, ~CF.name, ~units,
+    "tas", "air_temperature", "Kelvin",
+    "rlds", "surface_downwelling_longwave_flux_in_air", "W/m2",
+    "ps", "air_pressure", "Pascal",
+    "rsds", "surface_downwelling_shortwave_flux_in_air", "W/m2",
+    "uas", "eastward_wind", "m/s",
+    "vas", "northward_wind", "m/s",
+    "huss", "specific_humidity", "g/g",
+    "pr", "precipitation_flux", "kg/m2/s"
+  )
+
   for (i in seq_len(rows)) {
     year <- ylist[i]
-    ntime <- (14600)
+    # find start position of currently-wanted year in the 5-year DAP file
+    time_offset <- 1 + ((year-1) %% 5) * obs_per_year
+
+    PEcAn.logger::logger.debug(
+      sprintf(
+        "Downloading GFDL year %d (%d of %d)",
+        year, i, rows
+      )
+    )
+
+    loc.file <- file.path(
+      outfolder,
+      paste("GFDL", model, scenario, ensemble_member, year, "nc", sep = ".")
+    )
+
+    results$file[i]       <- loc.file
+    results$host[i]       <- PEcAn.remote::fqdn()
+    results$startdate[i]  <- paste0(year, "-01-01 00:00:00")
+    results$enddate[i]    <- paste0(year, "-12-31 23:59:59")
+    results$mimetype[i]   <- "application/x-netcdf"
+    results$formatname[i] <- "CF Meteorology"
     
-    loc.file <- file.path(outfolder,
-                          paste("GFDL", model, scenario, ensemble_member, year, "nc", sep = "."))
+    if (file.exists(loc.file) && !isTRUE(overwrite)) {
+      PEcAn.logger::logger.error("File already exists. Skipping to next year")
+      next
+    }
     
     met_start <- 2006
     met_block <- 5
     url_year  <- met_start + floor((year - met_start) / met_block) * met_block
     start_url <- paste0(url_year, "0101")
     end_url   <- paste0(url_year + met_block - 1, "1231")
-    
+
     ## Create dimensions
     lat <- ncdf4::ncdim_def(name = "latitude", units = "degree_north", vals = lat.in, create_dimvar = TRUE)
     lon <- ncdf4::ncdim_def(name = "longitude", units = "degree_east", vals = lon.in, create_dimvar = TRUE)
-    time <- ncdf4::ncdim_def(name = "time", units = "sec", vals = (1:2920) * 10800, 
-                      create_dimvar = TRUE, unlim = TRUE)
-    dim <- list(lat, lon, time)
-    
+    time <- ncdf4::ncdim_def(
+      name = "time",
+      units = paste("seconds since", results$startdate[i]),
+      vals = (1:obs_per_year) * 10800, # 3 hr interval * 3600 sec/hr
+      create_dimvar = TRUE,
+      unlim = TRUE
+    )
+    dim <- list(lat = lat, lon = lon, time = time)
+
     var.list <- list()
     dat.list <- list()
-    
+
     ## get data off OpenDAP
     for (j in seq_len(nrow(var))) {
-      dap_end <- paste0("-", model, "/", 
-                        scenario, "/3hr/atmos/3hr/", 
-                        ensemble_member, "/v20110601/", 
-                        var$DAP.name[j], "/", 
-                        var$DAP.name[j], "_3hr_GFDL-",
-                        model, "_", 
-                        scenario, "_", 
-                        ensemble_member, "_", 
-                        start_url, "00-", end_url, "23.nc")
+      PEcAn.logger::logger.debug(
+        sprintf(
+          "Downloading GFDL var %s (%d of %d)",
+          var$DAP.name[j], j, nrow(var)
+        )
+      )
+      dap_end <- paste0(
+        "-", model, "/",
+        scenario, "/3hr/atmos/3hr/",
+        ensemble_member, "/v20110601/",
+        var$DAP.name[j], "/",
+        var$DAP.name[j], "_3hr_GFDL-",
+        model, "_",
+        scenario, "_",
+        ensemble_member, "_",
+        start_url, "00-", end_url, "23.nc"
+      )
       dap_file <- paste0(dap_base, dap_end)
-      dap <- ncdf4::nc_open(dap_file)
-      dat.list[[j]] <- ncdf4::ncvar_get(dap, as.character(var$DAP.name[j]), 
-                                 c(lon_GFDL, lat_GFDL, 1), 
-                                 c(1, 1, ntime))
-      var.list[[j]] <- ncdf4::ncvar_def(name = as.character(var$CF.name[j]), 
-                                 units = as.character(var$units[j]), 
+      dap <- ncdf4::nc_open(dap_file, suppress_dimvals = TRUE)
+
+      # Sanity check:
+      # We're saving the data with timestamps at the end of the interval,
+      # while GFDL-supplied timestamps vary slightly -- some vars are
+      # timestamped in middle of interval, others at end.
+      # But if these disagree by more than 3 hours, we have a problem.
+      raw_time <- ncdf4::ncvar_get(dap, "time", start = time_offset, count = obs_per_year)
+      converted_time <- udunits2::ud.convert(raw_time, dap$dim$time$units, dim$time$units)
+      if(!all(diff(converted_time) == 3 * 60 * 60)){
+        PEcAn.logger::logger.error(
+          "Expected timestamps at 3-hour intervals, got",
+          paste(range(diff(converted_time)), collapse = "-"),
+          "seconds")
+      }
+      if(!all(abs(dim$time$vals - converted_time) < (3 * 60 * 60))){
+        PEcAn.logger::logger.error(
+          "Timestamps in GFDL source file differ from expected by more than 3 hours:",
+          "Expected", paste(range(dim$time$vals), collapse = "-"),
+          dim$time$units,
+          ", got", paste(range(converted_time), collapse = "-"),
+          ". Greatest difference from expected:",
+            max(abs(dim$time$vals - converted_time)), "seconds")
+      }
+
+      dat.list[[j]] <- ncdf4::ncvar_get(dap, as.character(var$DAP.name[j]),
+                                 start = c(lon_GFDL, lat_GFDL, time_offset),
+                                 count = c(1, 1, obs_per_year))
+      var.list[[j]] <- ncdf4::ncvar_def(name = as.character(var$CF.name[j]),
+                                 units = as.character(var$units[j]),
                                  dim = dim,
-                                 missval = -999, 
+                                 missval = -999,
                                  verbose = verbose)
       ncdf4::nc_close(dap)
-      
-    }
-    dat.list <- as.data.frame(dat.list)
-    if (year %% 5 == 1) {
-      dat.list <- dat.list[1:2920, ]
     }
-    if (year %% 5 == 2) {
-      dat.list <- dat.list[2920:5839, ]
-    }
-    if (year %% 5 == 3) {
-      dat.list <- dat.list[5840:8759, ]
-    }
-    if (year %% 5 == 4) {
-      dat.list <- dat.list[8760:11679, ]
-    }
-    if (year %% 5 == 0) {
-      dat.list <- dat.list[11680:14599, ]
-    }
-    
+
+
     ## put data in new file
     loc <- ncdf4::nc_create(filename = loc.file, vars = var.list, verbose = verbose)
     for (j in seq_len(nrow(var))) {
       ncdf4::ncvar_put(nc = loc, varid = as.character(var$CF.name[j]), vals = dat.list[[j]])
     }
     ncdf4::nc_close(loc)
-    
-    results$file[i]       <- loc.file
-    results$host[i]       <- PEcAn.remote::fqdn()
-    results$startdate[i]  <- paste0(year, "-01-01 00:00:00")
-    results$enddate[i]    <- paste0(year, "-12-31 23:59:59")
-    results$mimetype[i]   <- "application/x-netcdf"
-    results$formatname[i] <- "CF Meteorology"
+
   }
-  
+
   return(invisible(results))
 } # download.GFDL
diff --git a/modules/data.atmosphere/R/download.GLDAS.R b/modules/data.atmosphere/R/download.GLDAS.R
index e39145a4ead..2ba558807e5 100644
--- a/modules/data.atmosphere/R/download.GLDAS.R
+++ b/modules/data.atmosphere/R/download.GLDAS.R
@@ -7,8 +7,8 @@
 ##' @param start_date
 ##' @param end_date
 ##' @param site_id
-##' @param lat
-##' @param lon
+##' @param lat.in
+##' @param lon.in
 ##'
 ##' @author Christy Rollinson
 download.GLDAS <- function(outfolder, start_date, end_date, site_id, lat.in, lon.in,
@@ -127,10 +127,16 @@ download.GLDAS <- function(outfolder, start_date, end_date, site_id, lat.in, lon
         latlon <- RCurl::getURL(paste0(dap_file, "lat[0:1:599],lon[0:1:1439]"))
         lat.ind <- gregexpr("lat", latlon)
         lon.ind <- gregexpr("lon", latlon)
-        lats <- as.vector(read.table(con = textConnection(substr(latlon, lat.ind[[1]][3],
-                                                                 lon.ind[[1]][3] - 1)), sep = ",", fileEncoding = "\n", skip = 1))
-        lons <- as.vector(read.table(con = textConnection(substr(latlon, lon.ind[[1]][3],
-                                                                 nchar(latlon))), sep = ",", fileEncoding = "\n", skip = 1))
+        lats <- as.vector(utils::read.table(
+          con = textConnection(substr(latlon, lat.ind[[1]][3], lon.ind[[1]][3] - 1)),
+          sep = ",",
+          fileEncoding = "\n",
+          skip = 1))
+        lons <- as.vector(utils::read.table(
+          con = textConnection(substr(latlon, lon.ind[[1]][3], nchar(latlon))),
+          sep = ",",
+          fileEncoding = "\n",
+          skip = 1))
 
         lat.use <- which(lats - 0.25 / 2 <= lat.in & lats + 0.25 / 2 >= lat.in)
         lon.use <- which(lons - 0.25 / 2 <= lon.in & lons + 0.25 / 2 >= lon.in)
@@ -148,8 +154,10 @@ download.GLDAS <- function(outfolder, start_date, end_date, site_id, lat.in, lon
           var.now <- var$DAP.name[v]
           ind.1 <- gregexpr(paste(var.now, var.now, sep = "."), dap.out)
           end.1 <- gregexpr(paste(var.now, "time", sep = "."), dap.out)
-          dat.list[[v]][, , (j * 8) - 8 + h - 1] <-
-            read.delim(con = textConnection(substr(dap.out, ind.1[[1]][1], end.1[[1]][2])), sep = ",", fileEncoding = "\n")[1, 1]
+          dat.list[[v]][, , (j * 8) - 8 + h - 1] <- utils::read.delim(
+            con = textConnection(substr(dap.out, ind.1[[1]][1], end.1[[1]][2])),
+            sep = ",",
+            fileEncoding = "\n")[1, 1]
         }  # end variable loop
       }  # end hour
     }  # end day
diff --git a/modules/data.atmosphere/R/download.Geostreams.R b/modules/data.atmosphere/R/download.Geostreams.R
index 039d1244ea1..7828b5642d0 100644
--- a/modules/data.atmosphere/R/download.Geostreams.R
+++ b/modules/data.atmosphere/R/download.Geostreams.R
@@ -17,7 +17,7 @@
 #'  file and must contain a \code{<clowder>} key that specifies hostname, user, and
 #'  password for your Clowder server:
 #'
-#' \code{\preformatted{
+#' \preformatted{
 #'   <?xml version="1.0"?>
 #'   <pecan>
 #'     <clowder>
@@ -26,7 +26,7 @@
 #'       <password>superSecretPassw0rd</password>
 #'     </clowder>
 #'   </pecan>
-#' }}
+#' }
 #'
 #' @export
 #' @author Harsh Agrawal, Chris Black
@@ -57,9 +57,9 @@ download.Geostreams <- function(outfolder, sitename,
   sensor_info <- jsonlite::fromJSON(sensor_txt)
   sensor_id <- sensor_info$id
   sensor_mintime = lubridate::parse_date_time(sensor_info$min_start_time,
-                                              orders = c("ymd", "ymdHMS", "ymdHMSz"), tz = "UTC")
+                                              orders = "ymdHMSz", tz = "UTC")
   sensor_maxtime = lubridate::parse_date_time(sensor_info$max_end_time,
-                                              orders = c("ymd", "ymdHMS", "ymdHMSz"), tz = "UTC")
+                                              orders = "ymdHMSz", tz = "UTC")
   if (start_date < sensor_mintime) {
     PEcAn.logger::logger.severe("Requested start date", start_date, "is before data begin", sensor_mintime)
   }
@@ -71,8 +71,14 @@ download.Geostreams <- function(outfolder, sitename,
   for (year in lubridate::year(start_date):lubridate::year(end_date)) {
     query_args <- list(
       sensor_id = sensor_id,
-      since = max(start_date, lubridate::ymd(paste0(year, "-01-01"), tz="UTC")),
-      until = min(end_date, lubridate::ymd(paste0(year, "-12-31"), tz="UTC")),
+      since = strftime(
+        max(start_date, lubridate::ymd(paste0(year, "-01-01"), tz="UTC")),
+        format = "%Y-%m-%dT%H:%M:%SZ",
+        tz = "UTC"),
+      until = strftime(
+        min(end_date, lubridate::ymd(paste0(year, "-12-31"), tz="UTC")),
+        format = "%Y-%m-%dT%H:%M:%SZ",
+        tz = "UTC"),
       key = auth$key,
       ...)
 
diff --git a/modules/data.atmosphere/R/download.MACA.R b/modules/data.atmosphere/R/download.MACA.R
index e3e3ded91a4..b3cb02e6aba 100644
--- a/modules/data.atmosphere/R/download.MACA.R
+++ b/modules/data.atmosphere/R/download.MACA.R
@@ -14,9 +14,6 @@
 ##' @author James Simkins
 download.MACA <- function(outfolder, start_date, end_date, site_id, lat.in, lon.in, model='IPSL-CM5A-LR', scenario='rcp85', ensemble_member='r1i1p1', 
                           overwrite=FALSE, verbose=FALSE, ...){  
-  library(PEcAn.utils)
-  library(lubridate)
-  library(ncdf4)
   start_date <- as.POSIXlt(start_date, tz = "UTC")
   end_date <- as.POSIXlt(end_date, tz = "UTC")
   start_year <- lubridate::year(start_date)
@@ -103,7 +100,7 @@ download.MACA <- function(outfolder, start_date, end_date, site_id, lat.in, lon.
       ncdf4::nc_close(dap)
       } else {
         dat.list[[j]] <- NA
-        var.list[[j]] <- ncvar_def(name=as.character(var$CF.name[j]), units=as.character(var$units[j]), dim=dim, missval=-9999.0, verbose=verbose)}
+        var.list[[j]] <- ncdf4::ncvar_def(name=as.character(var$CF.name[j]), units=as.character(var$units[j]), dim=dim, missval=-9999.0, verbose=verbose)}
     }
     
     dat.list <- as.data.frame(dat.list)
@@ -135,7 +132,7 @@ download.MACA <- function(outfolder, start_date, end_date, site_id, lat.in, lon.
     }
     
     ## put data in new file
-    loc <- nc_create(filename=loc.file, vars=var.list, verbose=verbose)
+    loc <- ncdf4::nc_create(filename=loc.file, vars=var.list, verbose=verbose)
     for(j in seq_along(var$CF.name)){
       ncdf4::ncvar_put(nc=loc, varid=as.character(var$CF.name[j]), vals=dat.list[[j]])
     }
diff --git a/modules/data.atmosphere/R/download.MsTMIP_NARR.R b/modules/data.atmosphere/R/download.MsTMIP_NARR.R
index 58375c80f9d..73937411785 100644
--- a/modules/data.atmosphere/R/download.MsTMIP_NARR.R
+++ b/modules/data.atmosphere/R/download.MsTMIP_NARR.R
@@ -11,7 +11,6 @@
 ##' @author James Simkins
 download.MsTMIP_NARR <- function(outfolder, start_date, end_date, site_id, lat.in, lon.in,
                                  overwrite = FALSE, verbose = FALSE, ...) {
-  library(PEcAn.utils)
 
   start_date <- as.POSIXlt(start_date, tz = "UTC")
   end_date   <- as.POSIXlt(end_date, tz = "UTC")
diff --git a/modules/data.atmosphere/R/download.NARR.R b/modules/data.atmosphere/R/download.NARR.R
index 9b08012e611..364d3110dc6 100644
--- a/modules/data.atmosphere/R/download.NARR.R
+++ b/modules/data.atmosphere/R/download.NARR.R
@@ -7,6 +7,7 @@
 ##' @param verbose Turn on verbose output? Default=FALSE
 ##' @param method Method of file retrieval. Can set this using the options(download.ftp.method=[method]) in your Rprofile.
 ##' example options(download.ftp.method="ncftpget")
+##' @importFrom magrittr %>%
 ##' 
 ##' @examples
 ##' \dontrun{
@@ -18,8 +19,6 @@
 ##' @author Betsy Cowdery, Shawn Serbin
 download.NARR <- function(outfolder, start_date, end_date, overwrite = FALSE, verbose = FALSE, method, ...) {
   
-  library(PEcAn.utils)
-  
   start_date <- as.POSIXlt(start_date, tz = "UTC")
   end_date   <- as.POSIXlt(end_date, tz = "UTC")
   start_year <- lubridate::year(start_date)
diff --git a/modules/data.atmosphere/R/download.NARR_site.R b/modules/data.atmosphere/R/download.NARR_site.R
new file mode 100644
index 00000000000..e3b9e13a0bf
--- /dev/null
+++ b/modules/data.atmosphere/R/download.NARR_site.R
@@ -0,0 +1,466 @@
+#' Download NARR time series for a single site
+#'
+#' @param outfolder Target directory for storing output
+#' @param start_date Start date for met data
+#' @param end_date End date for met data
+#' @param lat.in Site latitude coordinate
+#' @param lon.in Site longitude coordinate
+#' @param overwrite Overwrite existing files?  Default=FALSE
+#' @param verbose Turn on verbose output? Default=FALSE
+#' @param parallel Download in parallel? Default = TRUE.
+#' @param ncores Number of cores for parallel download. Default is 
+#' `parallel::detectCores()`
+#'
+#' @examples
+#' 
+#' \dontrun{
+#' download.NARR_site(tempdir(), "2001-01-01", "2001-01-12", 43.372, -89.907)
+#' }
+#' 
+#'
+#' @export
+#'
+#' @author Alexey Shiklomanov
+download.NARR_site <- function(outfolder,
+                               start_date, end_date,
+                               lat.in, lon.in,
+                               overwrite = FALSE,
+                               verbose = FALSE,
+                               progress = TRUE,
+                               parallel = FALSE,
+                               ncores = if (parallel) parallel::detectCores() else NULL,
+                               ...) {
+
+  if (verbose) PEcAn.logger::logger.info("Downloading NARR data")
+  narr_data <- get_NARR_thredds(
+    start_date, end_date, lat.in, lon.in,
+    progress = progress,
+    parallel = parallel,
+    ncores = ncores
+  )
+  dir.create(outfolder, showWarnings = FALSE, recursive = TRUE)
+
+  date_limits_chr <- strftime(range(narr_data$datetime), "%Y-%m-%d %H:%M:%S", tz = "UTC")
+
+  narr_byyear <- narr_data %>%
+    dplyr::mutate(year = lubridate::year(datetime)) %>%
+    dplyr::group_by(year) %>%
+    tidyr::nest()
+
+  # Prepare result data frame
+  result_full <- narr_byyear %>%
+    dplyr::mutate(
+      file = file.path(outfolder, paste("NARR", year, "nc", sep = ".")),
+      host = PEcAn.remote::fqdn(),
+      start_date = date_limits_chr[1],
+      end_date = date_limits_chr[2],
+      mimetype = "application/x-netcdf",
+      formatname = "CF Meteorology",
+    )
+
+  lat <- ncdf4::ncdim_def(
+    name = "latitude",
+    units = "degree_north",
+    vals = lat.in,
+    create_dimvar = TRUE
+  )
+  lon <- ncdf4::ncdim_def(
+    name = "longitude",
+    units = "degree_east",
+    vals = lon.in,
+    create_dimvar = TRUE
+  )
+
+  narr_proc <- result_full %>%
+    dplyr::mutate(
+      data_nc = purrr::map2(data, file, prepare_narr_year, lat = lat, lon = lon)
+    )
+
+  results <- dplyr::select(result_full, -data)
+  return(invisible(results))
+} # download.NARR_site
+
+#' Write NetCDF file for a single year of data
+#'
+#' @param dat NARR tabular data for a single year ([get_NARR_thredds])
+#' @param file Full path to target file
+#' @param lat_nc `ncdim` object for latitude
+#' @param lon_nc `ncdim` object for longitude
+#' @param verbose 
+#' @return List of NetCDF variables in data. Creates NetCDF file containing 
+#' data as a side effect
+prepare_narr_year <- function(dat, file, lat_nc, lon_nc, verbose = FALSE) {
+  starttime <- min(dat$datetime)
+  starttime_f <- strftime(starttime, "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")
+  time <- difftime(dat$datetime, starttime) %>%
+    as.numeric() %>%
+    udunits2::ud.convert("seconds", "hours")
+  time_nc <- ncdf4::ncdim_def(
+    name = "time",
+    units = paste0("hours since ", starttime_f),
+    vals = time,
+    create_dimvar = TRUE,
+    unlim = TRUE
+  )
+  nc_values <- dplyr::select(dat, narr_all_vars$CF_name)
+  ncvar_list <- purrr::map(
+    colnames(nc_values),
+    col2ncvar,
+    dims = list(lat_nc, lon_nc, time_nc)
+  )
+  nc <- ncdf4::nc_create(file, ncvar_list, verbose = verbose)
+  on.exit(ncdf4::nc_close(nc))
+  purrr::iwalk(nc_values, ~ncdf4::ncvar_put(nc, .y, .x, verbose = verbose))
+  invisible(ncvar_list)
+}
+
+#' Create `ncvar` object from variable name
+#'
+#' @param variable CF variable name
+#' @param dims List of NetCDF dimension objects (passed to 
+#' `ncdf4::ncvar_def(..., dim)`)
+#' @return `ncvar` object (from `ncvar_def`)
+col2ncvar <- function(variable, dims) {
+  var_info <- narr_all_vars %>% dplyr::filter(CF_name == variable)
+  ncdf4::ncvar_def(
+    name = variable,
+    units = var_info$units,
+    dim = dims,
+    missval = -999,
+  )
+}
+
+#' Retrieve NARR data using thredds
+#'
+#' @param start_date Start date for meteorology
+#' @param end_date End date for meteorology
+#' @param lat.in Latitude coordinate
+#' @param lon.in Longitude coordinate
+#' @param progress Whether or not to show a progress bar (default = `TRUE`).  
+#' Requires the `progress` package to be installed.
+#' @param drop_outside Whether or not to drop dates outside of `start_date` to 
+#' `end_date` range (default = `TRUE`).
+#' @inheritParams download.NARR_site
+#' @return `tibble` containing time series of NARR data for the given site
+#' @author Alexey Shiklomanov
+#' @examples
+#' dat <- get_NARR_thredds("2008-01-01", "2008-01-15", 43.3724, -89.9071)
+#' @export
+get_NARR_thredds <- function(start_date, end_date, lat.in, lon.in,
+                             progress = TRUE,
+                             drop_outside = TRUE,
+                             parallel = TRUE,
+                             ncores = 1
+                             ) {
+
+  PEcAn.logger::severeifnot(
+    length(start_date) == 1,
+    msg = paste("Start date must be a scalar, but has length", length(start_date))
+  )
+
+  PEcAn.logger::severeifnot(
+    length(end_date) == 1,
+    msg = paste("End date must be a scalar, but has length", length(end_date))
+  )
+
+  PEcAn.logger::severeifnot(
+    length(lat.in) == 1,
+    msg = paste("Latitude must be a scalar, but has length", length(latitude))
+  )
+
+  PEcAn.logger::severeifnot(
+    length(lon.in) == 1,
+    msg = paste("Longitude must be a scalar, but has length", length(longitude))
+  )
+
+  narr_start <- lubridate::ymd("1979-01-01")
+  # NARR is updated monthly
+  # Set end day to the last day of the previous month
+  # (e.g. March 31 if today is April 10)
+  today <- lubridate::as_date(Sys.Date())
+  narr_end <- today - lubridate::days(lubridate::mday(today))
+
+  start_date <- lubridate::as_date(start_date)
+  end_date <- lubridate::as_date(end_date)
+
+  PEcAn.logger::severeifnot(
+    start_date >= narr_start,
+    msg = paste0(
+      "Start date ", start_date,
+      " is before NARR start date ", narr_start
+    )
+  )
+
+  PEcAn.logger::severeifnot(
+    end_date <= narr_end,
+    msg = paste0(
+      "End date ", end_date,
+      "is after NARR end date ", narr_end
+    )
+  )
+
+  dates <- seq(start_date, end_date, by = "1 day")
+  flx_df <- generate_narr_url(dates, TRUE)
+  sfc_df <- generate_narr_url(dates, FALSE)
+
+  # Load dimensions, etc. from first netCDF file
+  nc1 <- robustly(ncdf4::nc_open, n = 20, timeout = 0.5)(flx_df$url[1])
+  on.exit(ncdf4::nc_close(nc1))
+  xy <- latlon2narr(nc1, lat.in, lon.in)
+
+  if (parallel) {
+
+    # Load in parallel
+    PEcAn.logger::logger.info("Downloading in parallel")
+    flx_df$flx <- TRUE
+    sfc_df$flx <- FALSE
+    get_dfs <- dplyr::bind_rows(flx_df, sfc_df)
+    cl <- parallel::makeCluster(ncores)
+    doParallel::registerDoParallel(cl)
+    get_dfs$data <- foreach::`%dopar%`(
+      foreach::foreach(
+        url = get_dfs$url, flx = get_dfs$flx,
+        .packages = c("PEcAn.data.atmosphere", "magrittr"),
+        .export = c("get_narr_url", "robustly")
+      ),
+        robustly(get_narr_url)(url, xy = xy, flx = flx)
+    )
+    flx_data_raw <- dplyr::filter(get_dfs, flx)
+    sfc_data_raw <- dplyr::filter(get_dfs, !flx)
+  } else {
+
+    # Retrieve remaining variables by iterating over URLs
+    npb <- nrow(flx_df) * nrow(narr_flx_vars) +
+      nrow(sfc_df) * nrow(narr_sfc_vars)
+    if (progress && requireNamespace("progress")) {
+      pb <- progress::progress_bar$new(
+        total = npb,
+        format = "[:bar] :current/:total ETA: :eta"
+      )
+    } else {
+      pb <- NULL
+    }
+
+    flx_data_raw <- flx_df %>%
+      dplyr::mutate(
+        data = purrr::map(
+          url,
+          robustly(get_narr_url, n = 20, timeout = 1),
+          xy = xy,
+          flx = TRUE,
+          pb = pb
+        )
+      )
+
+    sfc_data_raw <- sfc_df %>%
+      dplyr::mutate(
+        data = purrr::map(
+          url,
+          robustly(get_narr_url, n = 20, timeout = 1),
+          xy = xy,
+          flx = FALSE,
+          pb = pb
+        )
+      )
+  }
+  flx_data <- post_process(flx_data_raw) %>%
+    dplyr::select(datetime, narr_flx_vars$CF_name)
+  sfc_data <- post_process(sfc_data_raw) %>%
+    dplyr::select(datetime, narr_sfc_vars$CF_name)
+  met_data <- dplyr::full_join(flx_data, sfc_data, by = "datetime") %>%
+    dplyr::arrange(datetime)
+
+  if (drop_outside) {
+    met_data <- met_data %>%
+      dplyr::filter(datetime >= start_date, datetime < (end_date + lubridate::days(1)))
+  }
+
+  met_data
+}
+
+#' Post process raw NARR downloaded data frame
+#'
+#' @param dat Nested `tibble` from mapped call to [get_narr_url]
+post_process <- function(dat) {
+  dat %>%
+    tidyr::unnest(data) %>%
+    dplyr::ungroup() %>%
+    dplyr::mutate(datetime = startdate + lubridate::dhours(dhours)) %>%
+    dplyr::select(-startdate, -dhours) %>%
+    dplyr::select(datetime, dplyr::everything()) %>%
+    dplyr::select(-url, url)
+}
+
+#' Generate NARR url from a vector of dates
+#'
+#' Figures out file names for the given dates, based on NARR's convoluted and 
+#' inconsistent naming scheme.
+#'
+#' @param dates Vector of dates for which to generate URL
+#' @param flx (Logical) If `TRUE`, format for `flx` variables. Otherwise, 
+#' format for `sfc` variables. See [narr_flx_vars].
+#' @author Alexey Shiklomanov
+generate_narr_url <- function(dates, flx) {
+  ngroup <- if (flx) 8 else 10
+  tag <- if (flx) "flx" else "sfc"
+  base_url <- paste(
+    # Have to login, so use Alexey Shiklomanov's account
+    "http://ashiklom%40bu.edu:Thisis4theNARR@rda.ucar.edu",
+    "thredds", "dodsC", "files", "g", "ds608.0", "3HRLY",
+    sep = "/"
+  )
+  tibble::tibble(date = dates) %>%
+    dplyr::mutate(
+      year = lubridate::year(date),
+      month = lubridate::month(date),
+      daygroup = daygroup(date, flx)
+    ) %>%
+    dplyr::group_by(year, month, daygroup) %>%
+    dplyr::summarize(
+      startdate = min(date),
+      url = sprintf(
+        "%s/%d/NARR%s_%d%02d_%s.tar",
+        base_url,
+        unique(year),
+        tag,
+        unique(year),
+        unique(month),
+        unique(daygroup)
+      )
+    ) %>%
+    dplyr::ungroup() %>%
+    dplyr::select(startdate, url)
+}
+
+#' Assign daygroup tag for a given date
+daygroup <- function(date, flx) {
+  mday <- lubridate::mday(date)
+  mmax <- lubridate::days_in_month(date)
+  if (flx) {
+    dplyr::case_when(
+      mday %in% 1:8 ~ "0108",
+      mday %in% 9:16 ~ "0916",
+      mday %in% 17:24 ~ "1724",
+      mday >= 25 ~ paste0(25, mmax)
+    )
+  } else {
+    dplyr::case_when(
+      mday %in% 1:9 ~ "0109",
+      mday %in% 10:19 ~ "1019",
+      mday >= 20 ~ paste0(20, mmax)
+    )
+  }
+}
+
+#' Retrieve NARR data from a given URL
+#'
+#' @param url Full URL to NARR thredds file
+#' @param xy Vector length 2 containing NARR coordinates
+#' @param pb Progress bar R6 object (default = `NULL`)
+#' @inheritParams generate_narr_url
+#' @author Alexey Shiklomanov
+get_narr_url <- function(url, xy, flx, pb = NULL) {
+  stopifnot(length(xy) == 2, length(url) == 1, is.character(url))
+  nc <- ncdf4::nc_open(url)
+  on.exit(ncdf4::nc_close(nc))
+  timevar <- if (flx) "time" else "reftime"
+  dhours <- ncdf4::ncvar_get(nc, timevar)
+  # HACK: Time variable seems inconsistent.
+  # Sometimes starts at 0, sometimes offset by 3.
+  # This is a hack to make it always start at zero
+  if (dhours[1] == 3) dhours <- dhours - 3
+  narr_vars <- if (flx) narr_flx_vars else narr_sfc_vars
+  result <- purrr::pmap(
+    narr_vars %>% dplyr::select(variable = NARR_name, unit = units),
+    read_narr_var,
+    nc = nc, xy = xy, flx = flx, pb = pb
+  )
+  names(result) <- narr_vars$CF_name
+  dplyr::bind_cols(dhours = dhours, result)
+}
+
+#' Read a specific variable from a NARR NetCDF file
+#'
+#' @param nc `ncdf4` connection object
+#' @param variable NARR name of variable to retrieve
+#' @param unit Output unit of variable to retrieve
+#' @inheritParams get_narr_url
+#' @author Alexey Shiklomanov
+read_narr_var <- function(nc, xy, variable, unit, flx, pb = NULL) {
+  if (flx) {
+    # Third dimension is height above ground -- first index is 2m above ground
+    start <- c(xy, 1, 1)
+    count <- c(1, 1, 1, -1)
+  } else {
+    # Third dimension is reference time; only has one index
+    start <- c(xy, 1, 1)
+    count <- c(1, 1, -1, -1)
+  }
+  nc_unit <- ncdf4::ncatt_get(nc, variable, "units")$value
+  out <- ncdf4::ncvar_get(nc, variable, start = start, count = count)
+  # Precipitation is a special case -- unit is actually precipitation per 3 hours
+  # So, divide by seconds in 3 hours and change unit accordingly
+  if (variable == "Total_precipitation_surface_3_Hour_Accumulation") {
+    nc_unit <- paste0(nc_unit, "/s")
+    out <- out / udunits2::ud.convert(3, "hours", "seconds")
+  }
+  final <- udunits2::ud.convert(out, nc_unit, unit)
+  if (!is.null(pb)) pb$tick()
+  final
+}
+
+#' NARR flux and sfc variables
+narr_flx_vars <- tibble::tribble(
+  ~CF_name, ~NARR_name, ~units,
+  "air_temperature", "Temperature_height_above_ground", "Kelvin",
+  "air_pressure", "Pressure_height_above_ground", "Pascal",
+  "eastward_wind", "u-component_of_wind_height_above_ground", "m/s",
+  "northward_wind", "v-component_of_wind_height_above_ground", "m/s",
+  "specific_humidity", "Specific_humidity_height_above_ground", "g/g"
+)
+
+#' @rdname narr_flx_vars
+narr_sfc_vars <- tibble::tribble(
+  ~CF_name, ~NARR_name, ~units,
+  "surface_downwelling_longwave_flux_in_air", "Downward_longwave_radiation_flux_surface_3_Hour_Average", "W/m2",
+  "surface_downwelling_shortwave_flux_in_air", "Downward_shortwave_radiation_flux_surface_3_Hour_Average", "W/m2",
+  "precipitation_flux", "Total_precipitation_surface_3_Hour_Accumulation", "kg/m2/s",
+)
+
+#' @rdname narr_flx_vars
+narr_all_vars <- dplyr::bind_rows(narr_flx_vars, narr_sfc_vars)
+
+#' Convert latitude and longitude coordinates to NARR indices
+#'
+#' @inheritParams read_narr_var
+#' @inheritParams get_NARR_thredds
+#' @return Vector length 2 containing NARR `x` and `y` indices, which can be 
+#' used in `ncdf4::ncvar_get` `start` argument.
+#' @author Alexey Shiklomanov
+latlon2narr <- function(nc, lat.in, lon.in) {
+  narr_x <- ncdf4::ncvar_get(nc, "x")
+  narr_y <- ncdf4::ncvar_get(nc, "y")
+  ptrans <- latlon2lcc(lat.in, lon.in)
+  x_ind <- which.min((ptrans$x - narr_x) ^ 2)
+  y_ind <- which.min((ptrans$y - narr_y) ^ 2)
+  c(x = x_ind, y = y_ind)
+}
+
+#' Convert latitude and longitude to x-y coordinates (in km) in Lambert 
+#' conformal conic projection (used by NARR)
+#'
+#' @inheritParams get_NARR_thredds
+#' @return `sp::SpatialPoints` object containing transformed x and y 
+#' coordinates, in km, which should match NARR coordinates
+#' @author Alexey Shiklomanov
+#' @export
+latlon2lcc <- function(lat.in, lon.in) {
+  pll <- sp::SpatialPoints(list(x = lon.in, y = lat.in), sp::CRS("+proj=longlat +datum=WGS84"))
+  CRS_narr_string <- paste(
+    "+proj=lcc +lat_1=20 +lat_2=60 +lat_0=40 +lon_0=-96",
+    "+x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=km +no_defs"
+  )
+  CRS_narr <- sp::CRS(CRS_narr_string)
+  ptrans <- sp::spTransform(pll, CRS_narr)
+  ptrans
+}
diff --git a/modules/data.atmosphere/R/download.NEONmet.R b/modules/data.atmosphere/R/download.NEONmet.R
index 2600772aa27..9e6d1b4c117 100644
--- a/modules/data.atmosphere/R/download.NEONmet.R
+++ b/modules/data.atmosphere/R/download.NEONmet.R
@@ -5,15 +5,17 @@
 ##' Uses NEON v0 API to download met data from NEON towers and convert to CF NetCDF
 ##' 
 ##' @export
-##' @param site the NEON ID of the site to be downloaded, used as file name prefix. 
+##' @param sitename the NEON ID of the site to be downloaded, used as file name prefix. 
 ##' The 4-letter SITE code  in \href{http://www.neonscience.org/science-design/field-sites/list}{list of NEON sites}
 ##' @param outfolder location on disk where outputs will be stored
 ##' @param start_date the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year and month of the date)
 ##' @param end_date the end date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year and month part of the date)
 ##' @param overwrite should existing files be overwritten
+##' @param verbose makes the function output more text
 ##' @examples 
+##' \dontrun{
 ##' result <- download.NEONmet('HARV','~/','2017-01-01','2017-01-31',overwrite=TRUE)
-##' @param verbose makes the function output more text
+##' }
 download.NEONmet <- function(sitename, outfolder, start_date, end_date, 
                                   overwrite = FALSE, verbose = FALSE,  ...) {
 
@@ -369,9 +371,9 @@ neonmet.getVals <- function(dates,product,site,datetime,
       #Extract and read 30 minute data from the highest vertical level among files returned
       #If belowground, then take top most level (lowest value)
       if (belowground==TRUE) {
-        url30 <- head(sort(urls[grep(urlstring,urls)]),1)        
+        url30 <- utils::head(sort(urls[grep(urlstring,urls)]),1)
       } else {
-        url30 <- tail(sort(urls[grep(urlstring,urls)]),1)        
+        url30 <- utils::tail(sort(urls[grep(urlstring,urls)]),1)
       }
       if (length(url30)!=0) {
         csvData <- nneo::nneo_file(product_code = product, site_code = site, year_month = mon, filename = url30) 
diff --git a/modules/data.atmosphere/R/download.NLDAS.R b/modules/data.atmosphere/R/download.NLDAS.R
index 903b42fcd62..c8a2fe00661 100644
--- a/modules/data.atmosphere/R/download.NLDAS.R
+++ b/modules/data.atmosphere/R/download.NLDAS.R
@@ -13,8 +13,6 @@
 ##' @author Christy Rollinson (with help from Ankur Desai)
 download.NLDAS <- function(outfolder, start_date, end_date, site_id, lat.in, lon.in,
                            overwrite = FALSE, verbose = FALSE, ...) {
-  library(PEcAn.utils)
-  library(RCurl)
 
   # Date stuff
   start_date <- as.POSIXlt(start_date, tz = "UTC")
@@ -66,19 +64,19 @@ download.NLDAS <- function(outfolder, start_date, end_date, site_id, lat.in, lon
       days.use <- 1:nday
     } else if (rows == 1) {
       # if we're working with only 1 year, lets only pull what we need to
-      day1 <- yday(start_date)
+      day1 <- lubridate::yday(start_date)
       # Now we need to check whether we're ending on the right day
-      day2 <- yday(end_date)
+      day2 <- lubridate::yday(end_date)
       days.use <- day1:day2
       nday <- length(days.use)  # Update nday
     } else if (i == 1) {
       # If this is the first of many years, we only need to worry about the start date
-      day1 <- yday(start_date)
+      day1 <- lubridate::yday(start_date)
       days.use <- day1:nday
       nday <- length(days.use)  # Update nday
     } else if (i == rows) {
       # If this is the last of many years, we only need to worry about the start date
-      day2 <- yday(end_date)
+      day2 <- lubridate::yday(end_date)
       days.use <- 1:day2
       nday <- length(days.use)  # Update nday
     }
@@ -100,7 +98,7 @@ download.NLDAS <- function(outfolder, start_date, end_date, site_id, lat.in, lon
 
     # Defining our dimensions up front
     for (j in 1:nrow(var)) {
-      var.list[[j]] <- ncvar_def(name = as.character(var$CF.name[j]),
+      var.list[[j]] <- ncdf4::ncvar_def(name = as.character(var$CF.name[j]),
                                  units = as.character(var$units[j]),
                                  dim = dim,
                                  missval = -999,
@@ -112,8 +110,8 @@ download.NLDAS <- function(outfolder, start_date, end_date, site_id, lat.in, lon
     ## get data off OpenDAP
     for (j in seq_along(days.use)) {
       date.now <- as.Date(days.use[j], origin = as.Date(paste0(year - 1, "-12-31")))
-      mo.now <- stringr::str_pad(month(date.now), 2, pad = "0")
-      day.mo <- stringr::str_pad(day(date.now), 2, pad = "0")
+      mo.now <- stringr::str_pad(lubridate::month(date.now), 2, pad = "0")
+      day.mo <- stringr::str_pad(lubridate::day(date.now), 2, pad = "0")
       doy <- stringr::str_pad(days.use[j], 3, pad = "0")
       for (h in seq_along(time.stamps)) {
         hr <- stringr::str_pad(time.stamps[h], 4, pad = "0")
@@ -121,12 +119,12 @@ download.NLDAS <- function(outfolder, start_date, end_date, site_id, lat.in, lon
                            mo.now, day.mo, ".", hr, ".002.grb.ascii?")
 
         # Query lat/lon
-        latlon <- getURL(paste0(dap_file, "lat[0:1:223],lon[0:1:463]"))
+        latlon <- RCurl::getURL(paste0(dap_file, "lat[0:1:223],lon[0:1:463]"))
         lat.ind <- gregexpr("lat", latlon)
         lon.ind <- gregexpr("lon", latlon)
-        lats <- as.vector(read.table(con <- textConnection(substr(latlon, lat.ind[[1]][3],
+        lats <- as.vector(utils::read.table(con <- textConnection(substr(latlon, lat.ind[[1]][3],
                                                                   lon.ind[[1]][3] - 1)), sep = ",", fileEncoding = "\n", skip = 1))
-        lons <- as.vector(read.table(con <- textConnection(substr(latlon, lon.ind[[1]][3],
+        lons <- as.vector(utils::read.table(con <- textConnection(substr(latlon, lon.ind[[1]][3],
                                                                   nchar(latlon))), sep = ",", fileEncoding = "\n", skip = 1))
 
         lat.use <- which(lats - 0.125 / 2 <= lat.in & lats + 0.125 / 2 >= lat.in)
@@ -144,13 +142,13 @@ download.NLDAS <- function(outfolder, start_date, end_date, site_id, lat.in, lon
         }
         dap_query <- substr(dap_query, 2, nchar(dap_query))
 
-        dap.out <- getURL(paste0(dap_file, dap_query))
+        dap.out <- RCurl::getURL(paste0(dap_file, dap_query))
         for (v in seq_len(nrow(var))) {
           var.now <- var$DAP.name[v]
           ind.1   <- gregexpr(paste(var.now, var.now, sep = "."), dap.out)
           end.1   <- gregexpr(paste(var.now, "time", sep = "."), dap.out)
           dat.list[[v]][, , j * 24 - 24 + h] <-
-            read.delim(con <- textConnection(substr(dap.out,
+            utils::read.delim(con <- textConnection(substr(dap.out,
                                                     ind.1[[1]][1], end.1[[1]][2])), sep = ",", fileEncoding = "\n")[1, 1]
         }  # end variable loop
       }  # end hour
diff --git a/modules/data.atmosphere/R/download.NOAA_GEFS.R b/modules/data.atmosphere/R/download.NOAA_GEFS.R
new file mode 100644
index 00000000000..e312f99e4ac
--- /dev/null
+++ b/modules/data.atmosphere/R/download.NOAA_GEFS.R
@@ -0,0 +1,273 @@
+##' @title Download NOAA GEFS Weather Data
+##' 
+##' @section Information on Units:
+##' Information on NOAA weather units can be found below. Note that the temperature is measured in degrees C, but is converted at the station and downlaoded
+##' in Kelvin.
+##' @references https://www.ncdc.noaa.gov/crn/measurements.html
+##' 
+##' @section NOAA_GEFS General Information:
+##' This function downloads NOAA GEFS weather data.  GEFS is an ensemble of 21 different weather forecast models.  A 16 day forecast is avaliable
+##' every 6 hours.  Each forecast includes information on a total of 8 variables.  These are transformed from the NOAA standard to the internal PEcAn
+##' standard.
+##' 
+##' @section Data Avaliability:
+##' NOAA GEFS weather data is avaliable on a rolling 12 day basis; dates provided in "start_date" must be within this range. The end date can be any point after
+##' that, but if the end date is beyond 16 days, only 16 days worth of forecast are recorded.  Times are rounded down to the previous 6 hour forecast.  NOAA
+##' GEFS weather data isn't always posted immediately, and to compensate, this function adjusts requests made in the last two hours
+##' back two hours (approximately the amount of time it takes to post the data) to make sure the most current forecast is used.
+##' 
+##' @section Data Save Format:
+##' Data is saved in the netcdf format to the specified directory.  File names reflect the precision of the data to the given range of days.
+##' NOAA.GEFS.willow creek.3.2018-06-08T06:00.2018-06-24T06:00.nc specifies the forecast, using ensemble nubmer 3 at willow creek on
+##' June 6th, 2018 at 6:00 a.m. to June 24th, 2018 at 6:00 a.m.
+##' 
+##' @return A list of data frames is returned containing information about the data file that can be used to locate it later.  Each
+##' data frame contains information about one file.
+##'
+##' @param outfolder Directory where results should be written
+##' @param start_date, end_date Range of dates/times to be downloaded (default assumed time of day is 0:00, midnight)
+##' @param lat site latitude in decimal degrees
+##' @param lon site longitude in decimal degrees
+##' @param sitename The unique ID given to each site. This is used as part of the file name.
+##' @param overwrite logical. Download a fresh version even if a local file with the same name already exists?
+##' @param verbose logical.  Print additional debug information.  Passed on to functions in the netcdf4 package to provide debugging info.
+##' @param ... Other arguments, currently ignored
+##' @export
+##' 
+##' @examples 
+##' \dontrun{
+##'  download.NOAA_GEFS(outfolder="~/Working/results", lat.in= 45.805925, lon.in = -90.07961, sitename="US-WCr")
+##' }
+##' 
+##' @author Luke Dramko
+##' 
+download.NOAA_GEFS <- function(outfolder, lat.in, lon.in, sitename, start_date = Sys.time(), end_date = (as.POSIXct(start_date, tz="UTC") + lubridate::days(16)),
+                             overwrite = FALSE, verbose = FALSE, ...) {
+  
+  start_date <- as.POSIXct(start_date, tz = "UTC")
+  end_date <- as.POSIXct(end_date, tz = "UTC")
+  
+  #It takes about 2 hours for NOAA GEFS weather data to be posted.  Therefore, if a request is made within that 2 hour window,
+  #we instead want to adjust the start time to the previous forecast, which is the most recent one avaliable.  (For example, if
+  #there's a request at 7:00 a.m., the data isn't up yet, so the function grabs the data at midnight instead.)
+  if (abs(as.numeric(Sys.time() - start_date, units="hours")) <= 2) {
+    start_date = start_date - lubridate::hours(2)
+    end_date = end_date - lubridate::hours(2)
+  }
+  
+  #Date/time error checking - Checks to see if the start date is before the end date
+  if (start_date > end_date) {
+    PEcAn.logger::logger.severe("Invalid dates: end date occurs before start date")
+  } else if (as.numeric(end_date - start_date, units="hours") < 6) { #Done separately to produce a more helpful error message.
+    PEcAn.logger::logger.severe("Times not far enough appart for a forecast to fall between them.  Forecasts occur every six hours; make sure start 
+                                and end dates are at least 6 hours appart.")
+  }
+  
+  #Set the end forecast date (default is the full 16 days)
+  if (end_date > start_date + lubridate::days(16)) {
+    end_date = start_date + lubridate::days(16)
+  }
+  
+  #Round the starting date/time down to the previous block of 6 hours.  Adjust the time frame to match.
+  forecast_hour = (lubridate::hour(start_date) %/% 6) * 6 #Integer division by 6 followed by re-multiplication acts like a "floor function" for multiples of 6
+  increments = as.integer(as.numeric(end_date - start_date, units = "hours") / 6) #Calculating the number of forecasts between start and end dates.
+  increments = increments + ((lubridate::hour(end_date) - lubridate::hour(start_date)) %/% 6) #These calculations are required to use the rnoaa package.
+  
+  end_hour = sprintf("%04d", ((forecast_hour + (increments * 6)) %% 24) * 100)  #Calculating the starting hour as a string, which is required type to access the 
+                                                                        #data via the rnoaa package
+  forecast_hour = sprintf("%04d", forecast_hour * 100)  #Having the end date as a string is useful later, too.
+  
+  #Recreate the adjusted start and end dates.
+  start_date = as.POSIXct(paste0(lubridate::year(start_date), "-", lubridate::month(start_date), "-", lubridate::day(start_date), " ", 
+                                 substring(forecast_hour, 1,2), ":00:00"), tz="UTC")
+  end_date = start_date + lubridate::hours(increments * 6)
+  
+  #Bounds date checking
+  #NOAA's GEFS database maintains a rolling 12 days of forecast data for access through this function.
+  #We do want Sys.Date() here - NOAA makes data unavaliable days at a time, not forecasts at a time.
+  NOAA_GEFS_Start_Date = as.POSIXct(Sys.Date(), tz="UTC") - lubridate::days(11)  #Subtracting 11 days is correct, not 12.
+  
+  #Check to see if start_date is valid. This must be done after date adjustment.
+  if (as.POSIXct(Sys.time(), tz="UTC") < start_date || start_date < NOAA_GEFS_Start_Date) {
+    PEcAn.logger::logger.severe(sprintf('Start date (%s) exceeds the NOAA GEFS range (%s to %s).',
+                                        start_date,
+                                        NOAA_GEFS_Start_Date, Sys.Date()))
+  }
+  
+  if (lubridate::hour(start_date) > 23) {
+    PEcAn.logger::logger.severe(sprintf("Start time %s is not a valid time", lubridate::hour(start_date)))
+  }
+  
+  if (lubridate::hour(end_date) > 23) {  #Done separately from the previous if statement in order to have more specific error messages.
+    PEcAn.logger::logger.severe(sprintf("End time %s is not a valid time", lubridate::hour(end_date)))
+  }
+  #End date/time error checking
+  
+  #################################################
+  #NOAA variable downloading
+  #Uses the rnoaa package to download data
+  
+  #We want data for each of the following variables. Here, we're just getting the raw data; later, we will convert it to the 
+  #cf standard format when relevant.
+  noaa_var_names = c("Temperature_height_above_ground_ens", "Pressure_surface_ens", "Relative_humidity_height_above_ground_ens", "Downward_Long-Wave_Radp_Flux_surface_6_Hour_Average_ens", 
+                   "Downward_Short-Wave_Radiation_Flux_surface_6_Hour_Average_ens", "Total_precipitation_surface_6_Hour_Accumulation_ens",
+                   "u-component_of_wind_height_above_ground_ens", "v-component_of_wind_height_above_ground_ens")
+  
+  #These are the cf standard names
+  cf_var_names = c("air_temperature", "air_pressure", "specific_humidity", "surface_downwelling_longwave_flux_in_air", 
+                      "surface_downwelling_shortwave_flux_in_air", "precipitation_flux", "eastward_wind", "northward_wind")
+  cf_var_units = c("K", "Pa", "1", "Wm-2", "Wm-2", "kgm-2s-1", "ms-1", "ms-1")  #Negative numbers indicate negative exponents
+  
+  # This debugging loop allows you to check if the cf variables are correctly mapped to the equivalent
+  # NOAA variable names.  This is very important, as much of the processing below will be erroneous if 
+  # these fail to match up.
+  # for (i in 1:length(cf_var_names)) {
+  #  print(sprintf("cf / noaa   :   %s / %s", cf_var_names[[i]], noaa_var_names[[i]]))
+  #}
+  
+  noaa_data = list()
+  
+  #Downloading the data here.  It is stored in a matrix, where columns represent time in intervals of 6 hours, and rows represent
+  #each ensemble member.  Each variable gets its own matrix, which is stored in the list noaa_data.
+  for (i in 1:length(noaa_var_names)) {
+    noaa_data[[i]] = rnoaa::gefs(noaa_var_names[i], lat.in, lon.in, raw=TRUE, time_idx = 1:increments, forecast_time = forecast_hour, date=format(start_date, "%Y%m%d"))$data
+  }
+  
+  #Fills in data with NaNs if there happens to be missing columns.
+  for (i in 1:length(noaa_var_names)) {
+    if (!is.null(ncol(noaa_data[[i]]))) { # Is a matrix
+      nans <- rep(NaN, nrow(noaa_data[[i]]))
+      while (ncol(noaa_data[[i]]) < increments) {
+        noaa_data[[i]] <- cbind(noaa_data[[i]], nans)
+      }
+    } else {   # Is a vector
+      while (length(noaa_data[[i]]) < increments) {
+        noaa_data[[i]] <- c(noaa_data[[i]], NaN);
+      }
+    }
+  }
+  
+  ###################################################
+  # Not all NOAA data units match the cf data standard.  In this next section, data are processed to
+  # confirm with the standard when necessary.
+  # The following is a list of variables which need to be processed:
+  # 1. NOAA's relative humidity must be converted to specific humidity
+  # 2. NOAA's measure of precipitation is the accumulation over 6 hours; cf's standard is precipitation per second
+
+  #Convert NOAA's relative humidity to specific humidity
+  humid_index = which(cf_var_names == "specific_humidity")
+  
+  #Temperature, pressure, and relative humidity are required to calculate specific humidity.
+  humid_data = noaa_data[[humid_index]]
+  temperature_data = noaa_data[[which(cf_var_names == "air_temperature")]]
+  pressure_data = noaa_data[[which(cf_var_names == "air_pressure")]]
+   
+  #Depending on the volume and dimensions of data you download, sometimes R stores it as a vector and sometimes
+  #as a matrix; the different cases must be processed with different loops.
+  #(The specific corner case in which a vector would be generated is if only one hour is requested; for example, 
+  #only the data at time_idx 1, for example).
+  if (as.logical(nrow(humid_data))) {
+     for (i in 1:length(humid_data)) {
+       humid_data[i] = PEcAn.data.atmosphere::rh2qair(humid_data[i], temperature_data[i], pressure_data[i])
+     }
+  } else {
+     for (i in 1:nrow(humid_data)) {
+       for (j in 1:ncol(humid_data)) {
+          humid_data[i,j] = PEcAn.data.atmosphere::rh2qair(humid_data[i,j], temperature_data[i,j], pressure_data[i,j])
+        }
+      }
+  }
+  
+  #Update the noaa_data list with the correct data
+  noaa_data[[humid_index]] <- humid_data
+  
+  # Convert NOAA's total precipitation (kg m-2) to precipitation flux (kg m-2 s-1)
+  #NOAA precipitation data is an accumulation over 6 hours.
+  precip_index = which(cf_var_names == "precipitation_flux")
+  
+  #The statement udunits2::ud.convert(1, "kg m-2 6 hr-1", "kg m-2 s-1") is equivalent to udunits2::ud.convert(1, "kg m-2 hr-1", "kg m-2 s-1") * 6,
+  #which is a little unintuitive. What will do the conversion we want is what's below:
+  noaa_data[[precip_index]] = udunits2::ud.convert(noaa_data[[precip_index]], "kg m-2 hr-1", "kg m-2 6 s-1")  #There are 21600 seconds in 6 hours
+  
+  #############################################
+  # Done with data processing.  Now writing the data to the specified directory. Each ensemble member is written to its own file, for a total
+  # of 21 files.  
+  if (!dir.exists(outfolder)) {
+    dir.create(outfolder, recursive=TRUE, showWarnings = FALSE)
+  }
+  
+  # Create a data frame with information about the file.  This data frame's format is an internal PEcAn standard, and is stored in the BETY database to
+  # locate the data file.  The data file is stored on the local machine where the download occured.  Because NOAA GEFS is an 
+  # ensemble of 21 different forecast models, each model gets its own data frame.  All of the information is the same for 
+  # each file except for the file name.
+  results = data.frame(
+    file = "",                            #Path to the file (added in loop below).
+    host = PEcAn.remote::fqdn(),          #Name of the server where the file is stored
+    mimetype = "application/x-netcdf",    #Format the data is saved in
+    formatname = "CF Meteorology",        #Type of data
+    startdate = paste0(format(start_date, "%Y-%m-%dT%H:%M:00")),    #starting date and time, down to the second
+    enddate = paste0(format(end_date, "%Y-%m-%dT%H:%M:00")),        #ending date and time, down to the second
+    dbfile.name = "NOAA_GEFS",            #Source of data (ensemble number will be added later)
+    stringsAsFactors = FALSE
+  )
+  
+  results_list = list()
+  
+  #Each ensemble gets its own file.
+  #These dimensions will be used for all 21 ncdf4 file members, so they're all declared once here.
+  #The data is really one-dimensional for each file (though we include lattitude and longitude dimensions
+  #to comply with the PEcAn standard).
+  time_dim = ncdf4::ncdim_def(name="time", 
+                              paste(units="hours since", format(start_date, "%Y-%m-%dT%H:%M")), 
+                              seq(6, 6 * increments, by = 6),
+                              create_dimvar = TRUE)
+  lat_dim = ncdf4::ncdim_def("latitude", "degree_north", lat.in, create_dimvar = TRUE)
+  lon_dim = ncdf4::ncdim_def("longitude", "degree_east", lon.in, create_dimvar = TRUE)
+  
+  dimensions_list = list(time_dim, lat_dim, lon_dim)
+  
+  nc_var_list = list()
+  for (i in 1:length(cf_var_names)) { #Each ensemble member will have data on each variable stored in their respective file.
+    nc_var_list[[i]] = ncdf4::ncvar_def(cf_var_names[i], cf_var_units[i], dimensions_list, missval=NaN)
+  }
+  
+  #For each ensemble
+  for (i in 1:21) { # i is the ensemble number
+    #Generating a unique identifier string that characterizes a particular data set.
+    identifier = paste("NOAA_GEFS", sitename, i, format(start_date, "%Y-%m-%dT%H:%M"), 
+          format(end_date, "%Y-%m-%dT%H:%M"), sep=".")
+    
+    ensemble_folder = file.path(outfolder, identifier)
+    
+    #Each file will go in its own folder.
+    if (!dir.exists(ensemble_folder)) {
+      dir.create(ensemble_folder, recursive=TRUE, showWarnings = FALSE)
+    }
+    
+    flname = file.path(ensemble_folder, paste(identifier, "nc", sep = "."))
+    
+    #Each ensemble member gets its own unique data frame, which is stored in results_list
+    #Object references in R work differently than in other languages. When adding an item to a list, R creates a copy of it
+    #for you instead of just inserting the object reference, so this works.
+    results$file <- flname
+    results$dbfile.name <- flname
+    results_list[[i]] <- results
+    
+    if (!file.exists(flname) | overwrite) {
+      nc_flptr = ncdf4::nc_create(flname, nc_var_list, verbose=verbose)
+      
+      #For each variable associated with that ensemble
+      for (j in 1:length(cf_var_names)) {
+        # "j" is the variable number.  "i" is the ensemble number. Remember that each row represents an ensemble
+        ncdf4::ncvar_put(nc_flptr, nc_var_list[[j]], noaa_data[[j]][i,])
+      }
+      
+      ncdf4::nc_close(nc_flptr)  #Write to the disk/storage
+    } else {
+      PEcAn.logger::logger.info(paste0("The file ", flname, " already exists.  It was not overwritten."))
+    }
+    
+  }
+  
+  return(results_list)
+} #download.NOAA_GEFS
diff --git a/modules/data.atmosphere/R/download.PalEON.R b/modules/data.atmosphere/R/download.PalEON.R
index ea8dffd4a34..f6bc4261833 100644
--- a/modules/data.atmosphere/R/download.PalEON.R
+++ b/modules/data.atmosphere/R/download.PalEON.R
@@ -4,14 +4,12 @@
 ##' @title download.PalEON
 ##' @export
 ##' @param outfolder
-##' @param start_year
-##' @param end_year
+##' @param start_date
+##' @param end_date
 ##' 
 ##' @author Betsy Cowdery
 download.PalEON <- function(sitename, outfolder, start_date, end_date, overwrite = FALSE, ...) {
   
-  library(PEcAn.utils)
-  
   if (sitename == "Harvard Forest - Lyford Plots (PalEON PHA)") {
     site <- "PHA"
   }  # 1-650 done
diff --git a/modules/data.atmosphere/R/download.PalEON_ENS.R b/modules/data.atmosphere/R/download.PalEON_ENS.R
index bf4147d85a8..9f2ed487bbd 100644
--- a/modules/data.atmosphere/R/download.PalEON_ENS.R
+++ b/modules/data.atmosphere/R/download.PalEON_ENS.R
@@ -2,8 +2,8 @@
 ##'
 ##' @export
 ##' @param outfolder
-##' @param start_year
-##' @param end_year
+##' @param start_date
+##' @param end_date
 ##' 
 ##' @author Betsy Cowdery, Mike Dietze
 download.PalEON_ENS <- function(sitename, outfolder, start_date, end_date, overwrite = FALSE, ...) {
diff --git a/modules/data.atmosphere/R/download.US_WCr.R b/modules/data.atmosphere/R/download.US_WCr.R
new file mode 100644
index 00000000000..5aaf55a0ef9
--- /dev/null
+++ b/modules/data.atmosphere/R/download.US_WCr.R
@@ -0,0 +1,115 @@
+##' @title download.US-WCr
+##' 
+##' @section General Description:
+##' Obtains data from Ankur Desai's Willow Creek flux tower, and selects certain variables (NEE and LE) to return
+##' Data is retruned at the given timestep in the given range.
+##' 
+##' This data includes information on a number of flux variables.
+##' 
+##' The timestep parameter is measured in hours, but is then converted to half hours because the data's timestep
+##' is every half hour.
+##' 
+##' @param start_date Start date/time data should be downloaded for
+##' @param end_date End date/time data should be downloaded for
+##' @param timestep How often to take data points from the file.  Must be a multiple of 0.5
+##' @export
+##' 
+##' @author Luke Dramko
+download.US_WCr <- function(start_date, end_date, timestep = 1) {
+  timestep = 2 * timestep #data is actually every half hour
+  
+  if (timestep != as.integer(timestep)) {
+    PEcAn.logger::logger.severe(paste0("Invalid timestep ", timestep/2, ". Timesteps must be at ",
+                                       "least every half hour (timestep = 0.5)."))
+  }
+  
+  start_date <- as.POSIXct(start_date, tz="UTC")
+  end_date <- as.POSIXct(end_date, tz="UTC")
+  
+  nee_col = 9  # Column number of NEE
+  le_col = 10  # Column number of LE
+  
+  # Data is found here
+  # Original url: http://flux.aos.wisc.edu/data/cheas/wcreek/flux/prelim/wcreek2018_flux.txt
+  base_url <- "http://flux.aos.wisc.edu/data/cheas/wcreek/flux/prelim/wcreek"
+  
+  flux = NULL;
+  
+  for (year in as.integer(format(start_date, "%Y")):as.integer(format(end_date, "%Y"))) {
+    url <- paste0(base_url, year, "_flux.txt") #Build proper url
+    PEcAn.logger::logger.info(paste0("Reading data for year ", year))
+    print(url)
+    influx <- tryCatch(read.table(url, sep="", header=FALSE), error=function(e) {NULL}, warning=function(e) {NULL})
+    if (is.null(influx)) { #Error encountered in data fetching.
+      PEcAn.logger::logger.warn(paste0("Data not avaliable for year ", year, ". All values for ", year, " will be NA."))
+      # Determine the number of days in the year
+      rows_in_year <- udunits2::ud.convert(lubridate::as.duration(lubridate::interval(as.POSIXct(paste0(year, "-01-01")), as.POSIXct(paste0(year + 1, "-01-01")))), "s", "day")
+      rows_in_year = rows_in_year * 48 # 48 measurements per day, one every half hour.
+      influx <- matrix(rep(-999, rows_in_year * 13), nrow=rows_in_year, ncol = 13)
+    }
+    flux <- rbind(flux, influx)
+  }
+  PEcAn.logger::logger.info("Flux data has been read.")
+  
+  # Contains only the data needed in a data frame
+  new.flux <- data.frame(DOY = flux[,3], 
+           HRMIN = flux[,4],
+           NEE = as.numeric(flux[,nee_col]),
+           LE = as.numeric(flux[,le_col]))
+  
+  # Calculate minutes from start year to find the right row to pull data from.
+  year_start <- as.POSIXct(format(start_date, "%Y-01-01 00:00:00"), tz="UTC")
+  
+  start_interval <- lubridate::interval(year_start, start_date)
+  days <- lubridate::as.duration(start_interval)  # Actually returns a number of seconds
+  days <- udunits2::ud.convert(as.integer(days), "s", "day") # Days, including fractional part, if any.
+  hours <- floor(udunits2::ud.convert(days - floor(days), "day", "hr"))  # Extract the hour component, round to the previous hour.
+  if (days - floor(days) >= 0.5) {  # Flux data is at half-hour precision
+    hours <- hours + 0.5
+  }
+  days <- floor(days) # Extract the whole day component
+  
+  start_row <- as.integer(days * 48 + hours * 2)
+  
+  data_interval <- lubridate::interval(start_date, end_date)
+  days <- lubridate::as.duration(data_interval) # a number of seconds
+  days <- udunits2::ud.convert(as.integer(days), "s", "day")
+  hours <- floor(udunits2::ud.convert(as.integer(days - floor(days)), "day", "hr")) # Round down to the nearest half hour
+  if (days - floor(days) >= 0.5) {
+    hours <- hours + 0.5
+  }
+  days <- floor(days)
+  end_row <- start_row + as.integer(days * 48 + hours * 2)
+  
+  # Calculations are one time point behind the actual start time; corrects the off-by-one error
+  start_row = start_row + 1;
+  end_row = end_row + 1;
+  
+  # Vectors that will contain the output data
+  out_nee = NULL
+  out_le = NULL
+  
+  PEcAn.logger::logger.info("Starting at row (nonconverted) ")
+  print(new.flux[start_row,]) #print gives a much more interpretable output than pasting in the logger call.
+  
+  for (d in seq(start_row, end_row, by=timestep)) {
+    row = new.flux[d,]
+    
+    # NEE values
+    val <- as.numeric(row$NEE)
+    if (val == -999) { val <- NA } else {
+        val <- PEcAn.utils::misc.convert(row$NEE, "umol C m-2 s-1", "kg C m-2 s-1")
+    }
+    out_nee <- c(out_nee, val)
+    
+    # LE values
+    val <- as.numeric(row$LE)
+    if (val == -999) { val <- NA }
+    out_le <- c(out_le, val)
+  }
+  
+  return(list(nee=out_nee[-1], qle=out_le[-1])) # Start time not included in the forecast
+} # download.wcr.R
+
+# This line is great for testing.
+# download.US_WCr('2018-07-23 06:00', '2018-08-08 06:00', timestep=12)
\ No newline at end of file
diff --git a/modules/data.atmosphere/R/download.raw.met.module.R b/modules/data.atmosphere/R/download.raw.met.module.R
index 5ae14cda40f..ed3b7e8f948 100644
--- a/modules/data.atmosphere/R/download.raw.met.module.R
+++ b/modules/data.atmosphere/R/download.raw.met.module.R
@@ -6,8 +6,21 @@
   pkg <- "PEcAn.data.atmosphere"
   fcn <- paste0("download.", met)
   
+  #Some data products can be forecasts instead of real time data.  Others can be ensembles of data instead of a single source.  Some can be both.
+  #Not all of the registration.xml files for each data source contains a <forecast> or <ensemble> tag; therefore, we must check for their 
+  #existence first.
+  forecast = FALSE
+  ensemble = FALSE
+  if (!is.null(register$forecast)) {
+    forecast = as.logical(register$forecast)
+  }
+  if (!is.null(register$ensemble) && !is.na(as.integer(register$ensemble)) && as.integer(register$ensemble) > 1) {
+    ensemble = as.integer(register$ensemble) #No ensembles is given by FALSE, while the presence of ensembles is given by the number of ensembles.
+    ifelse(is.na(ensemble), FALSE, ensemble) #If ensemble happens to be a character vector or something it can't convert, as.integer will evaluate to NA.
+  }
+  
   if (register$scale == "regional") {
-    raw.id <- PEcAn.utils::convert.input(input.id = NA, 
+    raw.id <- PEcAn.utils::convert.input(input.id = NA,
                             outfolder = outfolder, 
                             formatname = register$format$name, 
                             mimetype = register$format$mimetype,
@@ -35,8 +48,13 @@
                             fcn = fcn, 
                             con = con, host = host, browndog = NULL, 
                             write = TRUE, overwrite = overwrite, 
+                            forecast = forecast,
+                            ensemble = ensemble,
                             sitename = site$name, 
-                            username = username)
+                            username = username,
+                            lat.in = lat.in,
+                            lon.in = lon.in,
+                            pattern = met)
     
   } else {
     PEcAn.logger::logger.severe("Unknown register$scale")
diff --git a/modules/data.atmosphere/R/extract.nc.R b/modules/data.atmosphere/R/extract.nc.R
index 77412f9656a..3f4651175c5 100644
--- a/modules/data.atmosphere/R/extract.nc.R
+++ b/modules/data.atmosphere/R/extract.nc.R
@@ -16,8 +16,6 @@
 extract.nc <- function(in.path, in.prefix, outfolder, start_date, end_date, slat, slon,
                        overwrite = FALSE, verbose = FALSE, ...) {
   
-  library(PEcAn.utils)
-  
   in.path   <- as.character(in.path)
   in.prefix <- as.character(in.prefix)
   outfolder <- as.character(outfolder)
diff --git a/modules/data.atmosphere/R/extract.success.R b/modules/data.atmosphere/R/extract.success.R
index 307331f43d3..0c23d70e025 100644
--- a/modules/data.atmosphere/R/extract.success.R
+++ b/modules/data.atmosphere/R/extract.success.R
@@ -1,7 +1,5 @@
 extract.success <- function(in.path, in.prefix, outfolder) {
   
-  library(PEcAn.utils)
-  
   in.path   <- as.character(in.path)
   in.prefix <- as.character(in.prefix)
   outfolder <- as.character(outfolder)
diff --git a/modules/data.atmosphere/R/extract_local_CMIP5.R b/modules/data.atmosphere/R/extract_local_CMIP5.R
index 294376d873b..df5bab1c33c 100644
--- a/modules/data.atmosphere/R/extract_local_CMIP5.R
+++ b/modules/data.atmosphere/R/extract_local_CMIP5.R
@@ -39,9 +39,6 @@
 extract.local.CMIP5 <- function(outfolder, in.path, start_date, end_date, site_id, lat.in, lon.in, 
                                 model , scenario , ensemble_member = "r1i1p1", date.origin=NULL, no.leap=NULL,
                                 overwrite = FALSE, verbose = FALSE, ...){
-  library(lubridate)
-  library(ncdf4)
-  library(stringr)
   
   # Some GCMs don't do leap year; we'll have to deal with this separately
   # no.leap <- c("bcc-csm1-1", "CCSM4")
@@ -52,7 +49,7 @@ extract.local.CMIP5 <- function(outfolder, in.path, start_date, end_date, site_i
     } else if(scenario == "historical" & GCM!="MPI-ESM-P") {
       date.origin=as.Date("1850-01-01")
     } else {
-      logger.error("No date.origin specified and scenario not implemented yet")
+      PEcAn.logger::logger.error("No date.origin specified and scenario not implemented yet")
     }
   } 
   
@@ -146,7 +143,7 @@ extract.local.CMIP5 <- function(outfolder, in.path, start_date, end_date, site_i
   dat.time <- seq(start_date, end_date, by="day")  # Everything should end up being a day
   
   print("- Extracting files: ")
-  pb <- txtProgressBar(min=1, max=n.file, style=3)
+  pb <- utils::txtProgressBar(min=1, max=n.file, style=3)
   pb.ind=1
   # Loop through each variable so that we don't have to open files more than once
   for(v in 1:nrow(var)){
@@ -161,7 +158,7 @@ extract.local.CMIP5 <- function(outfolder, in.path, start_date, end_date, site_i
     # Figure out what file we need
     # file.ind <- which(files.var[[var.now]][i])
     for(i in 1:nrow(files.var[[var.now]])){
-      setTxtProgressBar(pb, pb.ind)
+      utils::setTxtProgressBar(pb, pb.ind)
       pb.ind=pb.ind+1
       f.now <- files.var[[var.now]][i,"file.name"]
       # print(f.now)
@@ -175,7 +172,7 @@ extract.local.CMIP5 <- function(outfolder, in.path, start_date, end_date, site_i
       nc.time <- ncdf4::ncvar_get(ncT, "time")
 
       # splt.ind <- ifelse(GCM %in% c("MPI-ESM-P"), 4, 3)
-      # date.origin <- as.Date(str_split(ncT$dim$time$units, " ")[[1]][splt.ind])
+      # date.origin <- as.Date(stringr::str_split(ncT$dim$time$units, " ")[[1]][splt.ind])
       nc.date <- date.origin + nc.time
       date.leaps <- seq(as.Date(paste0(files.var[[var.now]][i,"first.year"], "-01-01")), as.Date(paste0(files.var[[var.now]][i,"last.year"], "-12-31")), by="day")
       # Figure out if we're missing leap dat
@@ -257,12 +254,12 @@ extract.local.CMIP5 <- function(outfolder, in.path, start_date, end_date, site_i
 
   print("")
   print("- Writing to NetCDF: ")
-  pb <- txtProgressBar(min=1, max=rows, style=3)
+  pb <- utils::txtProgressBar(min=1, max=rows, style=3)
   for (i in 1:rows){
-    setTxtProgressBar(pb, i)
+    utils::setTxtProgressBar(pb, i)
     
     y.now = ylist[i]    
-    yr.ind <- which(year(dat.time)==y.now)
+    yr.ind <- which(lubridate::year(dat.time)==y.now)
     
     
     dpm <- lubridate::days_in_month(1:12)
@@ -277,15 +274,15 @@ extract.local.CMIP5 <- function(outfolder, in.path, start_date, end_date, site_i
     } else if(rows==1){
       # if we're working with only 1 year, lets only pull what we need to
       nday  = ifelse(lubridate::leap_year(y.now), 366, 365) # leap year or not; days per year
-      day1 <- yday(start_date)
+      day1 <- lubridate::yday(start_date)
       # Now we need to check whether we're ending on the right day
-      day2 <- yday(end_date)
+      day2 <- lubridate::yday(end_date)
       days.use = day1:day2
       nday=length(days.use) # Update nday
     } else if(i==1) {
       # If this is the first of many years, we only need to worry about the start date
       nday  = ifelse(lubridate::leap_year(y.now), 366, 365) # leap year or not; days per year
-      day1 <- yday(start_date)
+      day1 <- lubridate::yday(start_date)
       day2 = nday
       days.use = day1:day2
       nday=length(days.use) # Update nday
@@ -299,7 +296,7 @@ extract.local.CMIP5 <- function(outfolder, in.path, start_date, end_date, site_i
     }
     ntime = nday # leap year or not; time slice (coerce to daily)
     
-    loc.file <- file.path(outfolder, paste(model, scenario, ensemble_member, str_pad(y.now, width=4, side="left",  pad="0"), "nc", sep = "."))
+    loc.file <- file.path(outfolder, paste(model, scenario, ensemble_member, stringr::str_pad(y.now, width=4, side="left",  pad="0"), "nc", sep = "."))
     
     
     ## Create dimensions
diff --git a/modules/data.atmosphere/R/extract_local_NLDAS.R b/modules/data.atmosphere/R/extract_local_NLDAS.R
index 728f6767ff4..a879517426b 100644
--- a/modules/data.atmosphere/R/extract_local_NLDAS.R
+++ b/modules/data.atmosphere/R/extract_local_NLDAS.R
@@ -22,22 +22,19 @@
 ##' @param lat.in site latitude in decimal degrees
 ##' @param lon.in site longitude in decimal degrees
 ##' @param overwrite logical. Download a fresh version even if a local file with the same name already exists?
-##' @param verbose logical. Passed on to [ncdf4]{ncvar_def}} and [ncdf4]{nc_create}
+##' @param verbose logical. Passed on to \code{\link[ncdf4]{ncvar_def}} and \code{\link[ncdf4]{nc_create}}
 ##'   to control printing of debug info
 ##' @param ... Other arguments, currently ignored
 ##' @export
 # -----------------------------------
 extract.local.NLDAS <- function(outfolder, in.path, start_date, end_date, site_id, lat.in, lon.in, 
                                 overwrite = FALSE, verbose = FALSE, ...){
-  library(lubridate)
-  library(ncdf4)
-  library(stringr)
 
   # Date stuff
   start_date <- as.POSIXlt(start_date, tz = "GMT")
   end_date <- as.POSIXlt(end_date, tz = "GMT")
-  start_year <- year(start_date)
-  end_year   <- year(end_date)
+  start_year <- lubridate::year(start_date)
+  end_year   <- lubridate::year(end_date)
   
   lat.in = as.numeric(lat.in)
   lon.in = as.numeric(lon.in)
@@ -65,30 +62,30 @@ extract.local.NLDAS <- function(outfolder, in.path, start_date, end_date, site_i
     
     # figure out how many days we're working with
     if(rows>1 & i!=1 & i!=rows){ # If we have multiple years and we're not in the first or last year, we're taking a whole year
-      nday  = ifelse(lubridate:: leap_year(y.now), 366, 365) # leap year or not; days per year
+      nday  = ifelse(lubridate::leap_year(y.now), 366, 365) # leap year or not; days per year
       day1 = 1
       day2 = nday
       days.use = day1:day2
     } else if(rows==1){
       # if we're working with only 1 year, lets only pull what we need to
-      nday  = ifelse(lubridate:: leap_year(y.now), 366, 365) # leap year or not; days per year
-      day1 <- yday(start_date)
+      nday  = ifelse(lubridate::leap_year(y.now), 366, 365) # leap year or not; days per year
+      day1 <- lubridate::yday(start_date)
       # Now we need to check whether we're ending on the right day
-      day2 <- yday(end_date)
+      day2 <- lubridate::yday(end_date)
       days.use = day1:day2
       nday=length(days.use) # Update nday
     } else if(i==1) {
       # If this is the first of many years, we only need to worry about the start date
-      nday  = ifelse(lubridate:: leap_year(y.now), 366, 365) # leap year or not; days per year
-      day1 <- yday(start_date)
+      nday  = ifelse(lubridate::leap_year(y.now), 366, 365) # leap year or not; days per year
+      day1 <- lubridate::yday(start_date)
       day2 = nday
       days.use = day1:day2
       nday=length(days.use) # Update nday
     } else if(i==rows) {
       # If this is the last of many years, we only need to worry about the start date
-      nday  = ifelse(lubridate:: leap_year(y.now), 366, 365) # leap year or not; days per year
+      nday  = ifelse(lubridate::leap_year(y.now), 366, 365) # leap year or not; days per year
       day1 = 1
-      day2 <- yday(end_date)
+      day2 <- lubridate::yday(end_date)
       days.use = day1:day2
       nday=length(days.use) # Update nday
     }
@@ -97,9 +94,9 @@ extract.local.NLDAS <- function(outfolder, in.path, start_date, end_date, site_i
     loc.file = file.path(outfolder, paste("NLDAS",y.now,"nc",sep="."))
     
     ## Create dimensions
-    dim.lat <- ncdim_def(name='latitude', units='degree_north', vals=lat.in, create_dimvar=TRUE)
-    dim.lon <- ncdim_def(name='longitude', units='degree_east', vals=lon.in, create_dimvar=TRUE)
-    dim.time <- ncdim_def(name='time', units="sec", vals=seq((min(days.use)+1-1/24)*24*360, (max(days.use)+1-1/24)*24*360, length.out=ntime), create_dimvar=TRUE, unlim=TRUE)
+    dim.lat <- ncdf4::ncdim_def(name='latitude', units='degree_north', vals=lat.in, create_dimvar=TRUE)
+    dim.lon <- ncdf4::ncdim_def(name='longitude', units='degree_east', vals=lon.in, create_dimvar=TRUE)
+    dim.time <- ncdf4::ncdim_def(name='time', units="sec", vals=seq((min(days.use)+1-1/24)*24*360, (max(days.use)+1-1/24)*24*360, length.out=ntime), create_dimvar=TRUE, unlim=TRUE)
     nc.dim=list(dim.lat,dim.lon,dim.time)
     
     var.list = list()
@@ -107,7 +104,7 @@ extract.local.NLDAS <- function(outfolder, in.path, start_date, end_date, site_i
     
     # Defining our dimensions up front
     for(j in 1:nrow(var)){
-      var.list[[j]] = ncvar_def(name=as.character(var$CF.name[j]), units=as.character(var$units[j]), dim=nc.dim, missval=-999, verbose=verbose)
+      var.list[[j]] = ncdf4::ncvar_def(name=as.character(var$CF.name[j]), units=as.character(var$units[j]), dim=nc.dim, missval=-999, verbose=verbose)
       dat.list[[j]] <- array(NA, dim=c(length(lat.in), length(lon.in), ntime)) # Go ahead and make the arrays
     }
     names(var.list) <- names(dat.list) <- var$CF.name
@@ -116,25 +113,25 @@ extract.local.NLDAS <- function(outfolder, in.path, start_date, end_date, site_i
     # Progress bar just to help us track what's going on
     print("")
     print(y.now)
-    pb <- txtProgressBar(min=1, max=nday, style=3)
+    pb <- utils::txtProgressBar(min=1, max=nday, style=3)
     pb.index=1
     
     ## get data off OpenDAP
     for(j in 1:length(days.use)){
-      setTxtProgressBar(pb, pb.index)
+      utils::setTxtProgressBar(pb, pb.index)
       
       date.now <- as.Date(days.use[j], origin=as.Date(paste0(y.now-1,"-12-31")))
-      mo.now <- str_pad(month(date.now), 2, pad="0")
-      day.mo <- str_pad(day(date.now), 2, pad="0")
-      doy <- str_pad(days.use[j], 3, pad="0")
+      mo.now <- stringr::str_pad(lubridate::month(date.now), 2, pad="0")
+      day.mo <- stringr::str_pad(lubridate::day(date.now), 2, pad="0")
+      doy <- stringr::str_pad(days.use[j], 3, pad="0")
       
       # Local netcdf format is 1-file per day
       # NLDAS_FORA0125_H.A19790102.nc
-      dap_file <- nc_open(file.path(in.path,y.now,mo.now,paste0("NLDAS_FORA0125_H.A",y.now, mo.now,day.mo,".nc")))
+      dap_file <- ncdf4::nc_open(file.path(in.path,y.now,mo.now,paste0("NLDAS_FORA0125_H.A",y.now, mo.now,day.mo,".nc")))
       
       # Query lat/lon
-      lats <- ncvar_get(dap_file, "lat")
-      lons <- ncvar_get(dap_file, "lon")
+      lats <- ncdf4::ncvar_get(dap_file, "lat")
+      lons <- ncdf4::ncvar_get(dap_file, "lon")
       
       # Get the average resolution (without hard-coding and possibly making an error)
       x.inc <- mean(abs(diff(lons)))
@@ -151,12 +148,12 @@ extract.local.NLDAS <- function(outfolder, in.path, start_date, end_date, site_i
         # Variables have different dimensions (which is a pain in the butt)
         # so we need to check to see whether we're pulling 4 dimensions or just 3
         if(dap_file$var[[v.nldas]]$ndims == 4){
-          dat.list[[v.cf]][,,(j*24-23):(j*24)] <- ncvar_get(dap_file, v.nldas,
+          dat.list[[v.cf]][,,(j*24-23):(j*24)] <- ncdf4::ncvar_get(dap_file, v.nldas,
                                                             start=c(lon.use,lat.use,1,1), 
                                                             count=c(1,1,1,24)
           )
         } else {
-          dat.list[[v.cf]][,,(j*24-23):(j*24)] <- ncvar_get(dap_file, v.nldas, 
+          dat.list[[v.cf]][,,(j*24-23):(j*24)] <- ncdf4::ncvar_get(dap_file, v.nldas,
                                                             start=c(lon.use,lat.use,1), 
                                                             count=c(1,1,24)
           )
@@ -164,7 +161,7 @@ extract.local.NLDAS <- function(outfolder, in.path, start_date, end_date, site_i
         }
       } # end variable loop
       
-      nc_close(dap_file) # close file
+      ncdf4::nc_close(dap_file) # close file
       pb.index=pb.index+1 # Advance our progress bar
     } # end day
     
@@ -172,11 +169,11 @@ extract.local.NLDAS <- function(outfolder, in.path, start_date, end_date, site_i
     dat.list[["precipitation_flux"]] = dat.list[["precipitation_flux"]]/(60*60)
     
     ## put data in new file
-    loc <- nc_create(filename=loc.file, vars=var.list, verbose=verbose)
+    loc <- ncdf4::nc_create(filename=loc.file, vars=var.list, verbose=verbose)
     for(j in 1:nrow(var)){
-      ncvar_put(nc=loc, varid=as.character(var$CF.name[j]), vals=dat.list[[j]])
+      ncdf4::ncvar_put(nc=loc, varid=as.character(var$CF.name[j]), vals=dat.list[[j]])
     }
-    nc_close(loc)
+    ncdf4::nc_close(loc)
     
     results$file[i] <- loc.file
     # results$host[i] <- fqdn()
diff --git a/modules/data.atmosphere/R/get_cf_variables_table.R b/modules/data.atmosphere/R/get_cf_variables_table.R
new file mode 100644
index 00000000000..1f238a6983c
--- /dev/null
+++ b/modules/data.atmosphere/R/get_cf_variables_table.R
@@ -0,0 +1,40 @@
+#' Retrieve the current CF variables table from `cfconventions.org`
+#' and convert it into a `data.frame`
+#'
+#' @param cf_url URL of CF variables table XML. See also [build_cf_variables_table_url].
+#' @return CF variables table, as a `tibble`
+#' @author Alexey Shiklomanov
+#' @export
+get_cf_variables_table <- function(cf_url = build_cf_variables_table_url(57)) {
+  raw_xml <- XML::xmlParse(cf_url)
+  list_xml <- XML::xmlToList(raw_xml)
+  entries <- list_xml[names(list_xml) == "entry"]
+  entries_flat <- purrr::map(entries, unlist)
+  entries_df <- purrr::map(entries, as.list) %>%
+    purrr::transpose() %>%
+    purrr::map(~ifelse(purrr::map_lgl(.x, is.null), NA, .x)) %>%
+    purrr::map_dfc(unlist, recursive = TRUE)
+  entries_df %>%
+    dplyr::select(
+      cf_standard_name = .attrs,
+      unit = canonical_units,
+      description,
+      dplyr::everything()
+    )
+}
+#' Construct a URL to a specific version of the CF variables table XML
+#'
+#' This uses [sprintf] to construct the URL with the version number as
+#' the first argument.
+#'
+#' @param version CF variables table version number (integer/numeric)
+#' @param url_format_string A format string passed to [sprintf]. This
+#'   should contain the entire target URL with the version number
+#'   replaced by `"%d"`, and _no other string substitutions_.
+#' @return Complete URL, as a string
+#' @author Alexey Shiklomanov
+#' @export
+build_cf_variables_table_url <- function(version,
+                                         url_format_string = "http://cfconventions.org/Data/cf-standard-names/%d/src/src-cf-standard-name-table.xml") {
+  sprintf(url_format_string, version)
+}
diff --git a/modules/data.atmosphere/R/load.cfmet.R b/modules/data.atmosphere/R/load.cfmet.R
index b68ba703f0b..71fb8bce8d1 100644
--- a/modules/data.atmosphere/R/load.cfmet.R
+++ b/modules/data.atmosphere/R/load.cfmet.R
@@ -15,9 +15,6 @@
 ##' @author David LeBauer
 load.cfmet <- function(met.nc, lat, lon, start.date, end.date) {
   
-  library(data.table)
-  library(PEcAn.utils)
-  
   ## Lat and Lon
   Lat <- ncdf4::ncvar_get(met.nc, "latitude")
   Lon <- ncdf4::ncvar_get(met.nc, "longitude")
@@ -54,13 +51,13 @@ load.cfmet <- function(met.nc, lat, lon, start.date, end.date) {
 
   ## data table warns not to use POSIXlt, which is induced by round() 
   ## but POSIXlt moves times off by a second
-  suppressWarnings(all.dates <- data.table(index = seq(time.idx), date = round(date)))
+  suppressWarnings(all.dates <- data.table::data.table(index = seq(time.idx), date = round(date)))
   
   if (start.date + lubridate::days(1) < min(all.dates$date)) {
-   PEcAn.logger::logger.error("run start date", start.date, "before met data starts", min(all.dates$date))
+   PEcAn.logger::logger.severe("run start date", start.date, "before met data starts", min(all.dates$date))
   }
   if (end.date > max(all.dates$date)) {
-   PEcAn.logger::logger.error("run end date", end.date, "after met data ends", max(all.dates$date))
+   PEcAn.logger::logger.severe("run end date", end.date, "after met data ends", max(all.dates$date))
   }
   
   run.dates <- all.dates[date >= start.date & date <= end.date,
@@ -87,5 +84,5 @@ load.cfmet <- function(met.nc, lat, lon, start.date, end.date) {
 
   names(vars) <- gsub("surface_pressure", "air_pressure", variables)
 
-  return(cbind(run.dates, as.data.table(vars[!sapply(vars, is.null)])))
+  return(cbind(run.dates, data.table::as.data.table(vars[!sapply(vars, is.null)])))
 } # load.cfmet
diff --git a/modules/data.atmosphere/R/merge.met.variable.R b/modules/data.atmosphere/R/merge.met.variable.R
index abcd05c821d..f583d9906f3 100644
--- a/modules/data.atmosphere/R/merge.met.variable.R
+++ b/modules/data.atmosphere/R/merge.met.variable.R
@@ -5,8 +5,9 @@
 #' @param start_date  
 #' @param end_date 
 #' @param merge.file  path of file to be merged in
-#' @param overwrite 
-#' @param verbose 
+#' @param overwrite logical: replace output file if it already exists? 
+#' @param verbose logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}} functions
+#'   print debugging information as they run? 
 #' @param ... 
 #'
 #' @return
@@ -62,8 +63,8 @@ merge_met_variable <- function(in.path,in.prefix,start_date, end_date, merge.fil
     ncdf4::nc_close(merge.nc)
     return(NULL)
   }
-  if(lubridate::year(tail(merge.time.std,1)) < end_year){
-    PEcAn.logger::logger.error("merge.time < end_year", tail(merge.time.std,1),end_date)
+  if(lubridate::year(utils::tail(merge.time.std,1)) < end_year){
+    PEcAn.logger::logger.error("merge.time < end_year", utils::tail(merge.time.std,1),end_date)
     ncdf4::nc_close(merge.nc)
     return(NULL)
   }
@@ -123,7 +124,7 @@ merge_met_variable <- function(in.path,in.prefix,start_date, end_date, merge.fil
     
     
     ## interpolate merged data to target time
-    merge.interp <- approx(merge.sub$time,merge.sub$data, xout = target.time.std, 
+    merge.interp <- stats::approx(merge.sub$time,merge.sub$data, xout = target.time.std,
                            rule = 2, method = "linear", ties = mean)
     
     ## insert new variable
diff --git a/modules/data.atmosphere/R/met.process.R b/modules/data.atmosphere/R/met.process.R
index a6ce53c659c..9aec1f9fee2 100644
--- a/modules/data.atmosphere/R/met.process.R
+++ b/modules/data.atmosphere/R/met.process.R
@@ -21,17 +21,20 @@
 ##'
 ##'        list(download = FALSE, met2cf = TRUE, standardize = TRUE,  met2model = TRUE)
 ##'
-##' @importFrom PEcAn.DB db.query db.close dbfile.input.insert
 ##' @author Elizabeth Cowdery, Michael Dietze, Ankur Desai, James Simkins, Ryan Kelly
 met.process <- function(site, input_met, start_date, end_date, model,
                         host = "localhost", dbparms, dir, browndog = NULL, spin=NULL,
                         overwrite = FALSE) {
-
   # get met source and potentially determine where to start in the process
   if(is.null(input_met$source)){
     if(is.null(input_met$id)){
       PEcAn.logger::logger.warn("met.process only has a path provided, assuming path is model driver and skipping processing")
-      return(input_met$path)
+      
+      # Additional layer of list depth added for consistancy with other return statements.
+      temp_path = input_met$path
+      input_met$path <- list()
+      input_met$path$path1 <- temp_path
+      return(input_met)
     }else {
      PEcAn.logger::logger.warn("No met source specified")
       if(!is.null(input_met$id) & !is.null(input_met$path)){
@@ -86,17 +89,17 @@ met.process <- function(site, input_met, start_date, end_date, model,
                        password = dbparms$password)
   
   con <- bety$con
-  on.exit(db.close(con))
+  on.exit(PEcAn.DB::db.close(con))
   username <- ifelse(is.null(input_met$username), "pecan", input_met$username)
   machine.host <- ifelse(host == "localhost" || host$name == "localhost", PEcAn.remote::fqdn(), host$name)
-  machine <- db.query(paste0("SELECT * from machines where hostname = '", machine.host, "'"), con)
+  machine <- PEcAn.DB::db.query(paste0("SELECT * from machines where hostname = '", machine.host, "'"), con)
 
   # special case Brown Dog
   if (!is.null(browndog)) {
     result <- browndog.met(browndog, met, site, start_date, end_date, model, dir, username, con)
     
     if (is.data.frame(result)) {
-      dbfile.input.insert(in.path = dirname(result$file), 
+      dbentry = PEcAn.DB::dbfile.input.insert(in.path = dirname(result$file),
                           in.prefix = result$dbfile.name,
                           siteid = site$id, 
                           startdate = start_date, enddate = end_date,
@@ -104,7 +107,14 @@ met.process <- function(site, input_met, start_date, end_date, model,
                           formatname = result$formatname, 
                           parentid = NA, 
                           con = con, hostname = result$host)
-      return(invisible(result$file))
+      
+      # Additonal list depth added for consistancy with other return statements.
+      input_met$path <- list()
+      input_met$path$path1 <- result$file
+      input_met$id <- list()
+      input_met$id$id1 <- dbentry$input.id
+      
+      return(invisible(input_met))
     }
   }
   
@@ -115,14 +125,14 @@ met.process <- function(site, input_met, start_date, end_date, model,
   # first attempt at function that designates where to start met.process
   if (is.null(input_met$id)) {
     stage <- list(download.raw = TRUE, met2cf = TRUE, standardize = TRUE, met2model = TRUE)
-    format.vars <- query.format.vars(bety = bety, format.id = register$format$id)  # query variable info from format id
+    format.vars <- PEcAn.DB::query.format.vars(bety = bety, format.id = register$format$id)  # query variable info from format id
   } else {
     stage <- met.process.stage(input.id=input_met$id, raw.id=register$format$id, con)
-    format.vars <- query.format.vars(bety = bety, input.id = input_met$id)  # query DB to get format variable information if available
+    format.vars <- PEcAn.DB::query.format.vars(bety = bety, input.id = input_met$id)  # query DB to get format variable information if available
     # Is there a situation in which the input ID could be given but not the file path? 
     # I'm assuming not right now
     assign(stage$id.name, list(inputid = input_met$id,
-                               dbfileid = dbfile.check("Input",input_met$id,hostname = machine.host,con=con)$id))
+                               dbfileid = PEcAn.DB::dbfile.check("Input",input_met$id,hostname = machine.host,con=con)$id))
   }
   print(stage)
   
@@ -174,6 +184,10 @@ met.process <- function(site, input_met, start_date, end_date, model,
       input_met$id <- raw.id
       stage$met2cf <- FALSE
       stage$standardize <- FALSE
+    } else if (met %in% c("NOAA_GEFS")) { # Can sometimes have missing values, so the gapfilling step is required.
+      cf.id <- raw.id
+      input_met$id <-raw.id
+      stage$met2cf <- FALSE
     }
   }
   
@@ -202,31 +216,45 @@ met.process <- function(site, input_met, start_date, end_date, model,
   #--------------------------------------------------------------------------------------------------#
   # Change to Site Level - Standardized Met (i.e. ready for conversion to model specific format)
   if (stage$standardize) {
-    if (register$scale == "regional") {
-      #### Site extraction
-      ready.id <- .extract.nc.module(cf.id = cf.id, 
-                                     register = register, 
-                                     dir = dir, 
-                                     met = met, 
-                                     str_ns = str_ns, 
-                                     site = site, new.site = new.site, 
-                                     con = con, 
-                                     start_date = start_date, end_date = end_date, 
-                                     host = host, 
-                                     overwrite = overwrite$standardize)
-    } else if (register$scale == "site") {
-      ##### Site Level Processing
-      ready.id <- .metgapfill.module(cf.id = cf.id, 
-                                     register = register,
-                                     dir = dir,
-                                     met = met, 
-                                     str_ns = str_ns, 
-                                     site = site, new.site = new.site, 
-                                     con = con, 
-                                     start_date = start_date, end_date = end_date,
-                                     host = host, 
-                                     overwrite = overwrite$standardize)
+    standardize_result = list()
+    
+    for (i in 1:length(cf.id[[1]])) {
+      if (register$scale == "regional") {
+        #### Site extraction
+        standardize_result[[i]] <- .extract.nc.module(cf.id = list(input.id = cf.id$input.id[i], dbfile.id = cf.id$dbfile.id[i]), 
+                                       register = register, 
+                                       dir = dir, 
+                                       met = met, 
+                                       str_ns = str_ns, 
+                                       site = site, new.site = new.site, 
+                                       con = con, 
+                                       start_date = start_date, end_date = end_date, 
+                                       host = host, 
+                                       overwrite = overwrite$standardize)
+                                       # Expand to support ensemble names in the future
+      } else if (register$scale == "site") {
+        ##### Site Level Processing
+        standardize_result[[i]] <- .metgapfill.module(cf.id = list(input.id = cf.id$input.id[i], dbfile.id = cf.id$dbfile.id[i]), 
+                                       register = register,
+                                       dir = dir,
+                                       met = met, 
+                                       str_ns = str_ns, 
+                                       site = site, new.site = new.site, 
+                                       con = con, 
+                                       start_date = start_date, end_date = end_date,
+                                       host = host, 
+                                       overwrite = overwrite$standardize,
+                                       ensemble_name = i)
+      }
+      
+    } # End for loop
+    ready.id = list(input.id = NULL, dbfile.id = NULL)
+    
+    for (i in 1:length(standardize_result)) {
+      ready.id$input.id <- c(ready.id$input.id, standardize_result[[i]]$input.id)
+      ready.id$dbfile.id <- c(ready.id$dbfile.id, standardize_result[[i]]$dbfile.id)
     }
+    
   } else {
     ready.id = input_met$id
   }
@@ -239,42 +267,69 @@ met.process <- function(site, input_met, start_date, end_date, model,
     reg.model.xml <- system.file(paste0("register.", model, ".xml"), package = paste0("PEcAn.",model))
     reg.model <- XML::xmlToList(XML::xmlParse(reg.model.xml))
     
-    met2model.result <- .met2model.module(ready.id = ready.id, 
-                                          model = model, 
-                                          con = con,
-                                          host = host, 
-                                          dir = dir, 
-                                          met = met, 
-                                          str_ns = str_ns,
-                                          site = site, 
-                                          start_date = start_date, end_date = end_date, 
-                                          browndog = browndog, 
-                                          new.site = new.site,
-                                          overwrite = overwrite$met2model,
-                                          exact.dates = reg.model$exact.dates,
-                                          spin = spin)
+    met2model.result = list()
+    for (i in 1:length(ready.id[[1]])) {
+      met2model.result[[i]] <- .met2model.module(ready.id = list(input.id = ready.id$input.id[i], dbfile.id = ready.id$dbfile.id[i]), 
+                                    model = model, 
+                                    con = con,
+                                    host = host, 
+                                    dir = dir, 
+                                    met = met, 
+                                    str_ns = str_ns,
+                                    site = site, 
+                                    start_date = start_date, end_date = end_date, 
+                                    browndog = browndog, 
+                                    new.site = new.site,
+                                    overwrite = overwrite$met2model,
+                                    exact.dates = reg.model$exact.dates,
+                                    spin = spin,
+                                    register = register,
+                                    ensemble_name = i)
+    }
+    
+    model.id = list()
+    model.file.info = list()
+    model.file = list()
+    
+    for (i in 1:length(met2model.result)) {
+      model.id[[i]]  <- met2model.result[[i]]$model.id
+      model.file.info[[i]] <- PEcAn.DB::db.query(paste0("SELECT * from dbfiles where id = ", model.id[[i]]$dbfile.id), con)
+      model.file[[i]] <- file.path(model.file.info[[i]]$file_path, model.file.info[[i]]$file_name)
+    }
+    
+    
+    
+    # met.process now returns the entire $met portion of settings, updated with parellel lists containing
+    # the model-specific data files and their input ids.
+    
+    input_met$id <- list()
+    input_met$path <- list()
+    
+    for (i in 1:length(model.id)) {
+      input_met$id[[paste0("id", i)]] <- model.id[[i]]$input.id
+      input_met$path[[as.character(paste0("path", i))]] <- model.file[[i]]
+    }
     
-    model.id  <- met2model.result$model.id
-    model.file.info <- db.query(paste0("SELECT * from dbfiles where id = ", model.id$dbfile.id), con)
-    model.file <- file.path(model.file.info$file_path,model.file.info$file_name)
     
   } else {
+    # Because current ensemble data cannot reach this else statement, it only supports single source data.
     PEcAn.logger::logger.info("ready.id",ready.id,machine.host)
-    model.id  <- dbfile.check("Input", ready.id, con, hostname=machine.host)
-    if(is.null(model.id)|length(model.id)==0){
-      model.file <- input_met$path
-    }else{
+    model.id  <- PEcAn.DB::dbfile.check("Input", ready.id, con, hostname=machine.host)
+    if(!(is.null(model.id)|length(model.id)==0)) {
       model.id$dbfile.id  <- model.id$id 
-      model.file.info <- db.query(paste0("SELECT * from dbfiles where id = ", model.id$dbfile.id), con)
-      model.file <- file.path(model.file.info$file_path,model.file.info$file_name)
+      model.file.info <- PEcAn.DB::db.query(paste0("SELECT * from dbfiles where id = ", model.id$dbfile.id), con)
+      model.file <- file.path(model.file.info$file_path, model.file.info$file_name)
+    } else {
+      PEcAn.logger::logger.severe("Missing model id.")
     }
-    #PEcAn.logger::logger.info("model.file = ",model.file,input.met)
+    
+    input_met$path <- list() # for consistancy with the code in the if to this else.
+    input_met$path$path1 <- model.file
+    input_met$id <- model.id$container_id # This is the input id, whereas $id is the dbfile id.
     PEcAn.logger::logger.info("model.file = ",model.file,input_met)
   }
-  
-
     
-  return(model.file)
+  return(input_met) # Returns an updated $met entry for the settings object.
 } # met.process
 
 ################################################################################################################################# 
@@ -284,10 +339,9 @@ met.process <- function(site, input_met, start_date, end_date, model,
 ##' @export
 ##' @param site.id
 ##' @param con
-##' @importFrom PEcAn.DB db.query
 ##' @author Betsy Cowdery
 db.site.lat.lon <- function(site.id, con) {
-  site <- db.query(paste("SELECT id, ST_X(ST_CENTROID(geometry)) AS lon, ST_Y(ST_CENTROID(geometry)) AS lat FROM sites WHERE id =", 
+  site <- PEcAn.DB::db.query(paste("SELECT id, ST_X(ST_CENTROID(geometry)) AS lon, ST_Y(ST_CENTROID(geometry)) AS lat FROM sites WHERE id =", 
                          site.id), con)
   if (nrow(site) == 0) {
    PEcAn.logger::logger.error("Site not found")
@@ -373,7 +427,7 @@ browndog.met <- function(browndog, source, site, start_date, end_date, model, di
                           dbfile.name = basename(outputfile), 
                           stringsAsFactors = FALSE)
   } else if (model == "BIOCRO") {
-    metinfo <- db.query(paste0("select mimetypes.type_string, formats.name from mimetypes, formats, modeltypes, modeltypes_formats",
+    metinfo <- PEcAn.DB::db.query(paste0("select mimetypes.type_string, formats.name from mimetypes, formats, modeltypes, modeltypes_formats",
                                " where modeltype_id=modeltypes.id and format_id=formats.id and formats.mimetype_id=mimetypes.id",
                                " and tag='met' and modeltypes.name='", model, "'"), con)
 
@@ -404,15 +458,15 @@ browndog.met <- function(browndog, source, site, start_date, end_date, model, di
   
   userpass <- paste(browndog$username, browndog$password, sep = ":")
   curloptions <- list(userpwd = userpass, httpauth = 1L, followlocation = TRUE)
-  result <- postForm(paste0(browndog$url, formatname, "/"), 
-                     fileData = fileUpload("pecan.xml", xmldata, "text/xml"), .opts = curloptions)
+  result <- RCurl::postForm(paste0(browndog$url, formatname, "/"),
+                     fileData = RCurl::fileUpload("pecan.xml", xmldata, "text/xml"), .opts = curloptions)
   url <- gsub(".*<a.*>(.*)</a>.*", "\\1", result)
   PEcAn.logger::logger.info("browndog download url :", url)
-  downloadedfile <- download.url(url, outputfile, 600, curloptions)
+  downloadedfile <- PEcAn.utils::download.url(url, outputfile, 600, curloptions)
   
   # fix returned data
   if (model == "ED2") {
-    unzip(downloadedfile, exdir = folder)
+    utils::unzip(downloadedfile, exdir = folder)
     # fix ED_MET_DRIVER_HEADER
     x <- readLines(results$file)
     x[3] <- ifelse(grepl("/$", folder), folder, paste0(folder, "/"))
diff --git a/modules/data.atmosphere/R/met.process.stage.R b/modules/data.atmosphere/R/met.process.stage.R
index 98bc65e49a6..41b2c756166 100644
--- a/modules/data.atmosphere/R/met.process.stage.R
+++ b/modules/data.atmosphere/R/met.process.stage.R
@@ -8,7 +8,7 @@
 ##' @author Elizabeth Cowdery
 met.process.stage <- function(input.id, raw.id, con) {
   
-  format.id <- db.query(paste("SELECT format_id from inputs where id =", input.id), con)[[1]]
+  format.id <- PEcAn.DB::db.query(paste("SELECT format_id from inputs where id =", input.id), con)[[1]]
   cf.id     <- 33
   
   if (format.id == raw.id && format.id != cf.id) {
diff --git a/modules/data.atmosphere/R/met2CF.ALMA.R b/modules/data.atmosphere/R/met2CF.ALMA.R
index 3db0b3ebc7b..1fc714120fe 100644
--- a/modules/data.atmosphere/R/met2CF.ALMA.R
+++ b/modules/data.atmosphere/R/met2CF.ALMA.R
@@ -186,10 +186,6 @@ met2CF.PalEONregional <- function(in.path, in.prefix, outfolder, start_date, end
 met2CF.PalEON <- function(in.path, in.prefix, outfolder, start_date, end_date, lat, lon, overwrite = FALSE,
                           verbose = FALSE, ...) {
 
-  #---------------- Load libraries. -----------------------------------------------------------------#
-  library(PEcAn.utils)
-  #--------------------------------------------------------------------------------------------------#
-
   # get start/end year code works on whole years only
   start_year <- lubridate::year(start_date)
   end_year   <- lubridate::year(end_date)
@@ -334,7 +330,7 @@ met2CF.PalEON <- function(in.path, in.prefix, outfolder, start_date, end_date, l
 
     # add global attributes from original file
     for (j in seq_along(cp.global.atts)) {
-      ncatt_put(nc = nc2, varid = 0, attname = names(cp.global.atts)[j], attval = cp.global.atts[[j]])
+      ncdf4::ncatt_put(nc = nc2, varid = 0, attname = names(cp.global.atts)[j], attval = cp.global.atts[[j]])
     }
 
     # done, close file
@@ -470,7 +466,7 @@ met2CF.ALMA <- function(in.path, in.prefix, outfolder, start_date, end_date, ove
     print(latlon)
     var <- ncdf4::ncvar_def(name = "latitude", units = "degree_north", dim = (list(lat, lon, time)),
                      missval = as.numeric(-9999))
-    nc2 <- nc_create(filename = new.file, vars = var, verbose = verbose)
+    nc2 <- ncdf4::nc_create(filename = new.file, vars = var, verbose = verbose)
     ncdf4::ncvar_put(nc = nc2, varid = "latitude", vals = rep(latlon[1], tdim$len))
 
     # copy lon attribute to longitude
@@ -613,19 +609,19 @@ met2CF.ALMA <- function(in.path, in.prefix, outfolder, start_date, end_date, ove
     var <- ncdf4::ncvar_def(name = "eastward_wind", units = "m/s", dim = dim, missval = -6999, verbose = verbose)
     nc2 <- ncdf4::ncvar_add(nc = nc2, v = var, verbose = verbose)
     ncdf4::ncvar_put(nc = nc2, varid = "eastward_wind", vals = ew)
-    ncatt_put(nc = nc2, varid = "eastward_wind", attname = "valid_min", attval = -max)
-    ncatt_put(nc = nc2, varid = "eastward_wind", attname = "valid_max", attval = max)
+    ncdf4::ncatt_put(nc = nc2, varid = "eastward_wind", attname = "valid_min", attval = -max)
+    ncdf4::ncatt_put(nc = nc2, varid = "eastward_wind", attname = "valid_max", attval = max)
 
     var <- ncdf4::ncvar_def(name = "northward_wind", units = "m/s", dim = dim, missval = -6999, verbose = verbose)
     nc2 <- ncdf4::ncvar_add(nc = nc2, v = var, verbose = verbose)
     ncdf4::ncvar_put(nc = nc2, varid = "northward_wind", vals = nw)
-    ncatt_put(nc = nc2, varid = "northward_wind", attname = "valid_min", attval = -max)
-    ncatt_put(nc = nc2, varid = "northward_wind", attname = "valid_max", attval = max)
+    ncdf4::ncatt_put(nc = nc2, varid = "northward_wind", attname = "valid_min", attval = -max)
+    ncdf4::ncatt_put(nc = nc2, varid = "northward_wind", attname = "valid_max", attval = max)
 
     # add global attributes from original file
     cp.global.atts <- ncdf4::ncatt_get(nc = nc1, varid = 0)
     for (j in seq_along(cp.global.atts)) {
-      ncatt_put(nc = nc2, varid = 0, attname = names(cp.global.atts)[j], attval = cp.global.atts[[j]])
+      ncdf4::ncatt_put(nc = nc2, varid = 0, attname = names(cp.global.atts)[j], attval = cp.global.atts[[j]])
     }
 
     # done, close both files
diff --git a/modules/data.atmosphere/R/met2CF.Ameriflux.R b/modules/data.atmosphere/R/met2CF.Ameriflux.R
index 668c3de9323..fcc4d3a6361 100644
--- a/modules/data.atmosphere/R/met2CF.Ameriflux.R
+++ b/modules/data.atmosphere/R/met2CF.Ameriflux.R
@@ -74,9 +74,6 @@ getLatLon <- function(nc1) {
 met2CF.Ameriflux <- function(in.path, in.prefix, outfolder, start_date, end_date,
                              overwrite = FALSE, verbose = FALSE, ...) {
 
-  #---------------- Load libraries. -----------------------------------------------------------------#
-  library(geonames)  ## has to be loaded as a library
-  #--------------------------------------------------------------------------------------------------#
 
   # get start/end year code works on whole years only
   start_year <- lubridate::year(start_date)
@@ -129,8 +126,10 @@ met2CF.Ameriflux <- function(in.path, in.prefix, outfolder, start_date, end_date
     if ((tdimtz == "+") || (tdimtz == "-")) {
       lst <- tdimunit[length(tdimunit)]  #already in definition, leave it alone
     } else {
-      options(geonamesUsername = "carya")  #login to geoname server
-      lst <- GNtimezone(latlon[1], latlon[2], radius = 0)$gmtOffset
+      if (is.null(getOption("geonamesUsername"))) {
+        options(geonamesUsername = "carya")  #login to geoname server
+      }
+      lst <- geonames::GNtimezone(latlon[1], latlon[2], radius = 0)$gmtOffset
       if (lst >= 0) {
         lststr <- paste("+", lst, sep = "")
       } else {
diff --git a/modules/data.atmosphere/R/met2CF.AmerifluxLBL.R b/modules/data.atmosphere/R/met2CF.AmerifluxLBL.R
index 28ff1b6fad2..b9d37567af9 100644
--- a/modules/data.atmosphere/R/met2CF.AmerifluxLBL.R
+++ b/modules/data.atmosphere/R/met2CF.AmerifluxLBL.R
@@ -33,7 +33,7 @@ met2CF.AmerifluxLBL <- function(in.path, in.prefix, outfolder, start_date, end_d
       PEcAn.logger::logger.warn(length(files), ' met files found. Using first file: ', files[1])
       files <- files[1]
     }
-    somedat <- read.csv(files, 
+    somedat <- utils::read.csv(files, 
                        header = TRUE,
                        skip = format$skip, 
                        na.strings = format$na.strings,
diff --git a/modules/data.atmosphere/R/met2CF.FACE.R b/modules/data.atmosphere/R/met2CF.FACE.R
index 9428649d44a..52000cf94ac 100644
--- a/modules/data.atmosphere/R/met2CF.FACE.R
+++ b/modules/data.atmosphere/R/met2CF.FACE.R
@@ -1,18 +1,12 @@
-##' @name met2CF.FACE
-##' @title met2CF.FACE
+##' convert FACE files to CF files
 ##' @export
 ##' 
 ##' @param in.path
 ##' @param in.prefix
 ##' @param outfolder
-##' @param convert FACE files to CF files
 ##' @author Elizabeth Cowdery
 
-##' @importFrom ncdf4 ncvar_get ncdim_def ncatt_get ncvar_add ncvar_put nc_open nc_create nc_close
 met2CF.FACE <- function(in.path,in.prefix,outfolder,start_date,end_date,input.id,site,format, ...) {
-
-  
-  library(PEcAn.utils)
   
   files <- dir(in.path, in.prefix)
   file <- files[grep(pattern = "*.nc", files)]
@@ -37,27 +31,27 @@ met2CF.FACE <- function(in.path,in.prefix,outfolder,start_date,end_date,input.id
       #---------------------------------------------------------------------#
       # Latitude and Longitude
       
-      nc1 <- nc_open(f, write = TRUE)
+      nc1 <- ncdf4::nc_open(f, write = TRUE)
       
       time_units <- paste0("hours/2", unlist(strsplit(nc1$var$TIMEstp$units, "timesteps"))[2])
-      time <- ncdim_def(name = "time", units = time_units, vals = nc1$dim$tstep$vals)
-      lon <- ncdim_def("longitude", "degrees_east", as.numeric(site$lon)) # define netCDF dimensions for variables
-      lat <- ncdim_def("latitude", "degrees_north", as.numeric(site$lat))
+      time <- ncdf4::ncdim_def(name = "time", units = time_units, vals = nc1$dim$tstep$vals)
+      lon <- ncdf4::ncdim_def("longitude", "degrees_east", as.numeric(site$lon)) # define netCDF dimensions for variables
+      lat <- ncdf4::ncdim_def("latitude", "degrees_north", as.numeric(site$lat))
       dim <- list(lat, lon, time)
       
       # convert wind speed and wind direction to eastward_wind and northward_wind
       wd <- 0  # wind direction - not specified so I set to 0???
-      ws <- ncvar_get(nc = nc1, varid = "Wind")  #wind speed
+      ws <- ncdf4::ncvar_get(nc = nc1, varid = "Wind")  #wind speed
       ew <- ws * cos(wd * (pi / 180))
       nw <- ws * sin(wd * (pi / 180))
       
-      var <- ncvar_def(name = "eastward_wind", units = "m/s", dim = dim, missval = -6999, verbose = FALSE)
-      nc2 <- nc_create(filename = f.cf, vars = var, verbose = FALSE)
-      ncvar_put(nc = nc2, varid = "eastward_wind", vals = ew)
+      var <- ncdf4::ncvar_def(name = "eastward_wind", units = "m/s", dim = dim, missval = -6999, verbose = FALSE)
+      nc2 <- ncdf4::nc_create(filename = f.cf, vars = var, verbose = FALSE)
+      ncdf4::ncvar_put(nc = nc2, varid = "eastward_wind", vals = ew)
       
-      var <- ncvar_def(name = "northward_wind", units = "m/s", dim = dim, missval = -6999, verbose = FALSE)
-      nc2 <- ncvar_add(nc = nc2, v = var, verbose = FALSE)
-      ncvar_put(nc = nc2, varid = "northward_wind", vals = nw)
+      var <- ncdf4::ncvar_def(name = "northward_wind", units = "m/s", dim = dim, missval = -6999, verbose = FALSE)
+      nc2 <- ncdf4::ncvar_add(nc = nc2, v = var, verbose = FALSE)
+      ncdf4::ncvar_put(nc = nc2, varid = "northward_wind", vals = nw)
       
       #---------------------------------------------------------------------#
       # Loop through variables and convert 
@@ -83,7 +77,7 @@ met2CF.FACE <- function(in.path,in.prefix,outfolder,start_date,end_date,input.id
       
       # begin loop
       for (i in seq_len(nrow(vars_used))) {
-        vals <- ncvar_get(nc1, vars_used$input_name[i])
+        vals <- ncdf4::ncvar_get(nc1, vars_used$input_name[i])
         
         if (vars_used$input_units[i] == vars_used$pecan_units[i]) {
           print("match")
@@ -95,34 +89,34 @@ met2CF.FACE <- function(in.path,in.prefix,outfolder,start_date,end_date,input.id
                           vars_used$input_name[i], vars_used$input_units[i], 
                           vars_used$pecan_name[i], vars_used$pecan_units[i]))
             vals <- udunits2::ud.convert(vals, u1, u2)
-          } else if (misc.are.convertible(u1, u2)) {
+          } else if (PEcAn.utils::misc.are.convertible(u1, u2)) {
             print(sprintf("convert %s %s to %s %s", 
                           vars_used$input_name[i], u1, 
                           vars_used$pecan_name[i], u2))
-            vals <- misc.convert(x, u1, u2)
+            vals <- PEcAn.utils::misc.convert(x, u1, u2)
           } else {
             PEcAn.logger::logger.error("Units cannot be converted")
           } 
         }
         
-        var <- ncvar_def(name = vars_used$pecan_name[i], 
+        var <- ncdf4::ncvar_def(name = vars_used$pecan_name[i], 
                          units = vars_used$pecan_units[i], 
                          dim = dim, verbose = FALSE)
-        nc2 <- ncvar_add(nc = nc2, v = var, verbose = FALSE)
-        ncvar_put(nc = nc2, varid = vars_used$pecan_name[i], vals = vals)
+        nc2 <- ncdf4::ncvar_add(nc = nc2, v = var, verbose = FALSE)
+        ncdf4::ncvar_put(nc = nc2, varid = vars_used$pecan_name[i], vals = vals)
         
-        att <- ncatt_get(nc1,vars_used$input_name[i], "long_name")
+        att <- ncdf4::ncatt_get(nc1,vars_used$input_name[i], "long_name")
         if (att$hasatt) {
           val <- att$value
-          ncatt_put(nc = nc2, varid = vars_used$pecan_name[i], attname = "long_name", attval = val)
+          ncdf4::ncatt_put(nc = nc2, varid = vars_used$pecan_name[i], attname = "long_name", attval = val)
         }
       }
-      nc_close(nc2)
+      ncdf4::nc_close(nc2)
     
       
       # Split into annual files
       
-      year <- ncvar_get(nc1, "YEAR")
+      year <- ncdf4::ncvar_get(nc1, "YEAR")
       y <- year[1]:year[length(year)]
       n <- length(y)
       t <- -1
@@ -181,18 +175,18 @@ met2CF.FACE <- function(in.path,in.prefix,outfolder,start_date,end_date,input.id
 #   if (vars[k] %in% nc.vars) {
 #     # nc <- tncar_rename(nc,vars[k],nvars[k])
 #     
-#     vals <- ncvar_get(nc1, vars[k])
+#     vals <- ncdf4::ncvar_get(nc1, vars[k])
 #     
-#     units <- ncatt_get(nc1, varid = vars[k], attname = "units", verbose = FALSE)$value
+#     units <- ncdf4::ncatt_get(nc1, varid = vars[k], attname = "units", verbose = FALSE)$value
 #     
-#     var <- ncvar_def(name = nvars[k], units = units, dim = dim, verbose = FALSE)
-#     nc2 <- ncvar_add(nc = nc2, v = var, verbose = TRUE)
-#     ncvar_put(nc = nc2, varid = nvars[k], vals = vals)
+#     var <- ncdf4::ncvar_def(name = nvars[k], units = units, dim = dim, verbose = FALSE)
+#     nc2 <- ncdf4::ncvar_add(nc = nc2, v = var, verbose = TRUE)
+#     ncdf4::ncvar_put(nc = nc2, varid = nvars[k], vals = vals)
 #     
-#     att <- ncatt_get(nc1, vars[k], "long_name")
+#     att <- ncdf4::ncatt_get(nc1, vars[k], "long_name")
 #     if (att$hasatt) {
 #       val <- att$value
-#       ncatt_put(nc = nc2, varid = nvars[k], attname = "long_name", attval = val)
+#       ncdf4::ncatt_put(nc = nc2, varid = nvars[k], attname = "long_name", attval = val)
 #     }
 #   }
 # }
diff --git a/modules/data.atmosphere/R/met2CF.Geostreams.R b/modules/data.atmosphere/R/met2CF.Geostreams.R
index 442745c4398..b7f7357df34 100644
--- a/modules/data.atmosphere/R/met2CF.Geostreams.R
+++ b/modules/data.atmosphere/R/met2CF.Geostreams.R
@@ -53,12 +53,12 @@ met2CF.Geostreams <- function(in.path, in.prefix, outfolder,
 
     if (length(unique(dat$geometry.coordinates)) == 1) {
       # all lat/lons are are identical-- no need to store extra copies
-      raw_lat <- dat$geometry.coordinates[[1]][[1]]
-      raw_lon <- dat$geometry.coordinates[[1]][[2]]
+      raw_lon <- dat$geometry.coordinates[[1]][[1]]
+      raw_lat <- dat$geometry.coordinates[[1]][[2]]
     } else {
       # multiple coords in same file -- keep lat and lon as full-length vectors
-      raw_lat <- sapply(dat$geometry.coordinates, function(x)x[[1]])
-      raw_lon <- sapply(dat$geometry.coordinates, function(x)x[[2]])
+      raw_lon <- sapply(dat$geometry.coordinates, function(x)x[[1]])
+      raw_lat <- sapply(dat$geometry.coordinates, function(x)x[[2]])
     }
     
     lat <- ncdf4::ncdim_def(name = "latitude", units = "degrees_north", vals = raw_lat, create_dimvar = TRUE)
diff --git a/modules/data.atmosphere/R/met2CF.NARR.R b/modules/data.atmosphere/R/met2CF.NARR.R
index fbfc1c4828d..7ca69bdb8dd 100644
--- a/modules/data.atmosphere/R/met2CF.NARR.R
+++ b/modules/data.atmosphere/R/met2CF.NARR.R
@@ -14,8 +14,6 @@
 met2CF.NARR <- function(in.path, in.prefix, outfolder, start_date, end_date, 
                         overwrite = FALSE, verbose = FALSE, ...) {
   
-  library(PEcAn.utils)
-  
   dir.create(outfolder, showWarnings = FALSE, recursive = TRUE)
   
   vars <- c("pres.sfc", "dswrf", "dlwrf", "air.2m", "shum.2m", "prate", "uwnd.10m", "vwnd.10m")
diff --git a/modules/data.atmosphere/R/met2CF.csv.R b/modules/data.atmosphere/R/met2CF.csv.R
index 90dd9033e7c..559013eb1ba 100644
--- a/modules/data.atmosphere/R/met2CF.csv.R
+++ b/modules/data.atmosphere/R/met2CF.csv.R
@@ -26,7 +26,8 @@
 ##' @author Mike Dietze, David LeBauer, Ankur Desai
 ##' @examples
 ##' \dontrun{
-##' bety = list(user='bety', password='bety',host='localhost', dbname='bety', driver='PostgreSQL',write=TRUE)
+##' bety <- list(user='bety', password='bety', host='localhost',
+##'   dbname='bety', driver='PostgreSQL',write=TRUE)
 ##' con <- PEcAn.DB::db.open(bety)
 ##' bety$con <- con
 ##' start_date <- lubridate::ymd_hm('200401010000')
@@ -40,7 +41,10 @@
 ##' format$lon <- -92.0
 ##' format$lat <- 45.0
 ##' format$time_zone <- "America/Chicago"
-##' results<-PEcAn.data.atmosphere::met2CF.csv(in.path, in.prefix, outfolder,start_date, end_date,format, overwrite=TRUE)
+##' results <- PEcAn.data.atmosphere::met2CF.csv(
+##'   in.path, in.prefix, outfolder,
+##'   start_date, end_date, format,
+##'   overwrite=TRUE)
 ##' }
 met2CF.csv <- function(in.path, in.prefix, outfolder, start_date, end_date, format, lat = NULL, lon = NULL, 
                        nc_verbose = FALSE, overwrite = FALSE,...) {
@@ -128,7 +132,7 @@ met2CF.csv <- function(in.path, in.prefix, outfolder, start_date, end_date, form
       skiplog <- TRUE
       skiprows <- c(1:header - 1)
     }
-    alldat <- read.csv(files, 
+    alldat <- utils::read.csv(files, 
                        header = header,
                        skip = format$skip, 
                        na.strings = format$na.strings,
diff --git a/modules/data.atmosphere/R/met2model.module.R b/modules/data.atmosphere/R/met2model.module.R
index cdbb21f87ae..793c11510ab 100644
--- a/modules/data.atmosphere/R/met2model.module.R
+++ b/modules/data.atmosphere/R/met2model.module.R
@@ -1,6 +1,6 @@
 ##' @export
 .met2model.module <- function(ready.id, model, con, host, dir, met, str_ns, site, start_date, end_date, 
-                              browndog, new.site, overwrite = FALSE, exact.dates,spin) {
+                              browndog, new.site, overwrite = FALSE, exact.dates,spin, register, ensemble_name) {
   
   # Determine output format name and mimetype
   model_info <- PEcAn.DB::db.query(paste0("SELECT f.name, f.id, mt.type_string from modeltypes as m", " join modeltypes_formats as mf on m.id = mf.modeltype_id", 
@@ -19,6 +19,7 @@
     print("Convert to model format")
     
     input.id <- ready.id$input.id[1]
+    
     if(host$name == "localhost"){
       outfolder <- file.path(dir, paste0(met, "_", model, "_site_", str_ns))
     } else {
@@ -29,11 +30,18 @@
       }
     }
     
+    #Some data products can be forecasts instead of real time data.
+    #Not all of the registration.xml files for each data source contains a <forecast> tag.
+    forecast = FALSE
+    if (!is.null(register$forecast)) {
+      forecast = as.logical(register$forecast)
+    }
+    
     pkg <- paste0("PEcAn.", model)
     fcn <- paste0("met2model.", model)
     lst <- site.lst(site.id=site$id, con=con)
     
-    model.id <- PEcAn.utils::convert.input(input.id = input.id, 
+    model.id <- PEcAn.utils::convert.input(input.id = input.id,
                               outfolder = outfolder,
                               formatname = formatname, mimetype = mimetype, 
                               site.id = site$id, 
@@ -46,7 +54,10 @@
                               exact.dates = exact.dates,
                               spin_nyear = spin$nyear,
                               spin_nsample = spin$nsample,
-                              spin_resample = spin$resample)
+                              spin_resample = spin$resample,
+                              forecast = forecast,
+                              ensemble = !is.null(register$ensemble) && as.logical(register$ensemble),
+                              ensemble_name = ensemble_name)
   }
   
   PEcAn.logger::logger.info(paste("Finished Model Specific Conversion", model.id[1]))
diff --git a/modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R b/modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R
index ae340311ed5..1abb1d5bfdf 100644
--- a/modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R
+++ b/modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R
@@ -15,8 +15,9 @@ substrRight <- function(x, n) {
 ##' @param train_met - the observed dataset that will be used to train the modeled dataset in NC format. i.e. Flux Tower dataset 
 ##'                    (see download.Fluxnet2015 or download.Ameriflux) 
 ##' @param site.id
-##' @param overwrite 
-##' @param verbose
+##' @param overwrite logical: replace output file if it already exists? 
+##' @param verbose logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}} functions
+##'   print debugging information as they run?
 ##' @param swdn_method - Downwelling shortwave flux in air downscaling method (options are "sine", "spline", and "Waichler")
 ##' @param n_ens - numeric value with the number of ensembles to run
 ##' @param w_len - numeric value that is the window length in days  
@@ -298,15 +299,16 @@ met_temporal_downscale.Gaussian_ensemble <- function(in.path, in.prefix, outfold
     # matches our observations (1 significantly undervalues SW downwelling flux)
     if (swdn_method == "Waichler") {
       inter <- paste0(reso, " hour")
-      days <- seq(as.POSIXct(paste0(eph_year, "-01-01 00:00:00")), 
-                  as.POSIXct(paste0(eph_year, "-12-31 18:00:00")), 
+      days <- seq(as.POSIXct(paste0(eph_year, "-01-01 00:00:00"),tz="UTC"), 
+                  as.POSIXct(paste0(eph_year, "-12-31 18:00:00"),tz="UTC"), 
                   by = inter)
-      
-      Z <- RAtmosphere::SZA(days, lat_train, lon_train)
-      I <- 1000 * aspace::cos_d(Z)
+      days.doy <- as.numeric(format(days,"%j"))
+      days.hour <- lubridate::hour(days) + lubridate::minute(days) / 60 + lubridate::second(days) / 3600
+      cosZ <- PEcAn.data.atmosphere::cos_solar_zenith_angle(days.doy, lat_train, lon_train, inter, days.hour)
+      I <- 1000 * cosZ
       m <- vector()
       for (i in seq_len(12)) {
-        m[i] <- Hmisc::monthDays(as.Date(paste0(year, "-", i, "-01")))
+        m[i] <- lubridate::days_in_month(as.Date(paste0(year, "-", i, "-01")))
       }
       bmlist <- vector()
       
diff --git a/modules/data.atmosphere/R/metgapfill.NOAA_GEFS.R b/modules/data.atmosphere/R/metgapfill.NOAA_GEFS.R
new file mode 100644
index 00000000000..ac58f6559fd
--- /dev/null
+++ b/modules/data.atmosphere/R/metgapfill.NOAA_GEFS.R
@@ -0,0 +1,199 @@
+##'@title Gapfill NOAA_GEFS weather data
+##'@section Purpose:
+##'This function uses simple methods to gapfill NOAA GEFS met data
+##'Temperature and Precipitation are gapfilled with spline; other data sources are gapfilled with
+##'using linear models fitted to other fitted data.
+##'
+##'@param in.prefix the met file name
+##'@param in.path The location of the file
+##'@param outfolder The place to write the output file to
+##'@param start_date The start date of the contents of the file
+##'@param end_date The end date of the contents of the file
+##'@param overwrite Whether or not to overwrite the output file if it exists or not
+##'@param verbose Passed to nc writing functions for additional output
+##'@export
+##'
+##'@author Luke Dramko
+metgapfill.NOAA_GEFS <- function(in.prefix, in.path, outfolder, start_date, end_date,
+                                 overwrite = FALSE, verbose = FALSE, ...) {
+  
+  PEcAn.logger::logger.info("Starting metgapfill.NOAA_GEFS")
+  
+  # These are the variables cf NOAA_GEFS uses
+  cf_var_names = c("air_temperature", "air_pressure", "specific_humidity", "surface_downwelling_longwave_flux_in_air", 
+                   "surface_downwelling_shortwave_flux_in_air", "precipitation_flux", "eastward_wind", "northward_wind")
+  
+  # Variables whose gapfillings are not directly dependent on splines.
+  dependent_vars <- c("specific_humidity", "surface_downwelling_longwave_flux_in_air", "surface_downwelling_shortwave_flux_in_air",
+                      "air_pressure", "eastward_wind", "northward_wind")
+  
+  
+  escaped <- gsub("(\\W)", "\\\\\\1", in.prefix) # The file name may contain special characters that could mess up the regular expression.
+  matching_files <- grep(escaped, list.files(in.path), value=TRUE) 
+  if (length(matching_files) == 0) {
+    PEcAn.logger::logger.severe(paste0("No files found matching ", in.prefix, "; cannot process data."))
+  }
+  
+  # This function is supposed to process netcdf files, so we'll search for files the the extension .nc and use those first.
+  nc_file = grep("\\.nc$", matching_files)
+  if (length(nc_file) > 0) {
+    in.prefix <- matching_files[1]
+  } else { # no .nc files found... it could be that the extension was left off, or some other problem
+    PEcAn.logger::logger.warn("No files found with extension '.nc'.  Using the first file in the list below:")
+    PEcAn.logger::logger.warn(matching_files)
+    in.prefix <- matching_files[1]
+  }
+  
+  # Attach the path.  The above procedure doesn't require the path, but acutally opening the file does.
+  full.data.file <- file.path(in.path, in.prefix)
+  
+  if (!file.exists(full.data.file)) {
+    PEcAn.logger::logger.warn(paste0("File ", full.data.file, " not found.  Unable to perform gapfilling."))
+    return(data.frame())
+  }
+  
+  flptr = ncdf4::nc_open(full.data.file)
+  
+  # Put data into a matrix
+  var <- ncdf4::ncvar_get(flptr, "air_temperature")
+  allvars <- matrix(var, ncol=length(var), nrow=1)
+  var <- ncdf4::ncvar_get(flptr, "precipitation_flux")
+  allvars = rbind(allvars, var)
+  
+  for (i in 1:length(dependent_vars)) {
+    allvars <- rbind(allvars, ncdf4::ncvar_get(flptr, dependent_vars[i]))
+  }
+  
+  # Use this matrix to fill in missing days at the end of the forecast with data from the
+  # same time of day.
+  # First, count how far back needs going.
+  k <- ncol(allvars)
+  while (length(which(is.na(allvars[,k]))) > 0) {
+    k = k - 1;
+  }
+  
+  # i = column, row = j
+  for (i in 1:nrow(allvars)) {
+    for (j in k:ncol(allvars)) {
+      if (is.na(allvars[i,j])) {
+        allvars[i,j] = sample(na.omit(allvars[i,seq(j, 1, by = -4)]), 1)
+      }
+    }
+  }
+  
+  # Use a basic spline to fill in missing values for basic variables
+  # Other variables will be fit to these for internal consistency in gapfilling
+  air_temperature <- allvars[1,]
+  precipitation_flux <- allvars[2,]
+  
+  air_temperature <- zoo::na.spline(air_temperature)
+  precipitation_flux <- zoo::na.spline(precipitation_flux)
+  
+  fitted.data <- data.frame(air_temperature = air_temperature,
+                            precipitation_flux = precipitation_flux)
+  
+  # This loop does the gapfilling of the other variables, based on air_temperature and precipitation_flux.
+  # It does so in the following way:
+  # A linear model for a variabe (e.g. specific humidity) is fitted to temperature and precipitation
+  # A prediction is made using the predict function on what the values of the missing variables
+  # should be.
+  # The values that were missing in the original data are filled in with their corresponding 
+  # values in the output of the prediciton function.
+  # The new data is put into the data frame used to fit the next model
+  for (i in 1:length(dependent_vars)) {
+    var <- allvars[i,]
+    if(is.na(var[1])) {
+      var[1] <- mean(var, na.rm = TRUE)
+    }
+    
+    fitted.data[[dependent_vars[i]]] = var
+    
+    # Unfortunately, R is picky, and the data.frame[['var_as_string']] notation doesn't work
+    # for the lm function; only the $ notation does, hence this if/else if section.
+    if (dependent_vars[i] == "specific_humidity") {
+      reg <- lm(fitted.data$specific_humidity ~.,fitted.data)
+    } else if (dependent_vars[i] == "surface_downwelling_longwave_flux_in_air") {
+      reg <- lm(fitted.data$surface_downwelling_longwave_flux_in_air ~.,fitted.data)
+    } else if (dependent_vars[i] == "surface_downwelling_shortwave_flux_in_air") {
+      reg <- lm(fitted.data$surface_downwelling_shortwave_flux_in_air ~.,fitted.data)
+    } else if (dependent_vars[i] == "air_pressure") {
+      reg <- lm(fitted.data$air_pressure ~.,fitted.data)
+    } else if (dependent_vars[i] == "eastward_wind") {
+      reg <- lm(fitted.data$eastward_wind ~.,fitted.data)
+    } else if (dependent_vars[i] == "northward_wind") {
+      reg <- lm(fitted.data$northward_wind ~.,fitted.data)
+    }
+    prediction <- predict(reg, fitted.data)
+    
+    # Update the values in the data frame
+    for (j in 1:length(prediction)) {
+      if(is.na(fitted.data[[dependent_vars[i]]][j])) {
+        fitted.data[[dependent_vars[i]]][j] <- prediction[j]
+      }
+    }
+  }
+  
+  # Extract ensemble information from file name
+  ensemble <- regmatches(in.prefix, regexpr("NOAA_GEFS\\.[^.]*\\.[0-9]*", in.prefix))
+  ensemble <- regmatches(ensemble, regexpr("[0-9]+$", ensemble))
+  
+  # Each ensemble gets its own folder to keep things organized
+  out.data.file <- file.path(outfolder, paste0("NOAA_GEFS.", ensemble))
+  if (!dir.exists(out.data.file)) {
+    dir.create(out.data.file, recursive=TRUE, showWarnings = FALSE)
+  }
+  
+  # The file names are the same, but the data is in a different directory.
+  out.data.file <- file.path(out.data.file, in.prefix)
+  
+  # Write new, gapfilled file
+  if (!file.exists(out.data.file) || overwrite) {
+    # Setup netcdf dimensions and variables
+    # All variables should be of the same length.
+    time_dim = ncdf4::ncdim_def(name="time", 
+                                paste(units="hours since", start_date), 
+                                seq(6, 6 * length(air_temperature), by = 6),
+                                create_dimvar = TRUE)
+    lat <- ncdf4::ncvar_get(nc = flptr, varid = "latitude")
+    lon <- ncdf4::ncvar_get(nc = flptr, varid = "longitude")
+    lat_dim = ncdf4::ncdim_def("latitude", "degree_north", lat, create_dimvar = TRUE)
+    lon_dim = ncdf4::ncdim_def("longitude", "degree_east", lon, create_dimvar = TRUE)
+    
+    dimensions_list = list(time_dim, lat_dim, lon_dim)
+    
+    nc_var_list = list()
+    for (i in 1:length(cf_var_names)) {
+      units <- flptr$var[[cf_var_names[i]]]$units
+      nc_var_list[[i]] = ncdf4::ncvar_def(cf_var_names[i], units, dimensions_list, missval=NaN)
+    }
+    
+    # Open file
+    nc_flptr = ncdf4::nc_create(out.data.file, nc_var_list, verbose=verbose)
+    
+    # Write data to file
+    for (j in 1:length(cf_var_names)) {
+      ncdf4::ncvar_put(nc_flptr, nc_var_list[[j]], fitted.data[[cf_var_names[j]]])
+    }
+    
+    # Close file
+    ncdf4::nc_close(nc_flptr)
+  } else {
+    PEcAn.logger::logger.info(paste0("File ", out.data.file, " already exists.  It was not overwritten."))
+  }
+  
+  # We no longer need the original file
+  ncdf4::nc_close(flptr)
+  
+  # This table of results is used to insert the record of the file into the database.
+  results <- data.frame(file = out.data.file,                         # file name
+                        host = PEcAn.remote::fqdn(),                  # machine where file is located
+                        mimetype = "application/x-netcdf",            # type of file
+                        formatname = "CF (gapfilled)",                # file format
+                        startdate = start_date,                       # start date of file contents
+                        enddate = end_date,                           # end date of file contents
+                        dbfile.name = basename(out.data.file),        # output file name
+                        stringsAsFactors = FALSE)
+  
+  return(results)
+  
+} # metgapfill.NOAA_GEFS
\ No newline at end of file
diff --git a/modules/data.atmosphere/R/metgapfill.R b/modules/data.atmosphere/R/metgapfill.R
index 42641dbaaf7..756fb823bdb 100644
--- a/modules/data.atmosphere/R/metgapfill.R
+++ b/modules/data.atmosphere/R/metgapfill.R
@@ -14,14 +14,9 @@
 ##' @param verbose should the function be very verbose
 ##' @param lst is timezone offset from UTC, if timezone is available in time:units atribute in file, it will use that, default is to assume UTC
 ##' @author Ankur Desai
-##' @importFrom ncdf4 ncvar_get ncatt_get ncdim_def ncvar_def ncvar_add ncvar_put
 metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst = 0,
                        overwrite = FALSE, verbose = FALSE, ...) {
 
-  #REddyProc installed to ~/R/library by install.packages("REddyProc", repos="http://R-Forge.R-project.org", type="source")
-  #dependency minpack.lm may not install automatically, so install it first
-
-
 
   sEddyProc             <- REddyProc::sEddyProc
   fCalcVPDfromRHandTair <- REddyProc::fCalcVPDfromRHandTair
@@ -79,19 +74,19 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     ## Should probably check for variable names (need to install ncdf4-helpers package)
 
     # extract time, lat, lon
-    time <- ncvar_get(nc = nc, varid = "time")
-    lat  <- ncvar_get(nc = nc, varid = "latitude")
-    lon  <- ncvar_get(nc = nc, varid = "longitude")
+    time <- ncdf4::ncvar_get(nc = nc, varid = "time")
+    lat  <- ncdf4::ncvar_get(nc = nc, varid = "latitude")
+    lon  <- ncdf4::ncvar_get(nc = nc, varid = "longitude")
 
     ## create time lat lon dimensions for adding new variables
-    x <- ncdim_def("longitude", "degrees_east", lon)
-    y <- ncdim_def("latitude", "degrees_north", lat)
-    t <- ncdim_def("time", "days since 1700-01-01", time)
+    x <- ncdf4::ncdim_def("longitude", "degrees_east", lon)
+    y <- ncdf4::ncdim_def("latitude", "degrees_north", lat)
+    t <- ncdf4::ncdim_def("time", "days since 1700-01-01", time)
     xytdim <- list(x, y, t)
 
     # extract elevation and timezone for radiation calculations
-    elev  <- ncatt_get(nc = nc, varid = 0, "elevation")
-    tzone <- ncatt_get(nc = nc, varid = "time", "units")
+    elev  <- ncdf4::ncatt_get(nc = nc, varid = 0, "elevation")
+    tzone <- ncdf4::ncatt_get(nc = nc, varid = "time", "units")
     ## Future: query elevation from site.id
     if (elev$hasatt) {
       elevation <- as.numeric((unlist(strsplit(elev$value, " ")))[1])
@@ -107,12 +102,12 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     }
 
     ## Required to exist in file
-    Tair <- try(ncvar_get(nc = nc, varid = "air_temperature"), silent = TRUE)
+    Tair <- try(ncdf4::ncvar_get(nc = nc, varid = "air_temperature"), silent = TRUE)
     if (!is.numeric(Tair)) {
       PEcAn.logger::logger.error("air_temperature not defined in met file for metgapfill")
     }
     Tair_degC <- udunits2::ud.convert(Tair, "K", "degC")
-    precip <- try(ncvar_get(nc = nc, varid = "precipitation_flux"), silent = TRUE)
+    precip <- try(ncdf4::ncvar_get(nc = nc, varid = "precipitation_flux"), silent = TRUE)
     if (!is.numeric(precip)) {
       PEcAn.logger::logger.error("precipitation_flux not defined in met file for metgapfill")
     }
@@ -121,25 +116,25 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     missingarr <- as.numeric(array(NA, length(Tair)))
 
     ## One of these must exist, create the other one for gap-filling
-    Rg <- try(ncvar_get(nc = nc, varid = "surface_downwelling_shortwave_flux_in_air"), silent = TRUE)
+    Rg <- try(ncdf4::ncvar_get(nc = nc, varid = "surface_downwelling_shortwave_flux_in_air"), silent = TRUE)
     if (!is.numeric(Rg)) {
       Rg <- missingarr
-      myvar <- ncvar_def(name = "surface_downwelling_shortwave_flux_in_air",
+      myvar <- ncdf4::ncvar_def(name = "surface_downwelling_shortwave_flux_in_air",
                          units = "W m-2",
                          dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
 
-    PAR <- try(ncvar_get(nc = nc, varid = "surface_downwelling_photosynthetic_photon_flux_in_air"),
+    PAR <- try(ncdf4::ncvar_get(nc = nc, varid = "surface_downwelling_photosynthetic_photon_flux_in_air"),
                silent = TRUE)
     if (!is.numeric(PAR)) {
       PAR <- missingarr
-      myvar <- ncvar_def(name = "surface_downwelling_photosynthetic_photon_flux_in_air",
+      myvar <- ncdf4::ncvar_def(name = "surface_downwelling_photosynthetic_photon_flux_in_air",
                          units = "mol m-2 s-1",
                          dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
 
     # check to see if we have Rg values
@@ -189,22 +184,22 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
 
     ## If these don't exist, create blank ones that will be filled with default values, or imputed from
     ## other vars
-    co2 <- try(ncvar_get(nc = nc, varid = "mole_fraction_of_carbon_dioxide_in_air"), silent = TRUE)
+    co2 <- try(ncdf4::ncvar_get(nc = nc, varid = "mole_fraction_of_carbon_dioxide_in_air"), silent = TRUE)
     if (!is.numeric(co2)) {
       co2 <- missingarr
-      myvar <- ncvar_def(name = "mole_fraction_of_carbon_dioxide_in_air",
+      myvar <- ncdf4::ncvar_def(name = "mole_fraction_of_carbon_dioxide_in_air",
                          units = "mol mol-1",
                          dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
 
-    press <- try(ncvar_get(nc = nc, varid = "air_pressure"), silent = TRUE)
+    press <- try(ncdf4::ncvar_get(nc = nc, varid = "air_pressure"), silent = TRUE)
     if (!is.numeric(press)) {
       press <- missingarr
-      myvar <- ncvar_def(name = "air_pressure", units = "Pa", dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      myvar <- ncdf4::ncvar_def(name = "air_pressure", units = "Pa", dim = xytdim)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
     # default pressure (in Pascals) if no pressure observations are available (based on NOAA 1976
     # equation for pressure altitude for WMO international standard atmosphere)
@@ -213,45 +208,45 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
       press[is.na(press)] <- standard_pressure
     }
 
-    Lw <- try(ncvar_get(nc = nc, varid = "surface_downwelling_longwave_flux_in_air"), silent = TRUE)
+    Lw <- try(ncdf4::ncvar_get(nc = nc, varid = "surface_downwelling_longwave_flux_in_air"), silent = TRUE)
     if (!is.numeric(Lw)) {
       Lw <- missingarr
-      myvar <- ncvar_def(name = "surface_downwelling_longwave_flux_in_air",
+      myvar <- ncdf4::ncvar_def(name = "surface_downwelling_longwave_flux_in_air",
                          units = "W m-2",
                          dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
 
-    Ts1 <- try(ncvar_get(nc = nc, varid = "soil_temperature"), silent = TRUE)
+    Ts1 <- try(ncdf4::ncvar_get(nc = nc, varid = "soil_temperature"), silent = TRUE)
     if (!is.numeric(Ts1)) {
       Lw <- missingarr
-      myvar <- ncvar_def(name = "soil_temperature", units = "K", dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      myvar <- ncdf4::ncvar_def(name = "soil_temperature", units = "K", dim = xytdim)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
 
     ## one of these must exist, create the others
-    rH <- try(ncvar_get(nc = nc, varid = "relative_humidity"), silent = TRUE)
+    rH <- try(ncdf4::ncvar_get(nc = nc, varid = "relative_humidity"), silent = TRUE)
     if (!is.numeric(rH)) {
       rH <- missingarr
-      myvar <- ncvar_def(name = "relative_humidity", units = "%", dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      myvar <- ncdf4::ncvar_def(name = "relative_humidity", units = "%", dim = xytdim)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
-    sHum <- try(ncvar_get(nc = nc, varid = "specific_humidity"), silent = TRUE)
+    sHum <- try(ncdf4::ncvar_get(nc = nc, varid = "specific_humidity"), silent = TRUE)
     if (!is.numeric(sHum)) {
       sHum <- missingarr
-      myvar <- ncvar_def(name = "specific_humidity", units = "kg kg-1", dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      myvar <- ncdf4::ncvar_def(name = "specific_humidity", units = "kg kg-1", dim = xytdim)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
-    VPD <- try(ncvar_get(nc = nc, varid = "water_vapor_saturation_deficit"), silent = TRUE)
+    VPD <- try(ncdf4::ncvar_get(nc = nc, varid = "water_vapor_saturation_deficit"), silent = TRUE)
     if (!is.numeric(VPD)) {
       VPD <- missingarr
-      myvar <- ncvar_def(name = "water_vapor_saturation_deficit", units = "Pa", dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      myvar <- ncdf4::ncvar_def(name = "water_vapor_saturation_deficit", units = "Pa", dim = xytdim)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
 
     ## Fill these variables from each other
@@ -302,37 +297,40 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
 
     ##Once all are filled, do one more consistency check
     es <- get.es(Tair_degC) * 100
+
     rH[rH < 0] <- 0
     rH[rH > 100] <- 100
     VPD[VPD < 0] <- 0
+
     badVPD_es <- which(VPD > es)  
     VPD[badVPD_es] <- es[badVPD_es]  
+
     sHum[sHum < 0] <- 0
     
     ## one set of these must exist (either wind_speed or east+north wind)
-    ws <- try(ncvar_get(nc = nc, varid = "wind_speed"), silent = TRUE)
+    ws <- try(ncdf4::ncvar_get(nc = nc, varid = "wind_speed"), silent = TRUE)
     if (!is.numeric(ws)) {
       ws <- missingarr
-      myvar <- ncvar_def(name = "wind_speed", units = "m s-1", dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      myvar <- ncdf4::ncvar_def(name = "wind_speed", units = "m s-1", dim = xytdim)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
-    east_wind <- try(ncvar_get(nc = nc, varid = "eastward_wind"), silent = TRUE)
+    east_wind <- try(ncdf4::ncvar_get(nc = nc, varid = "eastward_wind"), silent = TRUE)
     if (!is.numeric(east_wind)) {
       east_wind <- missingarr
-      myvar <- ncvar_def(name = "eastward_wind", units = "m s-1", dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      myvar <- ncdf4::ncvar_def(name = "eastward_wind", units = "m s-1", dim = xytdim)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
-    north_wind <- try(ncvar_get(nc = nc, varid = "northward_wind"), silent = TRUE)
+    north_wind <- try(ncdf4::ncvar_get(nc = nc, varid = "northward_wind"), silent = TRUE)
     if (!is.numeric(north_wind)) {
       north_wind <- missingarr
-      myvar <- ncvar_def(name = "northward_wind", units = "m s-1", dim = xytdim)
-      nc <- ncvar_add(nc = nc, v = myvar)
-      ncvar_put(nc, varid = myvar, missingarr)
+      myvar <- ncdf4::ncvar_def(name = "northward_wind", units = "m s-1", dim = xytdim)
+      nc <- ncdf4::ncvar_add(nc = nc, v = myvar)
+      ncdf4::ncvar_put(nc, varid = myvar, missingarr)
     }
 
-    # Rn <- ncvar_get(nc=nc,varid='Rn') Ts2 <-ncvar_get(nc=nc,varid='TS2')
+    # Rn <- ncdf4::ncvar_get(nc=nc,varid='Rn') Ts2 <-ncdf4::ncvar_get(nc=nc,varid='TS2')
 
     ## make a data frame, convert -9999 to NA, convert to degrees C
     EddyData.F <- data.frame(Tair, Rg, rH, PAR, precip, sHum, Lw, Ts1,
@@ -365,7 +363,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
 
     # figure out datetime of nc file and convert to POSIX
     nelem <- length(time)
-    tunit <- ncatt_get(nc = nc, varid = "time", attname = "units", verbose = verbose)
+    tunit <- ncdf4::ncatt_get(nc = nc, varid = "time", attname = "units", verbose = verbose)
     origin <- "1900-01-01 00:00:00"
     time <- round(as.POSIXlt(udunits2::ud.convert(time, tunit$value, paste("seconds since", origin)),
                              origin = origin, tz = "UTC"), units = "mins")
@@ -485,7 +483,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(Tair_f))) > 0) {
       error <- c(error, "air_temperature")
     }
-    ncvar_put(nc, varid = "air_temperature", vals = Tair_f)
+    ncdf4::ncvar_put(nc, varid = "air_temperature", vals = Tair_f)
 
     if (("Rg_f" %in% colnames(Extracted))) {
       Rg_f <- Extracted[, "Rg_f"]
@@ -493,7 +491,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(Rg_f))) > 0) {
       error <- c(error, "surface_downwelling_shortwave_flux_in_air")
     }
-    ncvar_put(nc, varid = "surface_downwelling_shortwave_flux_in_air", vals = Rg_f)
+    ncdf4::ncvar_put(nc, varid = "surface_downwelling_shortwave_flux_in_air", vals = Rg_f)
 
     if (("rH_f" %in% colnames(Extracted))) {
       rH_f <- Extracted[, "rH_f"]
@@ -503,7 +501,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(rH_f))) > 0) {
       error <- c(error, "relative_humidity")
     }
-    ncvar_put(nc, varid = "relative_humidity", vals = rH_f)
+    ncdf4::ncvar_put(nc, varid = "relative_humidity", vals = rH_f)
 
     if (("PAR_f" %in% colnames(Extracted))) {
       PAR_f <- Extracted[, "PAR_f"]
@@ -511,7 +509,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(PAR_f))) > 0) {
       error <- c(error, "surface_downwelling_photosynthetic_photon_flux_in_air")
     }
-    ncvar_put(nc, varid = "surface_downwelling_photosynthetic_photon_flux_in_air", vals = PAR_f)
+    ncdf4::ncvar_put(nc, varid = "surface_downwelling_photosynthetic_photon_flux_in_air", vals = PAR_f)
 
     if (("precip_f" %in% colnames(Extracted))) {
       precip_f <- Extracted[, "precip_f"]
@@ -519,7 +517,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(precip_f))) > 0) {
       error <- c(error, "precipitation_flux")
     }
-    ncvar_put(nc, varid = "precipitation_flux", vals = precip_f)
+    ncdf4::ncvar_put(nc, varid = "precipitation_flux", vals = precip_f)
 
     if (("sHum_f" %in% colnames(Extracted))) {
       sHum_f <- Extracted[, "sHum_f"]
@@ -530,7 +528,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(sHum_f))) > 0) {
       error <- c(error, "specific_humidity")
     }
-    ncvar_put(nc, varid = "specific_humidity", vals = sHum_f)
+    ncdf4::ncvar_put(nc, varid = "specific_humidity", vals = sHum_f)
 
     if (("Lw_f" %in% colnames(Extracted))) {
       Lw_f <- Extracted[, "Lw_f"]
@@ -539,7 +537,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(Lw_f))) > 0) {
       error <- c(error, "surface_downwelling_longwave_flux_in_air")
     }
-    ncvar_put(nc, varid = "surface_downwelling_longwave_flux_in_air", vals = Lw_f)
+    ncdf4::ncvar_put(nc, varid = "surface_downwelling_longwave_flux_in_air", vals = Lw_f)
 
     if (("Ts1_f" %in% colnames(Extracted))) {
       Ts1_f <- udunits2::ud.convert(Extracted[, "Ts1_f"], "degC", "K")
@@ -550,13 +548,13 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
       tau <- 15 * DTS.n
       filt <- exp(-(1:length(Tair_ff)) / tau)
       filt <- (filt / sum(filt))
-      Ts_1ff <- convolve(Tair_ff, filt)
+      Ts_1ff <- stats::convolve(Tair_ff, filt)
       Ts1_f[is.na(Ts1_f)] <- Ts_1ff[is.na(Ts1_f)]
     }
     if (length(which(is.na(Ts1_f))) > 0) {
       error <- c(error, "soil_temperature")
     }
-    ncvar_put(nc, varid = "soil_temperature", vals = Ts1_f)
+    ncdf4::ncvar_put(nc, varid = "soil_temperature", vals = Ts1_f)
 
     if (("VPD_f" %in% colnames(Extracted))) {
       VPD_f <- udunits2::ud.convert(Extracted[, "VPD_f"], "kPa", "Pa")
@@ -564,14 +562,16 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
       if (("Tair_f" %in% colnames(Extracted))) {
         Tair_f_degC <- udunits2::ud.convert(Tair_f, "K", "degC")
         es <- get.es(Tair_f_degC) * 100
+
         badVPD_f <- which(VPD_f > es) 
         VPD_f[badVPD_f] <- es[badVPD_f] 
+
       }
     }
     if (length(which(is.na(VPD_f))) > 0) {
       error <- c(error, "water_vapor_saturation_deficit")
     }
-    ncvar_put(nc, varid = "water_vapor_saturation_deficit", vals = VPD_f)
+    ncdf4::ncvar_put(nc, varid = "water_vapor_saturation_deficit", vals = VPD_f)
 
     if (("ws_f" %in% colnames(Extracted))) {
       ws_f <- Extracted[, "ws_f"]
@@ -585,7 +585,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(co2_f))) > 0) {
       error <- c(error, "mole_fraction_of_carbon_dioxide_in_air")
     }
-    ncvar_put(nc, varid = "mole_fraction_of_carbon_dioxide_in_air", vals = co2_f)
+    ncdf4::ncvar_put(nc, varid = "mole_fraction_of_carbon_dioxide_in_air", vals = co2_f)
 
     if (("press_f" %in% colnames(Extracted))) {
       press_f <- Extracted[, "press_f"]
@@ -596,7 +596,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(press_f))) > 0) {
       error <- c(error, "air_pressure")
     }
-    ncvar_put(nc, varid = "air_pressure", vals = press_f)
+    ncdf4::ncvar_put(nc, varid = "air_pressure", vals = press_f)
 
     if (("east_wind_f" %in% colnames(Extracted))) {
       east_wind_f <- Extracted[, "east_wind_f"]
@@ -604,7 +604,7 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(east_wind_f))) > 0) {
       error <- c(error, "eastward_wind")
     }
-    ncvar_put(nc, varid = "eastward_wind", vals = east_wind_f)
+    ncdf4::ncvar_put(nc, varid = "eastward_wind", vals = east_wind_f)
 
     if (("north_wind_f" %in% colnames(Extracted))) {
       north_wind_f <- Extracted[, "north_wind_f"]
@@ -614,13 +614,13 @@ metgapfill <- function(in.path, in.prefix, outfolder, start_date, end_date, lst
     if (length(which(is.na(north_wind_f))) > 0) {
       error <- c(error, "northward_wind")
     }
-    ncvar_put(nc, varid = "northward_wind", vals = north_wind_f)
+    ncdf4::ncvar_put(nc, varid = "northward_wind", vals = north_wind_f)
 
     ws_f[is.na(ws_f)] <- sqrt(north_wind_f[is.na(ws_f)] ^ 2 + east_wind_f[is.na(ws_f)] ^ 2)
     if (length(which(is.na(ws_f))) > 0) {
       error <- c(error, "wind_speed")
     }
-    ncvar_put(nc, varid = "wind_speed", vals = ws_f)
+    ncdf4::ncvar_put(nc, varid = "wind_speed", vals = ws_f)
 
     ncdf4::nc_close(nc)
 
diff --git a/modules/data.atmosphere/R/metgapfill.module.R b/modules/data.atmosphere/R/metgapfill.module.R
index 2f76e7105a8..7c3433d54fd 100644
--- a/modules/data.atmosphere/R/metgapfill.module.R
+++ b/modules/data.atmosphere/R/metgapfill.module.R
@@ -1,5 +1,5 @@
 .metgapfill.module <- function(cf.id, register, dir, met, str_ns, site, new.site, con, 
-                               start_date, end_date, host, overwrite = FALSE) {
+                               start_date, end_date, host, overwrite = FALSE, ensemble_name = NULL) {
   PEcAn.logger::logger.info("Gapfilling")  # Does NOT take place on browndog!
   
   input.id   <- cf.id[1]
@@ -11,7 +11,19 @@
   mimetype   <- "application/x-netcdf"
   lst        <- site.lst(site.id=site$id, con=con)
   
-  ready.id <- PEcAn.utils::convert.input(input.id = input.id, 
+  if (!is.null(register$forecast)) {
+    forecast <- isTRUE(as.logical(register$forecast))
+  } else {
+    forecast <- FALSE
+  }
+  
+  # met products requiring special gapfilling functions (incompatable with metgapfill)
+  # Overrides default value of "fcn"
+  if (met %in% c("NOAA_GEFS")) {
+    fcn <- "metgapfill.NOAA_GEFS"
+  }
+  
+  ready.id <- PEcAn.utils::convert.input(input.id = input.id,
                             outfolder = outfolder, 
                             formatname = formatname, 
                             mimetype =  mimetype, 
@@ -21,7 +33,11 @@
                             write = TRUE, 
                             lst = lst, 
                             overwrite = overwrite,
-                            exact.dates = FALSE)
+                            exact.dates = FALSE,
+                            forecast = forecast,
+                            pattern = met,
+                            ensemble = !is.null(register$ensemble) && as.logical(register$ensemble),
+                            ensemble_name = ensemble_name)
   
   print(ready.id)
   
diff --git a/modules/data.atmosphere/R/metutils.R b/modules/data.atmosphere/R/metutils.R
index e8c6cd5db60..5c792076732 100644
--- a/modules/data.atmosphere/R/metutils.R
+++ b/modules/data.atmosphere/R/metutils.R
@@ -102,8 +102,8 @@ SatVapPres <- function(T) {
 ##' Relative Humidity and the Dewpoint Temperature in Moist Air
 ##' A Simple Conversion and Applications.)
 ##' @title get RH
-##' @param temp T in original equation
-##' @param dewpoint Td in original
+##' @param T temperature
+##' @param Td dewpoint
 ##' @return numeric vector
 ##' @export
 ##' @author David LeBauer
@@ -122,10 +122,9 @@ get.rh <- function(T, Td) {
 ##' @export
 ##' @author David LeBauer
 wide2long <- function(data.wide, lat, lon, var) {
-  library(reshape)
   colnames(data.wide) <- lon
   data.wide <- cbind(lat, data.wide)
-  data.long <- melt(data.wide, id = "lat")
+  data.long <- reshape2::melt(data.wide, id = "lat")
   colnames(data.long) <- c("lat", "lon", var)
   data.long$lon <- as.numeric(as.character(data.long$lon))
   return(data.long)
diff --git a/modules/data.atmosphere/R/modisWSDL.py b/modules/data.atmosphere/R/modisWSDL.py
deleted file mode 100644
index 2d2ac596815..00000000000
--- a/modules/data.atmosphere/R/modisWSDL.py
+++ /dev/null
@@ -1,435 +0,0 @@
-#!/home/db903833/dataLand01/enthoughtDistros/epd-7.2-2-rh5-x86/bin/python
-#!/home/db903833/dataLand01/enthoughtDistros/epd-7.3-1-rh5-x86/bin/python
-#!/usr/bin/env python
-"""
-Get MODIS data using the ORNL DAAC MODIS web service.
-http://daac.ornl.gov/MODIS/MODIS-menu/modis_webservice.html
-"""
-__author__ = "Tristan Quaife"
-__version__ = "0.3 (29.07.2010)"
-__email__ = "tquaife@gmail.com"
-
-import sys, os
-import numpy as np
-import optparse
-import pickle 
-import tempfile
-tempfile.tempdir="/scratch/ttviskar"
-from copy import copy
-from suds.client import *
-import netCDF4
-
-DEBUG_PRINTING=False
-
-defaultURL='http://daac.ornl.gov/cgi-bin/MODIS/GLBVIZ_1_Glb_subset/MODIS_webservice.wsdl'
-
-class modisData( object ):
-
-	def __init__( self ):
-	
-		self.server=None
-		self.product=None
-		self.latitude=None
-		self.longitude=None
-
-		self.band=None          
-		self.nrows=None         
-		self.ncols=None         
-		self.cellsize=None      
-		self.scale=None         
-		self.units=None         
-		self.yllcorner=None
-		self.xllcorner=None  
-		
-		self.kmAboveBelow=0
-		self.kmLeftRight=0
-
-		self.dateStr=[]
-		self.dateInt=[]
-		self.data=[]
-		self.QA=[]
-
-		#self.header=None        
-		#self.subset=None        
-
-		self.isScaled=False
-
-	
-	def getFilename( self ):
-	
-		d='.'
-	
-		fn=self.product
-		fn=fn+d+self.band
-		fn=fn+d+'LAT__'+str(self.latitude)
-		fn=fn+d+'LON__'+str(self.longitude)
-		fn=fn+d+self.dateStr[0]
-		fn=fn+d+self.dateStr[-1]
-		fn=fn+d+str(int(self.nrows))
-		fn=fn+d+str(int(self.ncols))
-		
-		
-		return fn
-
-
-	def pickle( self ):
-	
-		fn=self.getFilename()+'.'+'pkl'
-			
-		f=open( fn, 'w' )
-		pickle.dump( self, f )
-		f.close( )
-
-
-	def applyScale( self ):
-		
-		if self.isScaled==False:
-			self.data=self.data*self.scale
-			self.isScaled=True
-
-
-	def filterQA( self, QAOK, fill=np.nan ):
-
-		if np.size( self.data ) != np.size( self.QA ):
-			#should do this using an exception
-			print >> sys.stderr, 'data and QA are different sizes'
-			sys.exit()
-		
-		r=np.shape( self.data )[0]
-		c=np.shape( self.data )[1]
-	
-		for i in xrange( c ):
-			for j in xrange( r ):
-				if np.sum( QAOK == self.QA[j][i] ) == 0:
-					self.data[j][i] = fill
-
-
-
-def __getDummyDateList( ):
-	"""
-	Generate a dummy date list for testing without 
-	hitting the server
-	"""
-
-	D=[]
-	for y in xrange( 2001,2010 ):
-		for d in xrange( 1,365,1 ):
-			D.append( 'A%04d%03d'%(y,d) )
-		
-	return D
-
-
-
-def __error( msg ):
-	raise Exception, msg
-		
-def latLonErr( ):
-	__error( 'Latitude and longitude must both be specified' )
-	
-def serverDataErr( ):	
-	__error( 'Server not returning data (possibly busy)' )
-	
-
-def mkIntDate( s ):
-	"""
-	Convert the webserver formatted dates
-	to an integer format by stripping the
-	leading char and casting
-	"""
-	n=s.__len__( )
-	d=int( s[-(n-1):n] )
-
-	return d
-
-
-def setClient( wsdlurl=defaultURL ):
-		
-	return Client(wsdlurl)
-	
-
-def printList( l ):
-
-	for i in xrange( l.__len__() ):
-		print l[ i ]
-		
-		
-def printModisData( m ):
-
-		
-	print 'server:', m.server
-	print 'product:', m.product
-	print 'latitude:', m.latitude
-	print 'longitude:', m.longitude
-
-	print 'band:',m.band          
-	print 'nrows:',m.nrows        
-	print 'ncols:',m.ncols         
-	print 'cellsize:',m.cellsize      
-	print 'scale:',m.scale         
-	print 'units:',m.units         
-	print 'xllcorner:',m.yllcorner
-	print 'yllcorner:',m.xllcorner  
-
-	print 'kmAboveBelow:', m.kmAboveBelow
-	print 'kmLeftRight:', m.kmLeftRight
-
-	print 'dates:', m.dateStr
-
-	print 'QA:', m.QA
-	print m.data
-
-
-def __debugPrint( o ):
-
-	if DEBUG_PRINTING:
-		print >> sys.stderr,'DB> ',o
-		sys.stderr.flush
-
-
-def modisGetQA( m, QAname, client=None, chunkSize=8 ):
-
-	startDate=m.dateInt[0]
-	endDate=m.dateInt[-1]
-
-	q = modisClient( client, product=m.product, band=QAname, lat=m.latitude, lon=m.longitude, 
-			startDate=startDate, endDate=endDate, chunkSize=chunkSize, kmAboveBelow=m.kmAboveBelow, kmLeftRight=m.kmLeftRight )
-	
-	m.QA = copy( q.data )
-	
-			
-
-
-def modisClient( client=None, product=None, band=None, lat=None, lon=None, startDate=None, endDate=None, chunkSize=8, kmAboveBelow=0, kmLeftRight=0 ):
-	"""
-	modisClient: function for building a modisData object
-	"""
-
-	m=modisData()
-
-	m.kmABoveBelow=kmAboveBelow
-	m.kmLeftRight=kmLeftRight
-	
-	if client==None:
-		client=setClient( )
-		
-	m.server=client.wsdl.url	
-		
-	if product==None:
-		prodList=client.service.getproducts(  )
-		return prodList
-
-	m.product=product
-
-	if band==None:
-		bandList=client.service.getbands( product )
-		return bandList
-	
-	m.band=band
-	
-	if lat==None or lon==None:
-		latLonErr( )
-	
-	m.latitude=lat
-	m.longitude=lon
-	
-	# get the date list regardless so we can
-	# process it into appropriately sized chunks
-	 
-	dateList=client.service.getdates( lat, lon, product )
-		
-	if startDate==None or endDate==None:
-		return dateList
-
-
-
-	#count up the total number of dates
-	i=-1
-	nDates=0	
-	while i < dateList.__len__( )-1:	
-		i=i+1
-	
-		#__debugPrint( 'i=%d'%i )
-		
-		thisDate=mkIntDate( dateList[i] )
-		
-		if thisDate < startDate:
-			continue
-		if thisDate > endDate:
-			break	
-
-		nDates=nDates+1
-
-		m.dateInt.append( thisDate )
-		m.dateStr.append( dateList[i] )
-
-	__debugPrint( m.dateStr )
-	
-	n=0	
-	i=-1	
-	while i < dateList.__len__( )-1:	
-		i=i+1
-	
-		thisDate=mkIntDate( dateList[i] )
-		
-		if thisDate < startDate:
-			continue
-		if thisDate > endDate:
-			break	
-		
-		requestStart=dateList[i]
-		
-		j=min( chunkSize, dateList.__len__( )-i )
-		
-		__debugPrint( 'i=%d, j=%d, dateList__len__()=%d'%(i,j,dateList.__len__( ))  )
-		while mkIntDate( dateList[i+j-1] ) > endDate:
-			j=j-1
-		
-		
-		
-		requestEnd=dateList[i+j-1]
-		i=i+j-1
-		
-		#print >> sys.stderr, requestStart, requestEnd
-		
-		data = client.service.getsubset( lat, lon, product, band, requestStart, requestEnd, kmAboveBelow, kmLeftRight )
-		
-		
-		# now fill up the data structure with the returned data...
-
-		if n == 0:
-		
-			m.nrows=data.nrows         
-			m.ncols=data.ncols         
-			m.cellsize=data.cellsize      
-			m.scale=data.scale         
-			m.units=data.units         
-			m.yllcorner=data.yllcorner
-			m.xllcorner=data.xllcorner  	
-
-			m.data=np.zeros( (nDates,m.nrows*m.ncols) )
-
-		for j in xrange( data.subset.__len__( ) ):
-			kn=0
-			__debugPrint( data.subset	)		
-			for k in data.subset[j].split(",")[5:]:
-				__debugPrint( k )
-				try:
-					m.data[ n*chunkSize+j,kn] = int( k )
-				except ValueError:
-					serverDataErr( )
-				
-				kn=kn+1
-
-
-
-		n=n+1
-
-
-
-	return( m )
-
-
-
-#def m_data_to_netCDF(filename, varname, data):
-#	rootgrp = netCDF4.Dataset(filename, 'w', format='NETCDF3_64BIT')
-#	rootgrp.createDimension('ncol', data.shape[1])
-#	rootgrp.createDimension('nrow', data.shape[0])
-#	m_data = rootgrp.createVariable(varname, 'f8', ('nrow', 'ncol'))
-#	m_data[:] = data
-#	rootgrp.close()
-
-
-def m_data_to_netCDF(filename, m, k):
-	rootgrp = netCDF4.Dataset(filename, 'w', format='NETCDF3_64BIT')
-	rootgrp.createDimension('ncol', m.data.shape[1])
-	rootgrp.createDimension('nrow', m.data.shape[0])
-	rootgrp.createDimension('dates', len(m.dateInt))
-	m_data = rootgrp.createVariable('LAI', 'f8', ('nrow', 'ncol'))
-	m_std = rootgrp.createVariable('LAIStd', 'f8', ('nrow', 'ncol'))
-	m_date = rootgrp.createVariable('Dates', 'i7', ('dates'))
-	m_data[:] = m.data
-	m_std[:] = 0.1*k.data
-	m_date[:] = m.dateInt
-	rootgrp.close()
-
-#def m_date_to_netCDF(filename, varname, data):
-#	rootgrp = netCDF4.Dataset(filename, 'w', format='NETCDF3_64BIT')
-#	rootgrp.createDimension('ncol', data.shape[1])
-#	rootgrp.createDimension('nrow', data.shape[0])
-#	rootgrp.createDimension('ncol', len(data))
-#	m_data = rootgrp.createVariable(varname, 'S1', ('ncol'))
-#	m_data[:] = data
-#	rootgrp.close()
-
-
-def run_main(start_date=2004001, end_date=2004365, la=45.92, lo=-90.45, kmAB=0, kmLR=0, fname='m_data.nc'):
-
-	client=setClient( )
-
-	prodList = modisClient( client )
-#	printList( prodList )
-
-	bandList = modisClient( client, product='MOD15A2' )
-#	printList( bandList )
-	
-	dateList = modisClient( client, product='MOD15A2', band='Lai_1km', lat=45.92, lon=-90.45 )
-#	printList( dateList )
-	
-	m = modisClient( client, product='MOD15A2', band='Lai_1km', lat=la, lon=lo, startDate=start_date, endDate=end_date, kmAboveBelow=kmAB, kmLeftRight=kmLR)
-	if len(m.dateInt) == 0:
-		print "No data available for these dates"
-		return np.array([[]]), np.array([[]])
-	k = modisClient( client, product='MOD15A2', band='LaiStdDev_1km', lat=45.92, lon=-90.45, startDate=start_date, endDate=end_date, kmAboveBelow=kmAB, kmLeftRight=kmLR)
-	date = m.dateInt
-#	data[:] = m.data
-
-
-#	print(m.dateStr)
-
-	modisGetQA(m, 'FparLai_QC', client=client )
-	modisGetQA(k, 'FparLai_QC', client=client )
-		
-	m.applyScale()
-	m.filterQA( range(0,2**16,2), fill=-1 )
-
-	m_data_to_netCDF(fname, m, k)	
-
-#	print(len(m.data))
-#	print(len(k.data))
-
-	return m, k, date
-
-
-
-def main():
-	m, k, date = run_main()
-
-#	m_data_to_netCDF('m_data.nc', 'm_data', m.data)
-
-#	for i in range(m.data.shape[0]):
-#		for j in range(m.data.shape[1]):
-#			print "%12i%12i%19.14F"%(i+1,j+1,m.data[i,j])
-
-#	printModisData( m )
-
-
-#def get_m():
-if __name__ == "__main__":
-	main()
-
-#def load_m():
-#	f = open('MODIS_LAI.dat','rb')
-#	
-#	m = pickle.load(f)
-#	return m
-
- 
-#if __name__ == "__main__":
-#	get_m_data()
-#	get_m()
-#	m = load_m()
-#	m_data_to_netCDF('m_data.nc', m.data)
-#	for i in range(m.data.shape[0]):
-#		for j in range(m.data.shape[1]):
-#			print "%12i%12i%19.14F"%(i+1,j+1,m.data[i,j])
-#
diff --git a/modules/data.atmosphere/R/nc_merge.R b/modules/data.atmosphere/R/nc_merge.R
index 69d29ecb284..577fd9683dd 100644
--- a/modules/data.atmosphere/R/nc_merge.R
+++ b/modules/data.atmosphere/R/nc_merge.R
@@ -18,12 +18,11 @@
 ##' @param in.prefix - prefix of model string as character (e.g. IPSL.r1i1p1.rcp85)
 ##' @param start_date - yyyy-mm-dd
 ##' @param end_date - yyyy-mm-dd
-##' @param lat.in - latitude as numeric
-##' @param lon.in - longitude as numeric
 ##' @param upscale - Upscale can either be set for FALSE (leave alone) or to the temporal resolution you want to aggregate to
 #                    options are: "year", "doy" (day of year), or "hour"
-##' @param overwrite
-##' @param verbose
+##' @param overwrite logical: replace output file if it already exists?
+##' @param verbose logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}}
+##'   functions print debugging information as they run?
 ##' @export
 # -----------------------------------
 #----------------------------------------------------------------------
diff --git a/modules/data.atmosphere/R/pecan_standard_met_table.R b/modules/data.atmosphere/R/pecan_standard_met_table.R
new file mode 100644
index 00000000000..557e1322959
--- /dev/null
+++ b/modules/data.atmosphere/R/pecan_standard_met_table.R
@@ -0,0 +1,24 @@
+#' Conversion table for PEcAn standard meteorology
+#'
+#' @export
+pecan_standard_met_table <- tibble::tribble(
+  ~`cf_standard_name`                                     , ~units        , ~is_required,  ~bety               , ~isimip        , ~cruncep , ~narr   , ~ameriflux         ,
+  "air_temperature"                                       , "K"           ,         TRUE,  "airT"              , "tasAdjust"    , "tair"   , "air"   , "TA (C)"           ,
+  "air_temperature_max"                                   , "K"           ,        FALSE,  NA                  , "tasmaxAdjust" , NA       , "tmax"  , NA                 ,
+  "air_temperature_min"                                   , "K"           ,        FALSE,  NA                  , "tasminAdjust" , NA       , "tmin"  , NA                 ,
+  "air_pressure"                                          , "Pa"          ,         TRUE,  "air_pressure"      , NA             , NA       , NA      , "PRESS (KPa)"      ,
+  "mole_fraction_of_carbon_dioxide_in_air"                , "mol/mol"     ,        FALSE,  NA                  , NA             , NA       , NA      , "CO2"              ,
+  "moisture_content_of_soil_layer"                        , "kg m-2"      ,        FALSE,  NA                  , NA             , NA       , NA      , NA                 ,
+  "soil_temperature"                                      , "K"           ,        FALSE,  "soilT"             , NA             , NA       , NA      , "TS1 *(NOT DONE)*" ,
+  "relative_humidity"                                     , "%"           ,        FALSE,  "relative_humidity" , "rhurs"        , NA       , "rhum"  , "RH"               ,
+  "specific_humidity"                                     , "1"           ,         TRUE,  "specific_humidity" , NA             , "qair"   , "shum"  , "CALC(RH)"         ,
+  "water_vapor_saturation_deficit"                        , "Pa"          ,        FALSE,  "VPD"               , NA             , NA       , NA      , "VPD *(NOT DONE)*" ,
+  "surface_downwelling_longwave_flux_in_air"              , "W m-2"       ,         TRUE,  "same"              , "rldsAdjust"   , "lwdown" , "dlwrf" , "Rgl"              ,
+  "surface_downwelling_shortwave_flux_in_air"             , "W m-2"       ,         TRUE,  "solar_radiation"   , "rsdsAdjust"   , "swdown" , "dswrf" , "Rg"               ,
+  "surface_downwelling_photosynthetic_photon_flux_in_air" , "mol m-2 s-1" ,        FALSE,  "PAR"               , NA             , NA       , NA      , "PAR *(NOT DONE)*" ,
+  "precipitation_flux"                                    , "kg m-2 s-1"  ,         TRUE,  "cccc"              , "prAdjust"     , "rain"   , "acpc"  , "PREC (mm/s)"      ,
+  "wind_to_direction"                                     , "degrees"     ,        FALSE,  "wind_direction"    , NA             , NA       , NA      , "WD"               ,
+  "wind_speed"                                            , "m/s"         ,        FALSE,  "Wspd"              , NA             , NA       , NA      , "WS"               ,
+  "eastward_wind"                                         , "m/s"         ,         TRUE,  "eastward_wind"     , NA             , NA       , NA      , "CALC(WS+WD)"      ,
+  "northward_wind"                                        , "m/s"         ,         TRUE,  "northward_wind"    , NA             , NA       , NA      , "CALC(WS+WD)"
+)
diff --git a/modules/data.atmosphere/R/read.register.R b/modules/data.atmosphere/R/read.register.R
index 22f1cdbc852..d8af6455965 100644
--- a/modules/data.atmosphere/R/read.register.R
+++ b/modules/data.atmosphere/R/read.register.R
@@ -7,9 +7,6 @@
 ##' @author Betsy Cowdery
 read.register <- function(register.xml, con) {
   
-  library(PEcAn.DB)
-  library(PEcAn.utils)
-  
   register <- XML::xmlToList(XML::xmlParse(register.xml))
   print(as.data.frame(register))
   
@@ -38,13 +35,14 @@ read.register <- function(register.xml, con) {
     } else if ((!is.null(register$format$id) & is.null(register$format$name)) 
                | 
                (!is.null(register$format$id) & is.null(register$format$mimetype))) {
-      register$format$name <- db.query(paste("SELECT name from formats where id = ", register$format$id), 
-                                       con)[[1]]
-      register$format$mimetype <- db.query(paste("SELECT mime_type from formats where id = ", 
-                                                 register$format$id), con)[[1]]
+      register$format$name <- PEcAn.DB::db.query(
+        paste("SELECT name from formats where id = ", register$format$id), con)[[1]]
+      register$format$mimetype <- PEcAn.DB::db.query(
+        paste("SELECT mime_type from formats where id = ", register$format$id), con)[[1]]
     } else if (is.null(register$format$id) & !is.null(register$format$name) & !is.null(register$format$mimetype)) {
-      register$format$id <- db.query(paste0("SELECT id from formats where name = '", register$format$name, 
-                                            "' and mime_type = '", register$format$mimetype, "'"), con)[[1]]
+      register$format$id <- PEcAn.DB::db.query(
+        paste0("SELECT id from formats where name = '", register$format$name,
+               "' and mime_type = '", register$format$mimetype, "'"), con)[[1]]
     }
   }
   return(invisible(register))
diff --git a/modules/data.atmosphere/R/robustly.R b/modules/data.atmosphere/R/robustly.R
new file mode 100644
index 00000000000..d8cddfc3039
--- /dev/null
+++ b/modules/data.atmosphere/R/robustly.R
@@ -0,0 +1,32 @@
+#' Adverb to try calling a function `n` times before giving up
+#'
+#' @param .f Function to call.
+#' @param n Number of attempts to try
+#' @param timeout Timeout between attempts, in seconds
+#' @param silent Silence error messages?
+#' @return Modified version of input function
+#' @examples
+#' rlog <- robustly(log, timeout = 0.3)
+#' try(rlog("fail"))
+#' \dontrun{
+#'  nc_openr <- robustly(ncdf4::nc_open, n = 10, timeout = 0.5)
+#'  nc <- nc_openr(url)
+#'  # ...or just call the function directly
+#'  nc <- robustly(ncdf4::nc_open, n = 20)(url)
+#'  # Useful in `purrr` maps
+#'  many_vars <- purrr::map(varnames, robustly(ncdf4::ncvar_get), nc = nc)
+#' }
+#' @export
+robustly <- function(.f, n = 10, timeout = 0.2, silent = TRUE) {
+  .f <- purrr::as_mapper(.f)
+  function(...) {
+    attempt <- 1
+    while (attempt <= n) {
+      result <- try(.f(...), silent = silent)
+      if (!inherits(result, "try-error")) return(result)
+      attempt <- attempt + 1
+      if (!silent) PEcAn.logger::logger.info("Trying attempt ", attempt, " of ", n)
+    }
+    PEcAn.logger::logger.severe("Failed after", n, "attempts.")
+  }
+}
diff --git a/modules/data.atmosphere/R/site.lst.R b/modules/data.atmosphere/R/site.lst.R
index 6ab380b3e03..5ff3cfb733c 100644
--- a/modules/data.atmosphere/R/site.lst.R
+++ b/modules/data.atmosphere/R/site.lst.R
@@ -7,8 +7,6 @@
 ##' @param con
 ##' @author Betsy Cowdery
 site.lst <- function(site.id, con) {
-  library(geonames)
-  
   time.zone <- PEcAn.DB::db.query(paste("SELECT time_zone from SITES where id =", site.id), con)
 
   if (!is.na(time.zone) && !is.na(as.character(time.zone))) {
@@ -16,8 +14,10 @@ site.lst <- function(site.id, con) {
   } else {
     site <- PEcAn.DB::db.query(paste("SELECT ST_X(ST_CENTROID(geometry)) AS lon, ST_Y(ST_CENTROID(geometry)) AS lat",
       "FROM sites WHERE id =", site.id), con)
-    options(geonamesUsername = "carya")
-    lst <- GNtimezone(site$lat, site$lon, radius = 0)$gmtOffset
+    if (is.null(getOption("geonamesUsername"))) {
+      options(geonamesUsername = "carya")
+    }
+    lst <- geonames::GNtimezone(site$lat, site$lon, radius = 0)$gmtOffset
   }
   return(lst)
 } # site.lst
diff --git a/modules/data.atmosphere/R/spin.met.R b/modules/data.atmosphere/R/spin.met.R
index 64b24e7f69a..14bde6b6594 100644
--- a/modules/data.atmosphere/R/spin.met.R
+++ b/modules/data.atmosphere/R/spin.met.R
@@ -31,7 +31,10 @@
 #' \dontrun{
 #' if(!is.null(spin)){
 #'    ## if spinning up, extend processed met by resampling or cycling met
-#'    start_date <- PEcAn.data.atmosphere::spin.met(in.path,in.prefix,start_date,end_date,nyear,nsample,resample)
+#'    start_date <- PEcAn.data.atmosphere::spin.met(
+#'      in.path, in.prefix,
+#'      start_date, end_date,
+#'      nyear, nsample, resample)
 #' }
 #' }
 spin.met <- function(in.path, in.prefix, start_date, end_date, nyear = 1000, nsample = 50, resample = TRUE, run_start_date = start_date, overwrite = TRUE){
diff --git a/modules/data.atmosphere/R/split_wind.R b/modules/data.atmosphere/R/split_wind.R
index b6cca061f83..1aecec66186 100644
--- a/modules/data.atmosphere/R/split_wind.R
+++ b/modules/data.atmosphere/R/split_wind.R
@@ -4,8 +4,8 @@
 #' @param in.prefix   prefix of original data
 #' @param start_date  
 #' @param end_date 
-#' @param overwrite 
-#' @param verbose 
+#' @param overwrite logical: replace output file if it already exists? 
+#' @param verbose logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}} functions print debugging information as they run? 
 #' @param ... other arguments, currently ignored
 #'
 #' @return
@@ -69,7 +69,7 @@ split_wind <- function(in.path, in.prefix, start_date, end_date,
     wind_speed.attr <- ncdf4::ncatt_get(nc, "wind_speed")
     WD <- "wind_direction" %in% names(nc$var)
     if(WD){
-      wind_dir <- pi/2 - udunits2::ud_convert(ncdf4::ncvar_get(nc, "wind_direction"), wind_dir$units, "radians")
+      wind_dir <- pi/2 - udunits2::ud.convert(ncdf4::ncvar_get(nc, "wind_direction"), wind_dir$units, "radians")
       wind_dir.attr <- ncdf4::ncatt_get(nc, "wind_direction")
       east <- wind_speed*cos(wind_dir)
       north <- wind_speed*sin(wind_dir)
diff --git a/modules/data.atmosphere/R/tdm_generate_subdaily_models.R b/modules/data.atmosphere/R/tdm_generate_subdaily_models.R
index 494b8ab43e7..18d84b798ef 100644
--- a/modules/data.atmosphere/R/tdm_generate_subdaily_models.R
+++ b/modules/data.atmosphere/R/tdm_generate_subdaily_models.R
@@ -33,8 +33,8 @@
 ##'                     specific hours coefficients. Must be integer because we want statistics from the same time of day
 ##'                     for each day surrounding the model day
 ##' @param seed - seed for randomization to allow for reproducible results                    
-##' @param overwrite
-##' @param verbose
+##' @param overwrite logical: replace output file if it already exists?
+##' @param verbose logical, currently ignored
 ##' @param print.progress - print progress bar? (gets passed through)
 ##' @export
 # -----------------------------------
@@ -48,7 +48,7 @@ gen.subdaily.models <- function(outfolder, path.train, yrs.train, direction.filt
     verbose = FALSE, print.progress=FALSE) {
   
     # pb.index <- 1
-    # pb <- txtProgressBar(min = 1, max = 8, style = 3)
+    # pb <- utils::txtProgressBar(min = 1, max = 8, style = 3)
     
     # Just in case we have a capitalization or singular/plural issue 
     if(direction.filter %in% toupper( c("backward", "backwards"))) direction.filter="backward"
diff --git a/modules/data.atmosphere/R/tdm_lm_ensemble_sims.R b/modules/data.atmosphere/R/tdm_lm_ensemble_sims.R
index 2d953244767..fc9108a8f62 100644
--- a/modules/data.atmosphere/R/tdm_lm_ensemble_sims.R
+++ b/modules/data.atmosphere/R/tdm_lm_ensemble_sims.R
@@ -72,8 +72,8 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
   # # Set progress bar
   if(print.progress==TRUE){
     pb.index <- 1
-    pb <- txtProgressBar(min = 1, max = length(vars.list)*length(days.sim), style = 3)
-    setTxtProgressBar(pb, pb.index)
+    pb <- utils::txtProgressBar(min = 1, max = length(vars.list)*length(days.sim), style = 3)
+    utils::setTxtProgressBar(pb, pb.index)
   }
   
   # Figure out if we need to extract the approrpiate
@@ -145,11 +145,11 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
         
         # dat.temp <- merge(dat.temp, data.frame(ens=paste0("X", 1:n.ens)))
         if (i == 1) {
-          sim.lag <- stack(lags.init[[v]])
+          sim.lag <- utils::stack(lags.init[[v]])
           names(sim.lag) <- c(paste0("lag.", v), "ens")
           
         } else {
-          sim.lag <- stack(data.frame(array(0,dim = c(1, ncol(dat.sim[[v]])))))
+          sim.lag <- utils::stack(data.frame(array(0,dim = c(1, ncol(dat.sim[[v]])))))
           names(sim.lag) <- c(paste0("lag.", v), "ens")
         }
         dat.temp <- merge(dat.temp, sim.lag, all.x = TRUE)
@@ -159,18 +159,18 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
         
         # Set up the lags
         if (i == 1) { # First time through, so pull from our inital lags
-          sim.lag <- stack(lags.init$air_temperature)
+          sim.lag <- utils::stack(lags.init$air_temperature)
           names(sim.lag) <- c("lag.air_temperature", "ens")
           
-          sim.lag$lag.air_temperature_min <- stack(lags.init$air_temperature_min)[,1]
-          sim.lag$lag.air_temperature_max <- stack(lags.init$air_temperature_max)[,1]
+          sim.lag$lag.air_temperature_min <- utils::stack(lags.init$air_temperature_min)[,1]
+          sim.lag$lag.air_temperature_max <- utils::stack(lags.init$air_temperature_max)[,1]
         } else {
-          sim.lag <- stack(data.frame(array(dat.sim[["air_temperature"]][dat.mod$sim.day == (days.sim[i-1]) & 
+          sim.lag <- utils::stack(data.frame(array(dat.sim[["air_temperature"]][dat.mod$sim.day == (days.sim[i-1]) &
                                                                            dat.mod$hour == lag.time, ], 
                                             dim = c(1, ncol(dat.sim$air_temperature)))))
           names(sim.lag) <- c("lag.air_temperature", "ens")
-          sim.lag$lag.air_temperature_min <- stack(apply(dat.sim[["air_temperature"]][dat.mod$sim.day == days.sim[i-1], ], 2, min))[, 1]
-          sim.lag$lag.air_temperature_max <- stack(apply(dat.sim[["air_temperature"]][dat.mod$sim.day == days.sim[i-1], ], 2, max))[, 1]
+          sim.lag$lag.air_temperature_min <- utils::stack(apply(dat.sim[["air_temperature"]][dat.mod$sim.day == days.sim[i-1], ], 2, min))[, 1]
+          sim.lag$lag.air_temperature_max <- utils::stack(apply(dat.sim[["air_temperature"]][dat.mod$sim.day == days.sim[i-1], ], 2, max))[, 1]
         }
         dat.temp <- merge(dat.temp, sim.lag, all.x = TRUE)
       } else if (v == "precipitation_flux") {
@@ -184,11 +184,11 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
         # Set up the lags This is repeated differently because Precipitation
         # dat.temp is merged
         if (i == 1) {
-          sim.lag <- stack(lags.init[[v]])
+          sim.lag <- utils::stack(lags.init[[v]])
           names(sim.lag) <- c(paste0("lag.", v), "ens")
           
         } else {
-          sim.lag <- stack(data.frame(array(dat.sim[[v]][dat.mod$sim.day == days.sim[i-1] & 
+          sim.lag <- utils::stack(data.frame(array(dat.sim[[v]][dat.mod$sim.day == days.sim[i-1] &
                                                            dat.mod$hour == lag.time, ], 
                                             dim = c(1, ncol(dat.sim[[v]])))))
           names(sim.lag) <- c(paste0("lag.", v), "ens")
@@ -200,11 +200,11 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
         dat.temp <- dat.mod[rows.now, dat.info]
         
         if (i == 1) {
-          sim.lag <- stack(lags.init[[v]])
+          sim.lag <- utils::stack(lags.init[[v]])
           names(sim.lag) <- c(paste0("lag.", v), "ens")
           
         } else {
-          sim.lag <- stack(data.frame(array(dat.sim[[v]][dat.mod$sim.day == days.sim[i-1] & 
+          sim.lag <- utils::stack(data.frame(array(dat.sim[[v]][dat.mod$sim.day == days.sim[i-1] &
                                                            dat.mod$hour == lag.time, ], 
                                             dim = c(1, ncol(dat.sim[[v]])))))
           names(sim.lag) <- c(paste0("lag.", v), "ens")
@@ -235,7 +235,7 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
         # rows.beta[i] <- betas.tem
       # }
       # rows.beta <- as.numeric(rows.beta)
-      n.new <- round(n.ens/2)+1
+      n.new <- n.ens
       cols.redo <- 1:n.new
       sane.attempt=0
       betas_nc <- ncdf4::nc_open(file.path(path.model, v, paste0("betas_", v, "_", day.now, ".nc")))
@@ -249,7 +249,7 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
         
         # If we're starting from scratch, set up the prediction matrix
         if(sane.attempt==0){
-          dat.pred <- matrix(nrow=nrow(dat.temp), ncol=n.new)
+          dat.pred <- matrix(nrow=nrow(dat.temp), ncol=n.ens)
         }
         
         dat.pred[,cols.redo] <- subdaily_pred(newdata = dat.temp, model.predict = mod.save, 
@@ -309,21 +309,21 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
           } else {
             rows.filter <- which(dat.mod$sim.day <= days.sim[i] & dat.mod$sim.day >= days.sim[i]-14)
           }
-          dat.filter <- stack(dat.sim[[v]][rows.filter,])[,1]
+          dat.filter <- utils::stack(dat.sim[[v]][rows.filter,])[,1]
           
           filter.mean <- mean(dat.filter, na.rm=T) 
           filter.sd   <- sd(dat.filter, na.rm=T) 
         } else {
           
           if(v %in% vars.sqrt){
-            filter.mean <- mean(c(dat.pred^2, stack(dat.sim[[v]])[,1]), na.rm=T) 
-            filter.sd   <- sd(c(dat.pred^2, stack(dat.sim[[v]])[,1]), na.rm=T)
+            filter.mean <- mean(c(dat.pred^2, utils::stack(dat.sim[[v]])[,1]), na.rm=T)
+            filter.sd   <- sd(c(dat.pred^2, utils::stack(dat.sim[[v]])[,1]), na.rm=T)
           } else if(v %in% vars.log){
-            filter.mean <- mean(c(exp(dat.pred), stack(dat.sim[[v]])[,1]), na.rm=T)
-            filter.sd   <- sd(c(exp(dat.pred), stack(dat.sim[[v]])[,1]), na.rm=T)
+            filter.mean <- mean(c(exp(dat.pred), utils::stack(dat.sim[[v]])[,1]), na.rm=T)
+            filter.sd   <- sd(c(exp(dat.pred), utils::stack(dat.sim[[v]])[,1]), na.rm=T)
           } else {
-            filter.mean <- mean(c(dat.pred, stack(dat.sim[[v]])[,1]), na.rm=T) 
-            filter.sd   <- sd(c(dat.pred, stack(dat.sim[[v]])[,1]), na.rm=T) 
+            filter.mean <- mean(c(dat.pred, utils::stack(dat.sim[[v]])[,1]), na.rm=T)
+            filter.sd   <- sd(c(dat.pred, utils::stack(dat.sim[[v]])[,1]), na.rm=T)
           }
         }
         
@@ -408,7 +408,7 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
       # If we ran out of attempts, but want to foce sanity, do so now
       if(force.sanity & n.new>0){
         # If we're still struggling, but we have at least some workable columns, lets just duplicate those:
-        if(n.new<(round(n.ens/2)+1)){
+        if(n.new<n.ens){
           cols.safe <- 1:ncol(dat.pred)
           cols.safe <- cols.safe[!(cols.safe %in% cols.redo)]
           dat.pred[,cols.redo] <- dat.pred[,sample(cols.safe, n.new, replace=T)]
@@ -570,7 +570,7 @@ lm_ensemble_sims <- function(dat.mod, n.ens, path.model, direction.filter, lags.
       rm(mod.save)  # Clear out the model to save memory
 
       if(print.progress==TRUE){
-        setTxtProgressBar(pb, pb.index)
+        utils::setTxtProgressBar(pb, pb.index)
         pb.index <- pb.index + 1
       }
       
diff --git a/modules/data.atmosphere/R/tdm_predict_subdaily_met.R b/modules/data.atmosphere/R/tdm_predict_subdaily_met.R
index ce787bd2509..9f4da154249 100644
--- a/modules/data.atmosphere/R/tdm_predict_subdaily_met.R
+++ b/modules/data.atmosphere/R/tdm_predict_subdaily_met.R
@@ -32,8 +32,8 @@
 ##' @param resids - logical stating whether to pass on residual data or not
 ##' @param force.sanity - (logical) do we force the data to meet sanity checks?                             
 ##' @param sanity.tries - how many time should we try to predict a reasonable value before giving up?  We don't want to end up in an infinite loop
-##' @param overwrite
-##' @param verbose
+##' @param overwrite logical: replace output file if it already exists?
+##' @param verbose logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}} functions print debugging information as they run?
 ##' @param print.progress - print the progress bar?
 ##' @param seed - manually set seed for results to be reproducible
 ##' @export
@@ -60,7 +60,7 @@ predict_subdaily_met <- function(outfolder, in.path, in.prefix, path.train, dire
   
   if(direction.filter %in% toupper( c("backward", "backwards"))) direction.filter="backward"
   
-  if(!tolower(direction.filter) %in% c("backward", "forward", "backwards", "forwards")) logger.severe("Invalid direction.filter")
+  if(!tolower(direction.filter) %in% c("backward", "forward", "backwards", "forwards")) PEcAn.logger::logger.severe("Invalid direction.filter")
   
   vars.hour <- c("air_temperature", "precipitation_flux", "surface_downwelling_shortwave_flux_in_air", 
                  "surface_downwelling_longwave_flux_in_air", "air_pressure", "specific_humidity", 
@@ -179,8 +179,8 @@ predict_subdaily_met <- function(outfolder, in.path, in.prefix, path.train, dire
   # ----------------------------------
   # Set progress bar
   # pb.index <- 1
-  if(print.progress==TRUE) pb <- txtProgressBar(min = 0, max = length(yrs.tdm), style = 3)
-  # setTxtProgressBar(pb, pb.index)
+  if(print.progress==TRUE) pb <- utils::txtProgressBar(min = 0, max = length(yrs.tdm), style = 3)
+  # utils::setTxtProgressBar(pb, pb.index)
 
   for (y in 1:length(yrs.tdm)) {
     yr.train <- ifelse(lubridate::leap_year(yrs.tdm[y]), train.leap, train.nl)
@@ -228,7 +228,7 @@ predict_subdaily_met <- function(outfolder, in.path, in.prefix, path.train, dire
       
       lags.init[["air_temperature"]] <- data.frame(array(mean(met.out$dat.source$air_temperature_maximum[lag.use], met.out$dat.source$air_temperature_minimum[lag.use]), dim=c(1, n.ens)))
       lags.init[["air_temperature_min"]] <- data.frame(array(met.out$dat.source$air_temperature_minimum[lag.use], dim=c(1, n.ens)))
-      lags.init[["air_temperature_max"]] <- data.frame(array(met.out$dat.source$air_temperature_minimum[lag.use], dim=c(1, n.ens)))
+      lags.init[["air_temperature_max"]] <- data.frame(array(met.out$dat.source$air_temperature_maximum[lag.use], dim=c(1, n.ens)))
       for(v in vars.hour[2:length(vars.hour)]){
         lags.init[[v]] <- data.frame(array(met.out$dat.source[[v]][lag.use], dim=c(1,n.ens)))
       }
@@ -377,7 +377,7 @@ predict_subdaily_met <- function(outfolder, in.path, in.prefix, path.train, dire
         }
         ncdf4::nc_close(loc)
     } # End writing ensemble members 
-    if(print.progress==TRUE) setTxtProgressBar(pb, y)
+    if(print.progress==TRUE) utils::setTxtProgressBar(pb, y)
     # print(paste0("finished year ", yrs.tdm[y]))
     # -----------------------------------
     
diff --git a/modules/data.atmosphere/R/tdm_temporal_downscale_functions.R b/modules/data.atmosphere/R/tdm_temporal_downscale_functions.R
index 4da3de95a38..eaa013d1b3a 100644
--- a/modules/data.atmosphere/R/tdm_temporal_downscale_functions.R
+++ b/modules/data.atmosphere/R/tdm_temporal_downscale_functions.R
@@ -19,7 +19,6 @@
 # -----------------------------------
 ##' @param dat.train - training data generated by tdm_nc2dat.train.R
 ##' @param n.beta - number of betas to generate
-##' @param path.out - path to where the training models & betas will be stored
 ##' @param resids - whether or not to propogate residuals, set to FALSE
 ##' @param parallel - whether or not to run in parallel. this is a feature
 ##'                   still being worked on, set to FALSE
@@ -27,7 +26,7 @@
 ##' @param day.window - number of days surrounding current day we want to pull
 ##'                     statistics from
 ##' @param seed - allows this to be reproducible
-##' @param outfoulder = where the output should be stored
+##' @param outfolder = where the output should be stored
 ##' @param print.progress - print progress of model generation?
 ##' @export
 # -----------------------------------
@@ -39,8 +38,8 @@ temporal.downscale.functions <- function(dat.train, n.beta, day.window,
     
     if(print.progress==TRUE){
       pb.index <- 1
-      pb <- txtProgressBar(min = 1, max = 8, style = 3)
-      setTxtProgressBar(pb, pb.index)
+      pb <- utils::txtProgressBar(min = 1, max = 8, style = 3)
+      utils::setTxtProgressBar(pb, pb.index)
     }
     # Declare the variables of interest that will be called in the
     # overarching loop
@@ -224,7 +223,7 @@ temporal.downscale.functions <- function(dat.train, n.beta, day.window,
 
         if(print.progress==TRUE){
           pb.index <- pb.index + 1
-          setTxtProgressBar(pb, pb.index)
+          utils::setTxtProgressBar(pb, pb.index)
         }
     }  # end of the variable for loop
     
diff --git a/modules/data.atmosphere/R/temporal.downscaling.R b/modules/data.atmosphere/R/temporal.downscaling.R
index 96f8d97f649..27bebddbeea 100644
--- a/modules/data.atmosphere/R/temporal.downscaling.R
+++ b/modules/data.atmosphere/R/temporal.downscaling.R
@@ -10,7 +10,6 @@
 ##' @export
 ##' @author David LeBauer
 cfmet.downscale.time <- cruncep_hourly <- function(cfmet, output.dt = 1, lat = lat, ...) {
-  library(data.table)
   ## time step
   dt_hr <- as.numeric(round(difftime(cfmet$date[2], cfmet$date[1],  units = "hours")))
 
@@ -35,7 +34,7 @@ cfmet.downscale.time <- cruncep_hourly <- function(cfmet, output.dt = 1, lat = l
 
   if (dt_hr == 24) {
     if (all(c("tmax", "tmin") %in% colnames(cfmet))) {
-      setnames(cfmet, c("tmax", "tmin"), c("air_temperature_max", "air_temperature_min"))
+      data.table::setnames(cfmet, c("tmax", "tmin"), c("air_temperature_max", "air_temperature_min"))
     }
     downscaled.result <- cfmet.downscale.daily(dailymet = cfmet, output.dt = output.dt, lat = lat)
   } else if (dt_hr > 24) {
@@ -92,7 +91,7 @@ cfmet.downscale.subdaily <- function(subdailymet, output.dt = 1) {
       hrscale <- ifelse(var %in% c("surface_downwelling_shortwave_flux_in_air", "precipitation_flux"), 
                         output.dt, 1)
 
-      f <- splinefun(as.double(subdailymet$date), (subdailymet[[var]] / hrscale), method = "monoH.FC")
+      f <- stats::splinefun(as.double(subdailymet$date), (subdailymet[[var]] / hrscale), method = "monoH.FC")
       downscaled.result[[var]] <- f(as.double(new.date$date))
       downscaled.result[[var]][downscaled.result[[var]] < 0] <- 0
       if (var == "relative_humidity") {
@@ -101,7 +100,7 @@ cfmet.downscale.subdaily <- function(subdailymet, output.dt = 1) {
     }
   }
 
-  downscaled.result <- cbind(new.date, as.data.table(downscaled.result))
+  downscaled.result <- cbind(new.date, data.table::as.data.table(downscaled.result))
 } # cfmet.downscale.subdaily
 
 
@@ -123,10 +122,10 @@ cfmet.downscale.daily <- function(dailymet, output.dt = 1, lat) {
   tint <- 24/output.dt
   tseq <- 0:(23 * output.dt)/output.dt
   
-  setkeyv(dailymet, c("year", "doy"))
+  data.table::setkeyv(dailymet, c("year", "doy"))
   
   if (all(c("air_temperature_max", "air_temperature_min") %in% colnames(dailymet))) {
-    setnames(dailymet, c("air_temperature_max", "air_temperature_min"), c("tmax", "tmin"))
+    data.table::setnames(dailymet, c("air_temperature_max", "air_temperature_min"), c("tmax", "tmin"))
   }
   
   light <- dailymet[, lightME(DOY = doy, t.d = tseq, lat = lat), by = c("year", "doy")]
@@ -144,7 +143,7 @@ cfmet.downscale.daily <- function(dailymet, output.dt = 1, lat) {
   
   ## Relative Humidity
   RH <- dailymet[, list(RH = rep(relative_humidity, each = tint), hour = tseq), by = "year,doy"]
-  setkeyv(RH, c("year", "doy", "hour"))
+  data.table::setkeyv(RH, c("year", "doy", "hour"))
   
   # if(!'air_pressure' %in% colnames(dailymet)) air_pressure <-
   qair <- dailymet[, list(year, doy, tmin, tmax, air_pressure, air_temperature, qmin = rh2qair(rh = relative_humidity/100, 
@@ -177,7 +176,7 @@ cfmet.downscale.daily <- function(dailymet, output.dt = 1, lat) {
   ## Hour
   time <- dailymet[, list(hour = tseq), by = c("year", "doy")]
   
-  ans <- data.table(time, downwelling_photosynthetic_photon_flux = SolarR, air_temperature = udunits2::ud.convert(Temp, 
+  ans <- data.table::data.table(time, downwelling_photosynthetic_photon_flux = SolarR, air_temperature = udunits2::ud.convert(Temp, 
                                                                                                         "kelvin", "celsius"), relative_humidity = RH, wind = wind_speed, precipitation_flux = precip)
   return(ans)
 } # cfmet.downscale.daily
diff --git a/modules/data.atmosphere/R/upscale_met.R b/modules/data.atmosphere/R/upscale_met.R
index f44202c92a6..891b711a2a0 100644
--- a/modules/data.atmosphere/R/upscale_met.R
+++ b/modules/data.atmosphere/R/upscale_met.R
@@ -28,7 +28,7 @@ upscale_met <- function(outfolder, input_met, resolution = 1/24, overwrite = FAL
    PEcAn.logger::logger.severe("Output file", loc.file, "already exists. To replace it, set overwrite = TRUE")
   }
 
-  met_lookup <- read.csv(system.file("/data/met.lookup.csv", package = "PEcAn.data.atmosphere"),
+  met_lookup <- utils::read.csv(system.file("/data/met.lookup.csv", package = "PEcAn.data.atmosphere"),
                          header = TRUE, stringsAsFactors = FALSE)
   tem <- ncdf4::nc_open(input_met)
   dim <- tem$dim
diff --git a/modules/data.atmosphere/README.md b/modules/data.atmosphere/README.md
index 49188afcda1..0bbc556c844 100644
--- a/modules/data.atmosphere/README.md
+++ b/modules/data.atmosphere/README.md
@@ -10,6 +10,7 @@ Current list of input meteorological formats supported, functions are named `dow
 * Ameriflux
 * FACE
 * ALMA
+* NOAA GEFS
 * arbitrary csv files 
 
 
diff --git a/modules/data.atmosphere/data/narr_cruncep_ebifarm.RData b/modules/data.atmosphere/data/narr_cruncep_ebifarm.RData
index 95d9e9900c2..151896a703b 100644
Binary files a/modules/data.atmosphere/data/narr_cruncep_ebifarm.RData and b/modules/data.atmosphere/data/narr_cruncep_ebifarm.RData differ
diff --git a/modules/data.atmosphere/inst/registration/register.NOAA_GEFS.xml b/modules/data.atmosphere/inst/registration/register.NOAA_GEFS.xml
new file mode 100644
index 00000000000..a6eccef2ec0
--- /dev/null
+++ b/modules/data.atmosphere/inst/registration/register.NOAA_GEFS.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<NOAA_GEFS>
+  <scale>site</scale>
+  <ensemble>21</ensemble>
+  <forecast>TRUE</forecast>
+  <format>
+    <id>33</id>
+    <name>CF Meteorology</name>
+    <mimetype>application/x-netcdf</mimetype>
+    <inputtype>nc</inputtype>
+  </format>
+</NOAA_GEFS>
diff --git a/modules/data.atmosphere/inst/scripts/runtest-download.NOAA_GEFS.R b/modules/data.atmosphere/inst/scripts/runtest-download.NOAA_GEFS.R
new file mode 100644
index 00000000000..e38d1fe7191
--- /dev/null
+++ b/modules/data.atmosphere/inst/scripts/runtest-download.NOAA_GEFS.R
@@ -0,0 +1,38 @@
+#This program is to test the R script donload.NOAA.R during development.
+#It accepts a command line argument specifying the case test number to run, otherwise, it
+#defaults to the first case.
+
+test_no = 1
+args = commandArgs(trailingOnly = TRUE)
+if (length(args) > 0) {
+  test_no = as.integer(args[1])
+}
+
+devtools::load_all("~/pecan/modules/data.atmosphere/")
+
+##' @param Output directory
+##' @param lattitude of the site in decimal degrees
+##' @param longitude of the site in decimal degrees
+##' @param start date
+##' @param end date
+# Other parameters optional
+
+if (test_no == 1) { #Default case - should work - normal 16 day forecast
+  download.NOAA_GEFS("~/Working/results", lat.in= 45.805925, lon.in = -90.07961, "US-WCr")
+} else if (test_no == 2) { #Should be an Error - date out of bounds
+  download.NOAA_GEFS("~/Working/results", lat.in= 45.805925, lon.in = -90.07961, "US-WCr", Sys.time() - lubridate::days(12), Sys.time(), verbose = FALSE)
+} else if (test_no == 3) { #Should work - normal 16 day forecast
+  download.NOAA_GEFS("~/Working/results", lat.in= 45.805925, lon.in = -90.07961, "US-WCr", Sys.time() - lubridate::days(4), verbose = FALSE)
+} else if (test_no == 4) { #Should work - 1 day's worth of data
+  download.NOAA_GEFS("~/Working/results", llat.in= 45.805925, lon.in = -90.07961, "US-WCr", Sys.time() - lubridate::days(8), Sys.time() - lubridate::days(7),  verbose = FALSE)
+} else if (test_no == 5) { #Should be an error - date out of bounds 
+  download.NOAA_GEFS("~/Working/results", lat.in= 45.805925, lon.in = -90.07961, "US-WCr", Sys.Date() + lubridate::days(1), verbose = FALSE)
+} else if (test_no == 6) { #Should crash - timespan not large enough
+  download.NOAA_GEFS("~/Working/results", lat.in= 45.805925, lon.in = -90.07961, "US-WCr", Sys.time(), Sys.time(), verbose = FALSE)
+} else if (test_no == 7) { #Should work, but have the timespan shrunk by one day.  Output should be identical to default case.
+  download.NOAA_GEFS("~/Working/results", lat.in= 45.805925, lon.in = -90.07961, "US-WCr", Sys.time(), Sys.time() + lubridate::days(17), verbose = FALSE)
+}
+
+
+  
+  
diff --git a/modules/data.atmosphere/inst/scripts/runtests-download.NOAA_GEFS.sh b/modules/data.atmosphere/inst/scripts/runtests-download.NOAA_GEFS.sh
new file mode 100755
index 00000000000..c827fbe1846
--- /dev/null
+++ b/modules/data.atmosphere/inst/scripts/runtests-download.NOAA_GEFS.sh
@@ -0,0 +1,11 @@
+#Automatically runs all 7 test cases in runtest-download.NOAA_GEFS.R and writes the output
+#for each case out to their own separate files.
+#@author Luke Dramko
+
+runnum=1
+while [ $runnum -le 7 ];
+do
+  flname=out$runnum.txt
+  Rscript runtest.R $runnum &> $flname
+  (( runnum++ ))
+done
diff --git a/modules/data.atmosphere/man/align.met.Rd b/modules/data.atmosphere/man/align.met.Rd
index 920acc3ea7d..cd12add545e 100644
--- a/modules/data.atmosphere/man/align.met.Rd
+++ b/modules/data.atmosphere/man/align.met.Rd
@@ -5,8 +5,8 @@
 \title{align.met}
 \usage{
 align.met(train.path, source.path, yrs.train = NULL, yrs.source = NULL,
-  n.ens = NULL, pair.mems = FALSE, mems.train = NULL, seed = Sys.Date(),
-  print.progress = FALSE)
+  n.ens = NULL, pair.mems = FALSE, mems.train = NULL,
+  seed = Sys.Date(), print.progress = FALSE)
 }
 \arguments{
 \item{train.path}{- path to the dataset to be used to downscale the data}
@@ -75,3 +75,4 @@ Other debias - Debias & Align Meteorology Datasets into continuous time series:
 \author{
 Christy Rollinson
 }
+\concept{debias - Debias & Align Meteorology Datasets into continuous time series}
diff --git a/modules/data.atmosphere/man/browndog.met.Rd b/modules/data.atmosphere/man/browndog.met.Rd
index c24f13fd437..b28559ee7b2 100644
--- a/modules/data.atmosphere/man/browndog.met.Rd
+++ b/modules/data.atmosphere/man/browndog.met.Rd
@@ -4,8 +4,8 @@
 \alias{browndog.met}
 \title{get met data from browndog}
 \usage{
-browndog.met(browndog, source, site, start_date, end_date, model, dir, username,
-  con)
+browndog.met(browndog, source, site, start_date, end_date, model, dir,
+  username, con)
 }
 \arguments{
 \item{browndog, }{list with url, username and password to connect to browndog}
diff --git a/modules/data.atmosphere/man/build_cf_variables_table_url.Rd b/modules/data.atmosphere/man/build_cf_variables_table_url.Rd
new file mode 100644
index 00000000000..33e9472f812
--- /dev/null
+++ b/modules/data.atmosphere/man/build_cf_variables_table_url.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_cf_variables_table.R
+\name{build_cf_variables_table_url}
+\alias{build_cf_variables_table_url}
+\title{Construct a URL to a specific version of the CF variables table XML}
+\usage{
+build_cf_variables_table_url(version,
+  url_format_string = "http://cfconventions.org/Data/cf-standard-names/\%d/src/src-cf-standard-name-table.xml")
+}
+\arguments{
+\item{version}{CF variables table version number (integer/numeric)}
+
+\item{url_format_string}{A format string passed to [sprintf]. This
+should contain the entire target URL with the version number
+replaced by `"%d"`, and _no other string substitutions_.}
+}
+\value{
+Complete URL, as a string
+}
+\description{
+This uses [sprintf] to construct the URL with the version number as
+the first argument.
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/check_met_input_file.Rd b/modules/data.atmosphere/man/check_met_input_file.Rd
new file mode 100644
index 00000000000..fa8ff6b6a3c
--- /dev/null
+++ b/modules/data.atmosphere/man/check_met_input_file.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_met_input.R
+\name{check_met_input_file}
+\alias{check_met_input_file}
+\title{Check a meteorology data file for compliance with the PEcAn standard}
+\usage{
+check_met_input_file(metfile, variable_table = pecan_standard_met_table,
+  required_vars = variable_table \%>\% dplyr::filter(is_required) \%>\%
+  dplyr::pull(cf_standard_name), warn_unknown = TRUE)
+}
+\arguments{
+\item{metfile}{Path of met file to check, as a scalar character.}
+
+\item{variable_table}{`data.frame` linking standard names to their
+units. Must contain columns "cf_standard_name" and "units".
+Default is [pecan_standard_met_table].}
+
+\item{required_vars}{Character vector of required variables.
+Defaults to variables marked as required in `variable_table`.}
+
+\item{warn_unknown}{Logical. If `TRUE` (default), throw a warning
+for variables not in `variable_table`. Otherwise, ignore unknown
+variables.}
+}
+\value{
+`data.frame` summarizing the results of the tests.
+}
+\description{
+Check a meteorology data file for compliance with the PEcAn standard
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/check_unit.Rd b/modules/data.atmosphere/man/check_unit.Rd
new file mode 100644
index 00000000000..afb36e9ca78
--- /dev/null
+++ b/modules/data.atmosphere/man/check_unit.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/check_met_input.R
+\name{check_unit}
+\alias{check_unit}
+\title{Check that the unit of a variable in a NetCDF file is equivalent to
+the expected unit.}
+\usage{
+check_unit(variable, nc, variable_table, warn_unknown = TRUE)
+}
+\arguments{
+\item{variable}{Name of target variable, as a length 1 character}
+
+\item{nc}{NetCDF object containing target variable}
+
+\item{variable_table}{`data.frame` linking standard names to their
+units. Must contain columns "cf_standard_name" and "units".
+Default is [pecan_standard_met_table].}
+
+\item{warn_unknown}{Logical. If `TRUE` (default), throw a warning
+for variables not in `variable_table`. Otherwise, ignore unknown
+variables.}
+}
+\value{
+`TRUE` if unit is correct, or `try-error` object if there is a mismatch.
+}
+\description{
+Check that the unit of a variable in a NetCDF file is equivalent to
+the expected unit.
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/col2ncvar.Rd b/modules/data.atmosphere/man/col2ncvar.Rd
new file mode 100644
index 00000000000..ec2738697cf
--- /dev/null
+++ b/modules/data.atmosphere/man/col2ncvar.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{col2ncvar}
+\alias{col2ncvar}
+\title{Create `ncvar` object from variable name}
+\usage{
+col2ncvar(variable, dims)
+}
+\arguments{
+\item{variable}{CF variable name}
+
+\item{dims}{List of NetCDF dimension objects (passed to 
+`ncdf4::ncvar_def(..., dim)`)}
+}
+\value{
+`ncvar` object (from `ncvar_def`)
+}
+\description{
+Create `ncvar` object from variable name
+}
diff --git a/modules/data.atmosphere/man/daygroup.Rd b/modules/data.atmosphere/man/daygroup.Rd
new file mode 100644
index 00000000000..10dab9e98b6
--- /dev/null
+++ b/modules/data.atmosphere/man/daygroup.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{daygroup}
+\alias{daygroup}
+\title{Assign daygroup tag for a given date}
+\usage{
+daygroup(date, flx)
+}
+\description{
+Assign daygroup tag for a given date
+}
diff --git a/modules/data.atmosphere/man/db.site.lat.lon.Rd b/modules/data.atmosphere/man/db.site.lat.lon.Rd
index 670749cd9f9..46aa66c45fd 100644
--- a/modules/data.atmosphere/man/db.site.lat.lon.Rd
+++ b/modules/data.atmosphere/man/db.site.lat.lon.Rd
@@ -6,6 +6,9 @@
 \usage{
 db.site.lat.lon(site.id, con)
 }
+\description{
+db.site.lat.lon
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/data.atmosphere/man/debias.met.regression.Rd b/modules/data.atmosphere/man/debias.met.regression.Rd
index 9b65e781298..2d1d43b2eaa 100644
--- a/modules/data.atmosphere/man/debias.met.regression.Rd
+++ b/modules/data.atmosphere/man/debias.met.regression.Rd
@@ -60,7 +60,10 @@ without having to do do giant runs at once; if NULL will be numbered 1:n.ens}
 
 \item{n.cores}{- (experimental) how many cores to use in parallelization *Not implemented yet}
 
-\item{overwrite}{- overwrite existing files?}
+\item{overwrite}{- overwrite existing files? Currently ignored}
+
+\item{verbose}{logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}}
+functions print debugging information as they run?}
 }
 \description{
 This script debiases one dataset (e.g. GCM, re-analysis product) given another higher 
@@ -77,3 +80,4 @@ Other debias - Debias & Align Meteorology Datasets into continuous time series:
 \author{
 Christy Rollinson
 }
+\concept{debias - Debias & Align Meteorology Datasets into continuous time series}
diff --git a/modules/data.atmosphere/man/debias_met.Rd b/modules/data.atmosphere/man/debias_met.Rd
index 7e5e9bbf147..5a55c51eb74 100644
--- a/modules/data.atmosphere/man/debias_met.Rd
+++ b/modules/data.atmosphere/man/debias_met.Rd
@@ -5,8 +5,8 @@
 \alias{debias.met}
 \title{debias_met}
 \usage{
-debias.met(outfolder, input_met, train_met, site_id, de_method = "linear",
-  overwrite = FALSE, verbose = FALSE, ...)
+debias.met(outfolder, input_met, train_met, site_id,
+  de_method = "linear", overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
 \item{input_met}{- the source_met dataset that will be altered by the training dataset in NC format.}
@@ -14,6 +14,11 @@ debias.met(outfolder, input_met, train_met, site_id, de_method = "linear",
 \item{train_met}{- the observed dataset that will be used to train the modeled dataset in NC format}
 
 \item{de_method}{- select which debias method you would like to use, options are 'normal', 'linear regression'}
+
+\item{overwrite}{logical: replace output file if it already exists? Currently ignored.}
+
+\item{verbose}{logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}}
+functions print debugging information as they run?}
 }
 \description{
 debias.met takes input_met and debiases it based on statistics from a train_met dataset
diff --git a/modules/data.atmosphere/man/download.Ameriflux.Rd b/modules/data.atmosphere/man/download.Ameriflux.Rd
index e97d1b2cd38..8c9505436c8 100644
--- a/modules/data.atmosphere/man/download.Ameriflux.Rd
+++ b/modules/data.atmosphere/man/download.Ameriflux.Rd
@@ -8,6 +8,9 @@ download.Ameriflux(sitename, outfolder, start_date, end_date,
   overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
+\item{sitename}{the FLUXNET ID of the site to be downloaded, used as file name prefix. 
+The 'SITE_ID' field in \href{http://ameriflux.lbl.gov/sites/site-list-and-pages/}{list of Ameriflux sites}}
+
 \item{outfolder}{location on disk where outputs will be stored}
 
 \item{start_date}{the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)}
@@ -17,9 +20,6 @@ download.Ameriflux(sitename, outfolder, start_date, end_date,
 \item{overwrite}{should existing files be overwritten}
 
 \item{verbose}{should the function be very verbose}
-
-\item{site}{the FLUXNET ID of the site to be downloaded, used as file name prefix. 
-The 'SITE_ID' field in \href{http://ameriflux.lbl.gov/sites/site-list-and-pages/}{list of Ameriflux sites}}
 }
 \description{
 Download Ameriflux L2 netCDF files
diff --git a/modules/data.atmosphere/man/download.AmerifluxLBL.Rd b/modules/data.atmosphere/man/download.AmerifluxLBL.Rd
index 271f675a8cb..95156f4dbb5 100644
--- a/modules/data.atmosphere/man/download.AmerifluxLBL.Rd
+++ b/modules/data.atmosphere/man/download.AmerifluxLBL.Rd
@@ -5,9 +5,13 @@
 \title{Download Ameriflux LBL CSV files}
 \usage{
 download.AmerifluxLBL(sitename, outfolder, start_date, end_date,
-  overwrite = FALSE, verbose = FALSE, username = "pecan", method, ...)
+  overwrite = FALSE, verbose = FALSE, username = "pecan", method,
+  ...)
 }
 \arguments{
+\item{sitename}{the Ameriflux ID of the site to be downloaded, used as file name prefix. 
+The 'SITE_ID' field in \href{http://ameriflux.lbl.gov/sites/site-list-and-pages/}{list of Ameriflux sites}}
+
 \item{outfolder}{location on disk where outputs will be stored}
 
 \item{start_date}{the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)}
@@ -21,9 +25,6 @@ download.AmerifluxLBL(sitename, outfolder, start_date, end_date,
 \item{username}{Ameriflux username}
 
 \item{method}{Optional. download.file() function option.  Use this to set custom programs such as ncftp}
-
-\item{site}{the Ameriflux ID of the site to be downloaded, used as file name prefix. 
-The 'SITE_ID' field in \href{http://ameriflux.lbl.gov/sites/site-list-and-pages/}{list of Ameriflux sites}}
 }
 \description{
 download.AmerifluxLBL
@@ -32,7 +33,9 @@ download.AmerifluxLBL
 Uses Ameirflux LBL JSON API to download met data from Ameriflux towers in CSV format
 }
 \examples{
+\dontrun{
 result <- download.AmerifluxLBL("US-Akn","~/","2011-01-01","2011-12-31",overwrite=TRUE)
+}
 
 }
 \author{
diff --git a/modules/data.atmosphere/man/download.CRUNCEP.Rd b/modules/data.atmosphere/man/download.CRUNCEP.Rd
index 4fde088fa2f..242dda78059 100644
--- a/modules/data.atmosphere/man/download.CRUNCEP.Rd
+++ b/modules/data.atmosphere/man/download.CRUNCEP.Rd
@@ -5,7 +5,8 @@
 \title{Download CRUNCEP data}
 \usage{
 download.CRUNCEP(outfolder, start_date, end_date, site_id, lat.in, lon.in,
-  overwrite = FALSE, verbose = FALSE, maxErrors = 10, sleep = 2, ...)
+  overwrite = FALSE, verbose = FALSE, maxErrors = 10, sleep = 2,
+  ...)
 }
 \arguments{
 \item{outfolder}{Directory where results should be written}
diff --git a/modules/data.atmosphere/man/download.FACE.Rd b/modules/data.atmosphere/man/download.FACE.Rd
index a231dac29c1..95314e14b58 100644
--- a/modules/data.atmosphere/man/download.FACE.Rd
+++ b/modules/data.atmosphere/man/download.FACE.Rd
@@ -4,8 +4,8 @@
 \alias{download.FACE}
 \title{download.FACE}
 \usage{
-download.FACE(sitename, outfolder, start_date, end_date, overwrite = FALSE,
-  method, ...)
+download.FACE(sitename, outfolder, start_date, end_date,
+  overwrite = FALSE, method, ...)
 }
 \arguments{
 \item{method}{Optional. Passed to download.file() function.  Use this to set custom programs such as ncftp to use when
diff --git a/modules/data.atmosphere/man/download.Fluxnet2015.Rd b/modules/data.atmosphere/man/download.Fluxnet2015.Rd
index f4f220c8ff8..6a3e73897c3 100644
--- a/modules/data.atmosphere/man/download.Fluxnet2015.Rd
+++ b/modules/data.atmosphere/man/download.Fluxnet2015.Rd
@@ -8,6 +8,9 @@ download.Fluxnet2015(sitename, outfolder, start_date, end_date,
   overwrite = FALSE, verbose = FALSE, username = "pecan", ...)
 }
 \arguments{
+\item{sitename}{the FLUXNET ID of the site to be downloaded, used as file name prefix. 
+The 'SITE_ID' field in \href{http://fluxnet.fluxdata.org//sites/site-list-and-pages/}{list of Ameriflux sites}}
+
 \item{outfolder}{location on disk where outputs will be stored}
 
 \item{start_date}{the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)}
@@ -17,9 +20,6 @@ download.Fluxnet2015(sitename, outfolder, start_date, end_date,
 \item{overwrite}{should existing files be overwritten}
 
 \item{verbose}{should the function be very verbose}
-
-\item{site}{the FLUXNET ID of the site to be downloaded, used as file name prefix. 
-The 'SITE_ID' field in \href{http://fluxnet.fluxdata.org//sites/site-list-and-pages/}{list of Ameriflux sites}}
 }
 \description{
 Download Fluxnet 2015 CSV files
diff --git a/modules/data.atmosphere/man/download.GFDL.Rd b/modules/data.atmosphere/man/download.GFDL.Rd
index acbb12fc682..1571b8cce64 100644
--- a/modules/data.atmosphere/man/download.GFDL.Rd
+++ b/modules/data.atmosphere/man/download.GFDL.Rd
@@ -2,22 +2,38 @@
 % Please edit documentation in R/download.GFDL.R
 \name{download.GFDL}
 \alias{download.GFDL}
-\title{download.GFDL}
+\title{Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CF}
 \usage{
-download.GFDL(outfolder, start_date, end_date, site_id, lat.in, lon.in,
-  overwrite = FALSE, verbose = FALSE, model = "CM3", scenario = "rcp45",
-  ensemble_member = "r1i1p1", ...)
+download.GFDL(outfolder, start_date, end_date, lat.in, lon.in,
+  overwrite = FALSE, verbose = FALSE, model = "CM3",
+  scenario = "rcp45", ensemble_member = "r1i1p1", ...)
 }
 \arguments{
-\item{model}{, select which GFDL model to run (options are CM3, ESM2M, ESM2G)}
+\item{outfolder}{Directory for storing output}
 
-\item{scenario}{, select which scenario to run (options are rcp26, rcp45, rcp60, rcp85)}
+\item{start_date}{Start date for met (will be converted via [base::as.POSIXlt])}
 
-\item{ensemble_member}{, select which ensemble_member to initialize the run (options are r1i1p1, r3i1p1, r5i1p1)}
+\item{end_date}{End date for met (will be converted via [base::as.POSIXlt])}
+
+\item{lat.in}{Latitude coordinate for met}
+
+\item{lon.in}{Longitude coordinate for met}
+
+\item{overwrite}{Logical: Download a fresh version even if a local file with
+the same name already exists?}
+
+\item{verbose}{Logical, passed on to \code{\link[ncdf4]{ncvar_def}} and
+\code{\link[ncdf4]{nc_create}} to control printing of debug info}
+
+\item{model}{Which GFDL model to run (options are CM3, ESM2M, ESM2G)}
+
+\item{scenario}{Which scenario to run (options are rcp26, rcp45, rcp60, rcp85)}
+
+\item{ensemble_member}{Which ensemble_member to initialize the run (options are r1i1p1, r3i1p1, r5i1p1)}
 }
 \description{
 Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CF
 }
 \author{
-James Simkins
+James Simkins, Alexey Shiklomanov, Ankur Desai
 }
diff --git a/modules/data.atmosphere/man/download.GLDAS.Rd b/modules/data.atmosphere/man/download.GLDAS.Rd
index 92984267344..243ed301215 100644
--- a/modules/data.atmosphere/man/download.GLDAS.Rd
+++ b/modules/data.atmosphere/man/download.GLDAS.Rd
@@ -8,7 +8,7 @@ download.GLDAS(outfolder, start_date, end_date, site_id, lat.in, lon.in,
   overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
-\item{lon}{}
+\item{lon.in}{}
 }
 \description{
 Download and convert single grid point GLDAS to CF single grid point from hydro1.sci.gsfc.nasa.gov using OPENDAP interface
diff --git a/modules/data.atmosphere/man/download.Geostreams.Rd b/modules/data.atmosphere/man/download.Geostreams.Rd
index 4854cce420f..a8abd76a302 100644
--- a/modules/data.atmosphere/man/download.Geostreams.Rd
+++ b/modules/data.atmosphere/man/download.Geostreams.Rd
@@ -36,7 +36,7 @@ If using `~/.pecan.clowder.xml`, it must be a valid PEcAn-formatted XML settings
  file and must contain a \code{<clowder>} key that specifies hostname, user, and
  password for your Clowder server:
 
-\code{\preformatted{
+\preformatted{
   <?xml version="1.0"?>
   <pecan>
     <clowder>
@@ -45,7 +45,7 @@ If using `~/.pecan.clowder.xml`, it must be a valid PEcAn-formatted XML settings
       <password>superSecretPassw0rd</password>
     </clowder>
   </pecan>
-}}
+}
 }
 \examples{
 \dontrun{
diff --git a/modules/data.atmosphere/man/download.MACA.Rd b/modules/data.atmosphere/man/download.MACA.Rd
index 8f66356b32e..af79da3e75e 100644
--- a/modules/data.atmosphere/man/download.MACA.Rd
+++ b/modules/data.atmosphere/man/download.MACA.Rd
@@ -5,8 +5,9 @@
 \title{download.MACA}
 \usage{
 download.MACA(outfolder, start_date, end_date, site_id, lat.in, lon.in,
-  model = "IPSL-CM5A-LR", scenario = "rcp85", ensemble_member = "r1i1p1",
-  overwrite = FALSE, verbose = FALSE, ...)
+  model = "IPSL-CM5A-LR", scenario = "rcp85",
+  ensemble_member = "r1i1p1", overwrite = FALSE, verbose = FALSE,
+  ...)
 }
 \arguments{
 \item{start_date}{, of the format "YEAR-01-01 00:00:00"}
diff --git a/modules/data.atmosphere/man/download.MsTMIP_NARR.Rd b/modules/data.atmosphere/man/download.MsTMIP_NARR.Rd
index ae48540f5a5..a8362e01340 100644
--- a/modules/data.atmosphere/man/download.MsTMIP_NARR.Rd
+++ b/modules/data.atmosphere/man/download.MsTMIP_NARR.Rd
@@ -4,8 +4,8 @@
 \alias{download.MsTMIP_NARR}
 \title{download.MsTMIP_NARR}
 \usage{
-download.MsTMIP_NARR(outfolder, start_date, end_date, site_id, lat.in, lon.in,
-  overwrite = FALSE, verbose = FALSE, ...)
+download.MsTMIP_NARR(outfolder, start_date, end_date, site_id, lat.in,
+  lon.in, overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
 \item{start_date}{YYYY-MM-DD}
diff --git a/modules/data.atmosphere/man/download.NARR_site.Rd b/modules/data.atmosphere/man/download.NARR_site.Rd
new file mode 100644
index 00000000000..9f3306a002d
--- /dev/null
+++ b/modules/data.atmosphere/man/download.NARR_site.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{download.NARR_site}
+\alias{download.NARR_site}
+\title{Download NARR time series for a single site}
+\usage{
+download.NARR_site(outfolder, start_date, end_date, lat.in, lon.in,
+  overwrite = FALSE, verbose = FALSE, progress = TRUE,
+  parallel = FALSE, ncores = if (parallel) parallel::detectCores() else
+  NULL, ...)
+}
+\arguments{
+\item{outfolder}{Target directory for storing output}
+
+\item{start_date}{Start date for met data}
+
+\item{end_date}{End date for met data}
+
+\item{lat.in}{Site latitude coordinate}
+
+\item{lon.in}{Site longitude coordinate}
+
+\item{overwrite}{Overwrite existing files?  Default=FALSE}
+
+\item{verbose}{Turn on verbose output? Default=FALSE}
+
+\item{parallel}{Download in parallel? Default = TRUE.}
+
+\item{ncores}{Number of cores for parallel download. Default is 
+`parallel::detectCores()`}
+}
+\description{
+Download NARR time series for a single site
+}
+\examples{
+
+\dontrun{
+download.NARR_site(tempdir(), "2001-01-01", "2001-01-12", 43.372, -89.907)
+}
+
+
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/download.NEONmet.Rd b/modules/data.atmosphere/man/download.NEONmet.Rd
index 0a2e68f83e6..743dfe563cc 100644
--- a/modules/data.atmosphere/man/download.NEONmet.Rd
+++ b/modules/data.atmosphere/man/download.NEONmet.Rd
@@ -4,10 +4,13 @@
 \alias{download.NEONmet}
 \title{Download NEON Site Met CSV files}
 \usage{
-download.NEONmet(sitename, outfolder, start_date, end_date, overwrite = FALSE,
-  verbose = FALSE, ...)
+download.NEONmet(sitename, outfolder, start_date, end_date,
+  overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
+\item{sitename}{the NEON ID of the site to be downloaded, used as file name prefix. 
+The 4-letter SITE code  in \href{http://www.neonscience.org/science-design/field-sites/list}{list of NEON sites}}
+
 \item{outfolder}{location on disk where outputs will be stored}
 
 \item{start_date}{the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year and month of the date)}
@@ -17,9 +20,6 @@ download.NEONmet(sitename, outfolder, start_date, end_date, overwrite = FALSE,
 \item{overwrite}{should existing files be overwritten}
 
 \item{verbose}{makes the function output more text}
-
-\item{site}{the NEON ID of the site to be downloaded, used as file name prefix. 
-The 4-letter SITE code  in \href{http://www.neonscience.org/science-design/field-sites/list}{list of NEON sites}}
 }
 \description{
 download.NEONmet
@@ -28,5 +28,7 @@ download.NEONmet
 Uses NEON v0 API to download met data from NEON towers and convert to CF NetCDF
 }
 \examples{
+\dontrun{
 result <- download.NEONmet('HARV','~/','2017-01-01','2017-01-31',overwrite=TRUE)
 }
+}
diff --git a/modules/data.atmosphere/man/download.NOAA_GEFS.Rd b/modules/data.atmosphere/man/download.NOAA_GEFS.Rd
new file mode 100644
index 00000000000..31c2f861778
--- /dev/null
+++ b/modules/data.atmosphere/man/download.NOAA_GEFS.Rd
@@ -0,0 +1,75 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NOAA_GEFS.R
+\name{download.NOAA_GEFS}
+\alias{download.NOAA_GEFS}
+\title{Download NOAA GEFS Weather Data}
+\usage{
+download.NOAA_GEFS(outfolder, lat.in, lon.in, sitename,
+  start_date = Sys.time(), end_date = (as.POSIXct(start_date, tz =
+  "UTC") + lubridate::days(16)), overwrite = FALSE, verbose = FALSE,
+  ...)
+}
+\arguments{
+\item{outfolder}{Directory where results should be written}
+
+\item{sitename}{The unique ID given to each site. This is used as part of the file name.}
+
+\item{start_date, }{end_date Range of dates/times to be downloaded (default assumed time of day is 0:00, midnight)}
+
+\item{overwrite}{logical. Download a fresh version even if a local file with the same name already exists?}
+
+\item{verbose}{logical.  Print additional debug information.  Passed on to functions in the netcdf4 package to provide debugging info.}
+
+\item{...}{Other arguments, currently ignored}
+
+\item{lat}{site latitude in decimal degrees}
+
+\item{lon}{site longitude in decimal degrees}
+}
+\value{
+A list of data frames is returned containing information about the data file that can be used to locate it later.  Each
+data frame contains information about one file.
+}
+\description{
+Download NOAA GEFS Weather Data
+}
+\section{Information on Units}{
+
+Information on NOAA weather units can be found below. Note that the temperature is measured in degrees C, but is converted at the station and downlaoded
+in Kelvin.
+}
+
+\section{NOAA_GEFS General Information}{
+
+This function downloads NOAA GEFS weather data.  GEFS is an ensemble of 21 different weather forecast models.  A 16 day forecast is avaliable
+every 6 hours.  Each forecast includes information on a total of 8 variables.  These are transformed from the NOAA standard to the internal PEcAn
+standard.
+}
+
+\section{Data Avaliability}{
+
+NOAA GEFS weather data is avaliable on a rolling 12 day basis; dates provided in "start_date" must be within this range. The end date can be any point after
+that, but if the end date is beyond 16 days, only 16 days worth of forecast are recorded.  Times are rounded down to the previous 6 hour forecast.  NOAA
+GEFS weather data isn't always posted immediately, and to compensate, this function adjusts requests made in the last two hours
+back two hours (approximately the amount of time it takes to post the data) to make sure the most current forecast is used.
+}
+
+\section{Data Save Format}{
+
+Data is saved in the netcdf format to the specified directory.  File names reflect the precision of the data to the given range of days.
+NOAA.GEFS.willow creek.3.2018-06-08T06:00.2018-06-24T06:00.nc specifies the forecast, using ensemble nubmer 3 at willow creek on
+June 6th, 2018 at 6:00 a.m. to June 24th, 2018 at 6:00 a.m.
+}
+
+\examples{
+\dontrun{
+ download.NOAA_GEFS(outfolder="~/Working/results", lat.in= 45.805925, lon.in = -90.07961, sitename="US-WCr")
+}
+
+}
+\references{
+https://www.ncdc.noaa.gov/crn/measurements.html
+}
+\author{
+Luke Dramko
+}
diff --git a/modules/data.atmosphere/man/download.PalEON.Rd b/modules/data.atmosphere/man/download.PalEON.Rd
index 86a8d967be8..55e27b5cea1 100644
--- a/modules/data.atmosphere/man/download.PalEON.Rd
+++ b/modules/data.atmosphere/man/download.PalEON.Rd
@@ -4,11 +4,11 @@
 \alias{download.PalEON}
 \title{download.PalEON}
 \usage{
-download.PalEON(sitename, outfolder, start_date, end_date, overwrite = FALSE,
-  ...)
+download.PalEON(sitename, outfolder, start_date, end_date,
+  overwrite = FALSE, ...)
 }
 \arguments{
-\item{end_year}{}
+\item{end_date}{}
 }
 \description{
 Download PalEON files
diff --git a/modules/data.atmosphere/man/download.PalEON_ENS.Rd b/modules/data.atmosphere/man/download.PalEON_ENS.Rd
index 8ae9cdb6cc8..d268e4654a7 100644
--- a/modules/data.atmosphere/man/download.PalEON_ENS.Rd
+++ b/modules/data.atmosphere/man/download.PalEON_ENS.Rd
@@ -8,7 +8,10 @@ download.PalEON_ENS(sitename, outfolder, start_date, end_date,
   overwrite = FALSE, ...)
 }
 \arguments{
-\item{end_year}{}
+\item{end_date}{}
+}
+\description{
+Download PalEON met ensemble files
 }
 \author{
 Betsy Cowdery, Mike Dietze
diff --git a/modules/data.atmosphere/man/download.US_WCr.Rd b/modules/data.atmosphere/man/download.US_WCr.Rd
new file mode 100644
index 00000000000..3c3fcfa99d1
--- /dev/null
+++ b/modules/data.atmosphere/man/download.US_WCr.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.US_WCr.R
+\name{download.US_WCr}
+\alias{download.US_WCr}
+\title{download.US-WCr}
+\usage{
+download.US_WCr(start_date, end_date, timestep = 1)
+}
+\arguments{
+\item{start_date}{Start date/time data should be downloaded for}
+
+\item{end_date}{End date/time data should be downloaded for}
+
+\item{timestep}{How often to take data points from the file.  Must be a multiple of 0.5}
+}
+\description{
+download.US-WCr
+}
+\section{General Description}{
+
+Obtains data from Ankur Desai's Willow Creek flux tower, and selects certain variables (NEE and LE) to return
+Data is retruned at the given timestep in the given range.
+
+This data includes information on a number of flux variables.
+
+The timestep parameter is measured in hours, but is then converted to half hours because the data's timestep
+is every half hour.
+}
+
+\author{
+Luke Dramko
+}
diff --git a/modules/data.atmosphere/man/extract.local.CMIP5.Rd b/modules/data.atmosphere/man/extract.local.CMIP5.Rd
index 13fe0af0b9c..f0323cce02f 100644
--- a/modules/data.atmosphere/man/extract.local.CMIP5.Rd
+++ b/modules/data.atmosphere/man/extract.local.CMIP5.Rd
@@ -4,9 +4,10 @@
 \alias{extract.local.CMIP5}
 \title{extract.local.CMIP5}
 \usage{
-extract.local.CMIP5(outfolder, in.path, start_date, end_date, site_id, lat.in,
-  lon.in, model, scenario, ensemble_member = "r1i1p1", date.origin = NULL,
-  no.leap = NULL, overwrite = FALSE, verbose = FALSE, ...)
+extract.local.CMIP5(outfolder, in.path, start_date, end_date, site_id,
+  lat.in, lon.in, model, scenario, ensemble_member = "r1i1p1",
+  date.origin = NULL, no.leap = NULL, overwrite = FALSE,
+  verbose = FALSE, ...)
 }
 \arguments{
 \item{outfolder}{- directory where output files will be stored}
diff --git a/modules/data.atmosphere/man/extract.local.NLDAS.Rd b/modules/data.atmosphere/man/extract.local.NLDAS.Rd
index e4291992863..c0a0dae92a3 100644
--- a/modules/data.atmosphere/man/extract.local.NLDAS.Rd
+++ b/modules/data.atmosphere/man/extract.local.NLDAS.Rd
@@ -4,8 +4,8 @@
 \alias{extract.local.NLDAS}
 \title{extract.local.NLDAS}
 \usage{
-extract.local.NLDAS(outfolder, in.path, start_date, end_date, site_id, lat.in,
-  lon.in, overwrite = FALSE, verbose = FALSE, ...)
+extract.local.NLDAS(outfolder, in.path, start_date, end_date, site_id,
+  lat.in, lon.in, overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
 \item{outfolder}{- directory where output files will be stored}
@@ -24,6 +24,9 @@ extract.local.NLDAS(outfolder, in.path, start_date, end_date, site_id, lat.in,
 
 \item{overwrite}{logical. Download a fresh version even if a local file with the same name already exists?}
 
+\item{verbose}{logical. Passed on to \code{\link[ncdf4]{ncvar_def}} and \code{\link[ncdf4]{nc_create}}
+to control printing of debug info}
+
 \item{...}{Other arguments, currently ignored}
 }
 \description{
diff --git a/modules/data.atmosphere/man/gen.subdaily.models.Rd b/modules/data.atmosphere/man/gen.subdaily.models.Rd
index c22e7e6c819..bfd9872de36 100644
--- a/modules/data.atmosphere/man/gen.subdaily.models.Rd
+++ b/modules/data.atmosphere/man/gen.subdaily.models.Rd
@@ -6,8 +6,9 @@
 \usage{
 gen.subdaily.models(outfolder, path.train, yrs.train,
   direction.filter = "forward", in.prefix, n.beta, day.window,
-  seed = Sys.time(), resids = FALSE, parallel = FALSE, n.cores = NULL,
-  overwrite = TRUE, verbose = FALSE, print.progress = FALSE)
+  seed = Sys.time(), resids = FALSE, parallel = FALSE,
+  n.cores = NULL, overwrite = TRUE, verbose = FALSE,
+  print.progress = FALSE)
 }
 \arguments{
 \item{outfolder}{- directory where models will be stored *** storage required varies by size of training dataset, but prepare for >10 GB}
@@ -36,6 +37,10 @@ for each day surrounding the model day}
 
 \item{n.cores}{- deals with parallelization}
 
+\item{overwrite}{logical: replace output file if it already exists?}
+
+\item{verbose}{logical, currently ignored}
+
 \item{print.progress}{- print progress bar? (gets passed through)}
 }
 \description{
@@ -63,3 +68,4 @@ Other tdm - Temporally Downscale Meteorology: \code{\link{lm_ensemble_sims}},
 \author{
 Christy Rollinson, James Simkins
 }
+\concept{tdm - Temporally Downscale Meteorology}
diff --git a/modules/data.atmosphere/man/generate_narr_url.Rd b/modules/data.atmosphere/man/generate_narr_url.Rd
new file mode 100644
index 00000000000..40980a60db3
--- /dev/null
+++ b/modules/data.atmosphere/man/generate_narr_url.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{generate_narr_url}
+\alias{generate_narr_url}
+\title{Generate NARR url from a vector of dates}
+\usage{
+generate_narr_url(dates, flx)
+}
+\arguments{
+\item{dates}{Vector of dates for which to generate URL}
+
+\item{flx}{(Logical) If `TRUE`, format for `flx` variables. Otherwise, 
+format for `sfc` variables. See [narr_flx_vars].}
+}
+\description{
+Figures out file names for the given dates, based on NARR's convoluted and 
+inconsistent naming scheme.
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/get.ncvector.Rd b/modules/data.atmosphere/man/get.ncvector.Rd
index 85404da6b3e..e98e9f2690f 100644
--- a/modules/data.atmosphere/man/get.ncvector.Rd
+++ b/modules/data.atmosphere/man/get.ncvector.Rd
@@ -4,7 +4,8 @@
 \alias{get.ncvector}
 \title{Get time series vector from netCDF file}
 \usage{
-get.ncvector(var, lati = lati, loni = loni, run.dates = run.dates, met.nc)
+get.ncvector(var, lati = lati, loni = loni, run.dates = run.dates,
+  met.nc)
 }
 \arguments{
 \item{met.nc}{netcdf file with CF variable names}
diff --git a/modules/data.atmosphere/man/get.rh.Rd b/modules/data.atmosphere/man/get.rh.Rd
index fc02101ec23..d6bb66fd10f 100644
--- a/modules/data.atmosphere/man/get.rh.Rd
+++ b/modules/data.atmosphere/man/get.rh.Rd
@@ -7,9 +7,9 @@
 get.rh(T, Td)
 }
 \arguments{
-\item{temp}{T in original equation}
+\item{T}{temperature}
 
-\item{dewpoint}{Td in original}
+\item{Td}{dewpoint}
 }
 \value{
 numeric vector
diff --git a/modules/data.atmosphere/man/get_NARR_thredds.Rd b/modules/data.atmosphere/man/get_NARR_thredds.Rd
new file mode 100644
index 00000000000..5f934761900
--- /dev/null
+++ b/modules/data.atmosphere/man/get_NARR_thredds.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{get_NARR_thredds}
+\alias{get_NARR_thredds}
+\title{Retrieve NARR data using thredds}
+\usage{
+get_NARR_thredds(start_date, end_date, lat.in, lon.in, progress = TRUE,
+  drop_outside = TRUE, parallel = TRUE, ncores = 1)
+}
+\arguments{
+\item{start_date}{Start date for meteorology}
+
+\item{end_date}{End date for meteorology}
+
+\item{lat.in}{Latitude coordinate}
+
+\item{lon.in}{Longitude coordinate}
+
+\item{progress}{Whether or not to show a progress bar (default = `TRUE`).
+Requires the `progress` package to be installed.}
+
+\item{drop_outside}{Whether or not to drop dates outside of `start_date` to 
+`end_date` range (default = `TRUE`).}
+
+\item{parallel}{Download in parallel? Default = TRUE.}
+
+\item{ncores}{Number of cores for parallel download. Default is 
+`parallel::detectCores()`}
+}
+\value{
+`tibble` containing time series of NARR data for the given site
+}
+\description{
+Retrieve NARR data using thredds
+}
+\examples{
+dat <- get_NARR_thredds("2008-01-01", "2008-01-15", 43.3724, -89.9071)
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/get_cf_variables_table.Rd b/modules/data.atmosphere/man/get_cf_variables_table.Rd
new file mode 100644
index 00000000000..514260feaac
--- /dev/null
+++ b/modules/data.atmosphere/man/get_cf_variables_table.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_cf_variables_table.R
+\name{get_cf_variables_table}
+\alias{get_cf_variables_table}
+\title{Retrieve the current CF variables table from `cfconventions.org`
+and convert it into a `data.frame`}
+\usage{
+get_cf_variables_table(cf_url = build_cf_variables_table_url(57))
+}
+\arguments{
+\item{cf_url}{URL of CF variables table XML. See also [build_cf_variables_table_url].}
+}
+\value{
+CF variables table, as a `tibble`
+}
+\description{
+Retrieve the current CF variables table from `cfconventions.org`
+and convert it into a `data.frame`
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/get_narr_url.Rd b/modules/data.atmosphere/man/get_narr_url.Rd
new file mode 100644
index 00000000000..218e835c031
--- /dev/null
+++ b/modules/data.atmosphere/man/get_narr_url.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{get_narr_url}
+\alias{get_narr_url}
+\title{Retrieve NARR data from a given URL}
+\usage{
+get_narr_url(url, xy, flx, pb = NULL)
+}
+\arguments{
+\item{url}{Full URL to NARR thredds file}
+
+\item{xy}{Vector length 2 containing NARR coordinates}
+
+\item{flx}{(Logical) If `TRUE`, format for `flx` variables. Otherwise, 
+format for `sfc` variables. See [narr_flx_vars].}
+
+\item{pb}{Progress bar R6 object (default = `NULL`)}
+}
+\description{
+Retrieve NARR data from a given URL
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/latlon2lcc.Rd b/modules/data.atmosphere/man/latlon2lcc.Rd
new file mode 100644
index 00000000000..cbd47e269d9
--- /dev/null
+++ b/modules/data.atmosphere/man/latlon2lcc.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{latlon2lcc}
+\alias{latlon2lcc}
+\title{Convert latitude and longitude to x-y coordinates (in km) in Lambert 
+conformal conic projection (used by NARR)}
+\usage{
+latlon2lcc(lat.in, lon.in)
+}
+\arguments{
+\item{lat.in}{Latitude coordinate}
+
+\item{lon.in}{Longitude coordinate}
+}
+\value{
+`sp::SpatialPoints` object containing transformed x and y 
+coordinates, in km, which should match NARR coordinates
+}
+\description{
+Convert latitude and longitude to x-y coordinates (in km) in Lambert 
+conformal conic projection (used by NARR)
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/latlon2narr.Rd b/modules/data.atmosphere/man/latlon2narr.Rd
new file mode 100644
index 00000000000..3f99b2c53ed
--- /dev/null
+++ b/modules/data.atmosphere/man/latlon2narr.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{latlon2narr}
+\alias{latlon2narr}
+\title{Convert latitude and longitude coordinates to NARR indices}
+\usage{
+latlon2narr(nc, lat.in, lon.in)
+}
+\arguments{
+\item{nc}{`ncdf4` connection object}
+
+\item{lat.in}{Latitude coordinate}
+
+\item{lon.in}{Longitude coordinate}
+}
+\value{
+Vector length 2 containing NARR `x` and `y` indices, which can be 
+used in `ncdf4::ncvar_get` `start` argument.
+}
+\description{
+Convert latitude and longitude coordinates to NARR indices
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/lm_ensemble_sims.Rd b/modules/data.atmosphere/man/lm_ensemble_sims.Rd
index f8d50499846..8b4ae1bac0b 100644
--- a/modules/data.atmosphere/man/lm_ensemble_sims.Rd
+++ b/modules/data.atmosphere/man/lm_ensemble_sims.Rd
@@ -57,3 +57,4 @@ Other tdm - Temporally Downscale Meteorology: \code{\link{gen.subdaily.models}},
 \author{
 Christy Rollinson, James Simkins
 }
+\concept{tdm - Temporally Downscale Meteorology}
diff --git a/modules/data.atmosphere/man/merge_met_variable.Rd b/modules/data.atmosphere/man/merge_met_variable.Rd
index cd885bc341b..343cfdd023f 100644
--- a/modules/data.atmosphere/man/merge_met_variable.Rd
+++ b/modules/data.atmosphere/man/merge_met_variable.Rd
@@ -18,9 +18,10 @@ merge_met_variable(in.path, in.prefix, start_date, end_date, merge.file,
 
 \item{merge.file}{path of file to be merged in}
 
-\item{overwrite}{}
+\item{overwrite}{logical: replace output file if it already exists?}
 
-\item{verbose}{}
+\item{verbose}{logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}} functions
+print debugging information as they run?}
 
 \item{...}{}
 }
diff --git a/modules/data.atmosphere/man/met.process.Rd b/modules/data.atmosphere/man/met.process.Rd
index 9ea29df213b..09b5da424df 100644
--- a/modules/data.atmosphere/man/met.process.Rd
+++ b/modules/data.atmosphere/man/met.process.Rd
@@ -4,8 +4,9 @@
 \alias{met.process}
 \title{met.process}
 \usage{
-met.process(site, input_met, start_date, end_date, model, host = "localhost",
-  dbparms, dir, browndog = NULL, spin = NULL, overwrite = FALSE)
+met.process(site, input_met, start_date, end_date, model,
+  host = "localhost", dbparms, dir, browndog = NULL, spin = NULL,
+  overwrite = FALSE)
 }
 \arguments{
 \item{site}{Site info from settings file}
@@ -36,6 +37,9 @@ met.process(site, input_met, start_date, end_date, model, host = "localhost",
 
        list(download = FALSE, met2cf = TRUE, standardize = TRUE,  met2model = TRUE)}
 }
+\description{
+met.process
+}
 \author{
 Elizabeth Cowdery, Michael Dietze, Ankur Desai, James Simkins, Ryan Kelly
 }
diff --git a/modules/data.atmosphere/man/met.process.stage.Rd b/modules/data.atmosphere/man/met.process.stage.Rd
index a0d653fd5d3..fe3eaa0122a 100644
--- a/modules/data.atmosphere/man/met.process.stage.Rd
+++ b/modules/data.atmosphere/man/met.process.stage.Rd
@@ -9,6 +9,9 @@ met.process.stage(input.id, raw.id, con)
 \arguments{
 \item{raw.id}{}
 }
+\description{
+met.process.stage
+}
 \author{
 Elizabeth Cowdery
 }
diff --git a/modules/data.atmosphere/man/met2CF.AmerifluxLBL.Rd b/modules/data.atmosphere/man/met2CF.AmerifluxLBL.Rd
index 08f0f04faea..89b287f49ea 100644
--- a/modules/data.atmosphere/man/met2CF.AmerifluxLBL.Rd
+++ b/modules/data.atmosphere/man/met2CF.AmerifluxLBL.Rd
@@ -4,8 +4,8 @@
 \alias{met2CF.AmerifluxLBL}
 \title{met2CF.AmerifluxLBL}
 \usage{
-met2CF.AmerifluxLBL(in.path, in.prefix, outfolder, start_date, end_date, format,
-  overwrite = FALSE, verbose = FALSE, ...)
+met2CF.AmerifluxLBL(in.path, in.prefix, outfolder, start_date, end_date,
+  format, overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
 \item{in.path}{location on disk where inputs are stored}
diff --git a/modules/data.atmosphere/man/met2CF.FACE.Rd b/modules/data.atmosphere/man/met2CF.FACE.Rd
index 6505a82c72f..9b2a1a075f6 100644
--- a/modules/data.atmosphere/man/met2CF.FACE.Rd
+++ b/modules/data.atmosphere/man/met2CF.FACE.Rd
@@ -2,13 +2,13 @@
 % Please edit documentation in R/met2CF.FACE.R
 \name{met2CF.FACE}
 \alias{met2CF.FACE}
-\title{met2CF.FACE}
+\title{convert FACE files to CF files}
 \usage{
-met2CF.FACE(in.path, in.prefix, outfolder, start_date, end_date, input.id, site,
-  format, ...)
+met2CF.FACE(in.path, in.prefix, outfolder, start_date, end_date, input.id,
+  site, format, ...)
 }
-\arguments{
-\item{convert}{FACE files to CF files}
+\description{
+convert FACE files to CF files
 }
 \author{
 Elizabeth Cowdery
diff --git a/modules/data.atmosphere/man/met2CF.PalEON.Rd b/modules/data.atmosphere/man/met2CF.PalEON.Rd
index 572523b3592..d8d55827954 100644
--- a/modules/data.atmosphere/man/met2CF.PalEON.Rd
+++ b/modules/data.atmosphere/man/met2CF.PalEON.Rd
@@ -4,8 +4,8 @@
 \alias{met2CF.PalEON}
 \title{met2CF.PalEON}
 \usage{
-met2CF.PalEON(in.path, in.prefix, outfolder, start_date, end_date, lat, lon,
-  overwrite = FALSE, verbose = FALSE, ...)
+met2CF.PalEON(in.path, in.prefix, outfolder, start_date, end_date, lat,
+  lon, overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
 \item{in.path}{location on disk where inputs are stored}
diff --git a/modules/data.atmosphere/man/met2CF.csv.Rd b/modules/data.atmosphere/man/met2CF.csv.Rd
index ac8beb37923..8149b63e65f 100644
--- a/modules/data.atmosphere/man/met2CF.csv.Rd
+++ b/modules/data.atmosphere/man/met2CF.csv.Rd
@@ -5,7 +5,8 @@
 \title{met2CF.csv}
 \usage{
 met2CF.csv(in.path, in.prefix, outfolder, start_date, end_date, format,
-  lat = NULL, lon = NULL, nc_verbose = FALSE, overwrite = FALSE, ...)
+  lat = NULL, lon = NULL, nc_verbose = FALSE, overwrite = FALSE,
+  ...)
 }
 \arguments{
 \item{format}{data frame or list with elements as described below
@@ -27,9 +28,13 @@ Units for datetime field are the lubridate function that will be used to parse t
 
 \item{nc_verbose}{logical: run ncvar_add in verbose mode?}
 }
+\description{
+met2CF.csv
+}
 \examples{
 \dontrun{
-bety = list(user='bety', password='bety',host='localhost', dbname='bety', driver='PostgreSQL',write=TRUE)
+bety <- list(user='bety', password='bety', host='localhost',
+  dbname='bety', driver='PostgreSQL',write=TRUE)
 con <- PEcAn.DB::db.open(bety)
 bety$con <- con
 start_date <- lubridate::ymd_hm('200401010000')
@@ -43,7 +48,10 @@ format <- PEcAn.DB::query.format.vars(format.id=format.id,bety = bety)
 format$lon <- -92.0
 format$lat <- 45.0
 format$time_zone <- "America/Chicago"
-results<-PEcAn.data.atmosphere::met2CF.csv(in.path, in.prefix, outfolder,start_date, end_date,format, overwrite=TRUE)
+results <- PEcAn.data.atmosphere::met2CF.csv(
+  in.path, in.prefix, outfolder,
+  start_date, end_date, format,
+  overwrite=TRUE)
 }
 }
 \author{
diff --git a/modules/data.atmosphere/man/met_temporal_downscale.Gaussian_ensemble.Rd b/modules/data.atmosphere/man/met_temporal_downscale.Gaussian_ensemble.Rd
index ffd43b6eb33..96d22450da8 100644
--- a/modules/data.atmosphere/man/met_temporal_downscale.Gaussian_ensemble.Rd
+++ b/modules/data.atmosphere/man/met_temporal_downscale.Gaussian_ensemble.Rd
@@ -18,7 +18,10 @@ met_temporal_downscale.Gaussian_ensemble(in.path, in.prefix, outfolder,
 \item{train_met}{- the observed dataset that will be used to train the modeled dataset in NC format. i.e. Flux Tower dataset 
 (see download.Fluxnet2015 or download.Ameriflux)}
 
-\item{overwrite}{}
+\item{overwrite}{logical: replace output file if it already exists?}
+
+\item{verbose}{logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}} functions
+print debugging information as they run?}
 
 \item{swdn_method}{- Downwelling shortwave flux in air downscaling method (options are "sine", "spline", and "Waichler")}
 
diff --git a/modules/data.atmosphere/man/metgapfill.NOAA_GEFS.Rd b/modules/data.atmosphere/man/metgapfill.NOAA_GEFS.Rd
new file mode 100644
index 00000000000..a6d126cbb9c
--- /dev/null
+++ b/modules/data.atmosphere/man/metgapfill.NOAA_GEFS.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metgapfill.NOAA_GEFS.R
+\name{metgapfill.NOAA_GEFS}
+\alias{metgapfill.NOAA_GEFS}
+\title{Gapfill NOAA_GEFS weather data}
+\usage{
+metgapfill.NOAA_GEFS(in.prefix, in.path, outfolder, start_date, end_date,
+  overwrite = FALSE, verbose = FALSE, ...)
+}
+\arguments{
+\item{in.prefix}{the met file name}
+
+\item{in.path}{The location of the file}
+
+\item{outfolder}{The place to write the output file to}
+
+\item{start_date}{The start date of the contents of the file}
+
+\item{end_date}{The end date of the contents of the file}
+
+\item{overwrite}{Whether or not to overwrite the output file if it exists or not}
+
+\item{verbose}{Passed to nc writing functions for additional output}
+}
+\description{
+Gapfill NOAA_GEFS weather data
+}
+\section{Purpose}{
+
+This function uses simple methods to gapfill NOAA GEFS met data
+Temperature and Precipitation are gapfilled with spline; other data sources are gapfilled with
+using linear models fitted to other fitted data.
+}
+
+\author{
+Luke Dramko
+}
diff --git a/modules/data.atmosphere/man/model.train.Rd b/modules/data.atmosphere/man/model.train.Rd
index b03c43633fe..ab173e23221 100644
--- a/modules/data.atmosphere/man/model.train.Rd
+++ b/modules/data.atmosphere/man/model.train.Rd
@@ -4,7 +4,8 @@
 \alias{model.train}
 \title{model.train}
 \usage{
-model.train(dat.subset, v, n.beta, resids = resids, threshold = NULL, ...)
+model.train(dat.subset, v, n.beta, resids = resids, threshold = NULL,
+  ...)
 }
 \arguments{
 \item{dat.subset}{data.frame containing lags, next, and downscale period data}
@@ -37,3 +38,4 @@ Other tdm - Temporally Downscale Meteorology: \code{\link{gen.subdaily.models}},
 \author{
 Christy Rollinson, James Simkins
 }
+\concept{tdm - Temporally Downscale Meteorology}
diff --git a/modules/data.atmosphere/man/narr_flx_vars.Rd b/modules/data.atmosphere/man/narr_flx_vars.Rd
new file mode 100644
index 00000000000..c2da49226d6
--- /dev/null
+++ b/modules/data.atmosphere/man/narr_flx_vars.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\docType{data}
+\name{narr_flx_vars}
+\alias{narr_flx_vars}
+\alias{narr_sfc_vars}
+\alias{narr_all_vars}
+\title{NARR flux and sfc variables}
+\format{An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 5 rows and 3 columns.}
+\usage{
+narr_flx_vars
+
+narr_sfc_vars
+
+narr_all_vars
+}
+\description{
+NARR flux and sfc variables
+}
+\keyword{datasets}
diff --git a/modules/data.atmosphere/man/nc.merge.Rd b/modules/data.atmosphere/man/nc.merge.Rd
index e239478f844..03c0c320205 100644
--- a/modules/data.atmosphere/man/nc.merge.Rd
+++ b/modules/data.atmosphere/man/nc.merge.Rd
@@ -4,8 +4,8 @@
 \alias{nc.merge}
 \title{nc.merge}
 \usage{
-nc.merge(outfolder, in.path, in.prefix, start_date, end_date, upscale = FALSE,
-  overwrite = FALSE, verbose = FALSE, ...)
+nc.merge(outfolder, in.path, in.prefix, start_date, end_date,
+  upscale = FALSE, overwrite = FALSE, verbose = FALSE, ...)
 }
 \arguments{
 \item{outfolder}{- directory where output will be stored}
@@ -20,9 +20,10 @@ nc.merge(outfolder, in.path, in.prefix, start_date, end_date, upscale = FALSE,
 
 \item{upscale}{- Upscale can either be set for FALSE (leave alone) or to the temporal resolution you want to aggregate to}
 
-\item{lat.in}{- latitude as numeric}
+\item{overwrite}{logical: replace output file if it already exists?}
 
-\item{lon.in}{- longitude as numeric}
+\item{verbose}{logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}}
+functions print debugging information as they run?}
 }
 \description{
 This is the 1st function for the tdm (Temporally Downscale Meteorology) workflow. The nc2dat.train function
@@ -46,3 +47,4 @@ Other tdm - Temporally Downscale Meteorology: \code{\link{gen.subdaily.models}},
 \author{
 James Simkins, Christy Rollinson
 }
+\concept{tdm - Temporally Downscale Meteorology}
diff --git a/modules/data.atmosphere/man/pecan_standard_met_table.Rd b/modules/data.atmosphere/man/pecan_standard_met_table.Rd
new file mode 100644
index 00000000000..9108ca6f6c2
--- /dev/null
+++ b/modules/data.atmosphere/man/pecan_standard_met_table.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pecan_standard_met_table.R
+\docType{data}
+\name{pecan_standard_met_table}
+\alias{pecan_standard_met_table}
+\title{Conversion table for PEcAn standard meteorology}
+\format{An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 18 rows and 8 columns.}
+\usage{
+pecan_standard_met_table
+}
+\description{
+Conversion table for PEcAn standard meteorology
+}
+\keyword{datasets}
diff --git a/modules/data.atmosphere/man/post_process.Rd b/modules/data.atmosphere/man/post_process.Rd
new file mode 100644
index 00000000000..633a81c7b13
--- /dev/null
+++ b/modules/data.atmosphere/man/post_process.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{post_process}
+\alias{post_process}
+\title{Post process raw NARR downloaded data frame}
+\usage{
+post_process(dat)
+}
+\arguments{
+\item{dat}{Nested `tibble` from mapped call to [get_narr_url]}
+}
+\description{
+Post process raw NARR downloaded data frame
+}
diff --git a/modules/data.atmosphere/man/predict_subdaily_met.Rd b/modules/data.atmosphere/man/predict_subdaily_met.Rd
index 0b22caed980..4fe464ccb6c 100644
--- a/modules/data.atmosphere/man/predict_subdaily_met.Rd
+++ b/modules/data.atmosphere/man/predict_subdaily_met.Rd
@@ -37,6 +37,10 @@ ensemble rather than overwriting with a default naming scheme}
 
 \item{sanity.tries}{- how many time should we try to predict a reasonable value before giving up?  We don't want to end up in an infinite loop}
 
+\item{overwrite}{logical: replace output file if it already exists?}
+
+\item{verbose}{logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}} functions print debugging information as they run?}
+
 \item{seed}{- manually set seed for results to be reproducible}
 
 \item{print.progress}{- print the progress bar?}
@@ -79,3 +83,4 @@ Other tdm - Temporally Downscale Meteorology: \code{\link{gen.subdaily.models}},
 \author{
 Christy Rollinson, James Simkins
 }
+\concept{tdm - Temporally Downscale Meteorology}
diff --git a/modules/data.atmosphere/man/prepare_narr_year.Rd b/modules/data.atmosphere/man/prepare_narr_year.Rd
new file mode 100644
index 00000000000..237bec25fc9
--- /dev/null
+++ b/modules/data.atmosphere/man/prepare_narr_year.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{prepare_narr_year}
+\alias{prepare_narr_year}
+\title{Write NetCDF file for a single year of data}
+\usage{
+prepare_narr_year(dat, file, lat_nc, lon_nc, verbose = FALSE)
+}
+\arguments{
+\item{dat}{NARR tabular data for a single year ([get_NARR_thredds])}
+
+\item{file}{Full path to target file}
+
+\item{lat_nc}{`ncdim` object for latitude}
+
+\item{lon_nc}{`ncdim` object for longitude}
+
+\item{verbose}{}
+}
+\value{
+List of NetCDF variables in data. Creates NetCDF file containing 
+data as a side effect
+}
+\description{
+Write NetCDF file for a single year of data
+}
diff --git a/modules/data.atmosphere/man/read.register.Rd b/modules/data.atmosphere/man/read.register.Rd
index 36304429c16..d7c63d55f15 100644
--- a/modules/data.atmosphere/man/read.register.Rd
+++ b/modules/data.atmosphere/man/read.register.Rd
@@ -11,6 +11,9 @@ read.register(register.xml, con)
 
 \item{con}{betydb connection}
 }
+\description{
+read.register
+}
 \author{
 Betsy Cowdery
 }
diff --git a/modules/data.atmosphere/man/read_narr_var.Rd b/modules/data.atmosphere/man/read_narr_var.Rd
new file mode 100644
index 00000000000..59e0c16002a
--- /dev/null
+++ b/modules/data.atmosphere/man/read_narr_var.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/download.NARR_site.R
+\name{read_narr_var}
+\alias{read_narr_var}
+\title{Read a specific variable from a NARR NetCDF file}
+\usage{
+read_narr_var(nc, xy, variable, unit, flx, pb = NULL)
+}
+\arguments{
+\item{nc}{`ncdf4` connection object}
+
+\item{xy}{Vector length 2 containing NARR coordinates}
+
+\item{variable}{NARR name of variable to retrieve}
+
+\item{unit}{Output unit of variable to retrieve}
+
+\item{flx}{(Logical) If `TRUE`, format for `flx` variables. Otherwise, 
+format for `sfc` variables. See [narr_flx_vars].}
+
+\item{pb}{Progress bar R6 object (default = `NULL`)}
+}
+\description{
+Read a specific variable from a NARR NetCDF file
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/data.atmosphere/man/robustly.Rd b/modules/data.atmosphere/man/robustly.Rd
new file mode 100644
index 00000000000..29a9d4f0e63
--- /dev/null
+++ b/modules/data.atmosphere/man/robustly.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/robustly.R
+\name{robustly}
+\alias{robustly}
+\title{Adverb to try calling a function `n` times before giving up}
+\usage{
+robustly(.f, n = 10, timeout = 0.2, silent = TRUE)
+}
+\arguments{
+\item{.f}{Function to call.}
+
+\item{n}{Number of attempts to try}
+
+\item{timeout}{Timeout between attempts, in seconds}
+
+\item{silent}{Silence error messages?}
+}
+\value{
+Modified version of input function
+}
+\description{
+Adverb to try calling a function `n` times before giving up
+}
+\examples{
+rlog <- robustly(log, timeout = 0.3)
+try(rlog("fail"))
+\dontrun{
+ nc_openr <- robustly(ncdf4::nc_open, n = 10, timeout = 0.5)
+ nc <- nc_openr(url)
+ # ...or just call the function directly
+ nc <- robustly(ncdf4::nc_open, n = 20)(url)
+ # Useful in `purrr` maps
+ many_vars <- purrr::map(varnames, robustly(ncdf4::ncvar_get), nc = nc)
+}
+}
diff --git a/modules/data.atmosphere/man/save.betas.Rd b/modules/data.atmosphere/man/save.betas.Rd
index 31641042b18..0a8e50bbdd1 100644
--- a/modules/data.atmosphere/man/save.betas.Rd
+++ b/modules/data.atmosphere/man/save.betas.Rd
@@ -32,3 +32,4 @@ Other tdm - Temporally Downscale Meteorology: \code{\link{gen.subdaily.models}},
 \author{
 Christy Rollinson, James Simkins
 }
+\concept{tdm - Temporally Downscale Meteorology}
diff --git a/modules/data.atmosphere/man/save.model.Rd b/modules/data.atmosphere/man/save.model.Rd
index 06b4cfd22f4..87008e0e97e 100644
--- a/modules/data.atmosphere/man/save.model.Rd
+++ b/modules/data.atmosphere/man/save.model.Rd
@@ -32,3 +32,4 @@ Other tdm - Temporally Downscale Meteorology: \code{\link{gen.subdaily.models}},
 \author{
 Christy Rollinson, James Simkins
 }
+\concept{tdm - Temporally Downscale Meteorology}
diff --git a/modules/data.atmosphere/man/site_from_tag.Rd b/modules/data.atmosphere/man/site_from_tag.Rd
index 8f417a7e532..d47159342dd 100644
--- a/modules/data.atmosphere/man/site_from_tag.Rd
+++ b/modules/data.atmosphere/man/site_from_tag.Rd
@@ -6,6 +6,9 @@
 \usage{
 site_from_tag(sitename, tag)
 }
+\description{
+site_from_tag
+}
 \author{
 Betsy Cowdery
 
diff --git a/modules/data.atmosphere/man/spin.met.Rd b/modules/data.atmosphere/man/spin.met.Rd
index 7db9f2ef9a5..b85997a356e 100644
--- a/modules/data.atmosphere/man/spin.met.Rd
+++ b/modules/data.atmosphere/man/spin.met.Rd
@@ -51,7 +51,10 @@ resample   <- TRUE
 \dontrun{
 if(!is.null(spin)){
    ## if spinning up, extend processed met by resampling or cycling met
-   start_date <- PEcAn.data.atmosphere::spin.met(in.path,in.prefix,start_date,end_date,nyear,nsample,resample)
+   start_date <- PEcAn.data.atmosphere::spin.met(
+     in.path, in.prefix,
+     start_date, end_date,
+     nyear, nsample, resample)
 }
 }
 }
diff --git a/modules/data.atmosphere/man/split_wind.Rd b/modules/data.atmosphere/man/split_wind.Rd
index f48dcc93cb4..9155c63e568 100644
--- a/modules/data.atmosphere/man/split_wind.Rd
+++ b/modules/data.atmosphere/man/split_wind.Rd
@@ -16,9 +16,9 @@ split_wind(in.path, in.prefix, start_date, end_date, overwrite = FALSE,
 
 \item{end_date}{}
 
-\item{overwrite}{}
+\item{overwrite}{logical: replace output file if it already exists?}
 
-\item{verbose}{}
+\item{verbose}{logical: should \code{\link[ncdf4:ncdf4-package]{ncdf4}} functions print debugging information as they run?}
 
 \item{...}{other arguments, currently ignored}
 }
diff --git a/modules/data.atmosphere/man/subdaily_pred.Rd b/modules/data.atmosphere/man/subdaily_pred.Rd
index a416352599e..28e7c6fec40 100644
--- a/modules/data.atmosphere/man/subdaily_pred.Rd
+++ b/modules/data.atmosphere/man/subdaily_pred.Rd
@@ -43,3 +43,4 @@ Other tdm - Temporally Downscale Meteorology: \code{\link{gen.subdaily.models}},
 \author{
 Christy Rollinson, James Simkins
 }
+\concept{tdm - Temporally Downscale Meteorology}
diff --git a/modules/data.atmosphere/man/temporal.downscale.functions.Rd b/modules/data.atmosphere/man/temporal.downscale.functions.Rd
index 6d47d4ebfe5..e22868fefa1 100644
--- a/modules/data.atmosphere/man/temporal.downscale.functions.Rd
+++ b/modules/data.atmosphere/man/temporal.downscale.functions.Rd
@@ -4,9 +4,10 @@
 \alias{temporal.downscale.functions}
 \title{temporal_downscale_functions}
 \usage{
-temporal.downscale.functions(dat.train, n.beta, day.window, resids = FALSE,
-  parallel = FALSE, n.cores = NULL, seed = format(Sys.time(), "\%m\%d"),
-  outfolder, print.progress = FALSE, ...)
+temporal.downscale.functions(dat.train, n.beta, day.window,
+  resids = FALSE, parallel = FALSE, n.cores = NULL,
+  seed = format(Sys.time(), "\%m\%d"), outfolder,
+  print.progress = FALSE, ...)
 }
 \arguments{
 \item{dat.train}{- training data generated by tdm_nc2dat.train.R}
@@ -25,11 +26,9 @@ still being worked on, set to FALSE}
 
 \item{seed}{- allows this to be reproducible}
 
-\item{print.progress}{- print progress of model generation?}
-
-\item{path.out}{- path to where the training models & betas will be stored}
+\item{outfolder}{= where the output should be stored}
 
-\item{outfoulder}{= where the output should be stored}
+\item{print.progress}{- print progress of model generation?}
 }
 \description{
 This function contains the functions that do the heavy lifting in gen.subdaily.models()
@@ -56,3 +55,4 @@ Other tdm - Temporally Downscale Meteorology: \code{\link{gen.subdaily.models}},
 \author{
 Christy Rollinson, James Simkins
 }
+\concept{tdm - Temporally Downscale Meteorology}
diff --git a/modules/data.atmosphere/tests/testthat/helper.R b/modules/data.atmosphere/tests/testthat/helper.R
new file mode 100644
index 00000000000..3a014c85f35
--- /dev/null
+++ b/modules/data.atmosphere/tests/testthat/helper.R
@@ -0,0 +1,37 @@
+#' Expectation: Does PEcAn logger produce warning/debug/error?
+#'
+#' Tests whether PEcAn.logger produced the expected output.
+#' Modeled after testthat::expect_message, but looks for output on stderr
+#' (where PEcAn.logger writes it) rather than a message() object
+#'
+#' @param object object to test, probably a PEcAn function call
+#' @param regexp pattern expected in the output
+#' @param ... other arguments passed on to \code{\link[testthat]{expect_match}}
+#' @examples
+#' expect_log(PEcAn.logger::logger.debug("test"), "DEBUG.*test")
+#' expect_log(PEcAn.utils::get.model.output(), "update your workflow")
+#' expect_log(cat("Hello", file = stderr()), "Hello")
+#' # Only messages on stderr are recognized
+#' expect_failure(expect_log("Hello", "Hello"))
+#'
+expect_log <- function(object, regexp, ...){
+	qobj <- rlang::enquo(object)
+	msg <- capture.output(
+		{val <- rlang::eval_tidy(qobj)},
+		type = "message")
+	label = rlang::expr_label(rlang::get_expr(qobj))
+
+	expect(
+		length(msg) > 0,
+		sprintf("%s did not produce any log messages", label))
+	msg = paste(msg, collapse = "\n")
+	expect(
+		grepl(regexp, msg,  ...),
+		sprintf(
+			"%s does not match %s.\nActual value: \"%s\"",
+			label,
+			encodeString(regexp, quote = "\""),
+			encodeString(msg)))
+
+	invisible(val)
+}
diff --git a/modules/data.atmosphere/tests/testthat/test-download.GFDLR.R b/modules/data.atmosphere/tests/testthat/test-download.GFDLR.R
new file mode 100644
index 00000000000..b8c154bdd05
--- /dev/null
+++ b/modules/data.atmosphere/tests/testthat/test-download.GFDLR.R
@@ -0,0 +1,42 @@
+context("Checking GFDL download")
+
+tmpdir = tempfile(pattern="GFDLtest")
+dir.create(tmpdir)
+teardown(unlink(tmpdir, recursive = TRUE))
+
+test_that("download works and returns a valid CF file", {
+  # Download is too slow for Travis -- please run locally before committing!
+  skip_on_travis()
+
+  PEcAn.logger::logger.setLevel("WARN")
+
+  result <- download.GFDL(outfolder = tmpdir,
+                             start_date = "2007-01-01",
+                             end_date = "2007-12-31",
+                             site_id = 753,
+                             lat.in = 40,
+                             lon.in = -88)
+  cf <- ncdf4::nc_open(result$file)
+  teardown(ncdf4::nc_close(cf))
+
+  # Expect that reference times are present and set to start date
+  cf_units <- cf$dim$time$units
+  expect_equal(cf_units, "seconds since 2007-01-01 00:00:00")
+
+  expect_equal(cf$dim$latitude$len, 1)
+  expect_equal(cf$dim$longitude$len, 1)
+  expect_equal(cf$dim$time$len, 365*(24/3)) # one year at 3-hr interval, leap days ignored
+  expect_equal(cf$nvar, 8)
+
+  # Expect that overwrite argument is respected
+  expect_log(
+    download.GFDL(
+      outfolder = tmpdir,
+      start_date = "2007-01-01",
+      end_date = "2007-12-31",
+      site_id = 753,
+      lat.in = 40,
+      lon.in = -88,
+      overwrite = FALSE),
+    "already exists. Skipping")
+})
diff --git a/modules/data.atmosphere/tests/testthat/test.cf-downscaling.R b/modules/data.atmosphere/tests/testthat/test.cf-downscaling.R
index 7857e5e5d8d..1dd969d34c0 100644
--- a/modules/data.atmosphere/tests/testthat/test.cf-downscaling.R
+++ b/modules/data.atmosphere/tests/testthat/test.cf-downscaling.R
@@ -3,14 +3,13 @@ context("downscaling")
 daily.nc <- ncdf4::nc_open("data/urbana_daily_test.nc")
 on.exit(ncdf4::nc_close(daily.nc))
 daily.cf <- load.cfmet(met.nc = daily.nc, lat = 39.75, lon = -87.25,
-                       start.date = "1951-01-02", end.date = "1951-06-01")
+                       start.date = "1951-01-02", end.date = "1951-05-31")
 
 test_that(
   paste("cfmet.downscale.time works\n",
         "these are capturing the current state of the downscale algorithms;\n", 
         "actual values will need to be revised if (when) algorithms change"), 
 {
-  skip("Broken test #1343")
   b <- cfmet.downscale.time(cfmet = daily.cf, lat = 40)
   expect_equal(b[,unique(year)], 1951)
   expect_equal(b[,range(doy)], c(2,151))
@@ -24,6 +23,8 @@ test_that(
 
 
 test_that("get.ncvector works",{
-  run.dates <- data.table(index = 1:2, date = c(lubridate::ymd("1951-01-01 UTC"), lubridate::ymd("1951-01-02 UTC")))
-  c <- get.ncvector("air_temperature", lati = 1, loni = 1, run.dates, met.nc = daily.nc)
+  run.dates <- data.table::data.table(index = 1:2, date = c(lubridate::ymd("1951-01-01 UTC"), lubridate::ymd("1951-01-02 UTC")))
+  res <- get.ncvector("air_temperature", lati = 1, loni = 1, run.dates, met.nc = daily.nc)
+  expect_type(res, "double")
+  expect_equal(length(res), nrow(run.dates))
 })
diff --git a/modules/data.atmosphere/tests/testthat/test.check_met_file.R b/modules/data.atmosphere/tests/testthat/test.check_met_file.R
new file mode 100644
index 00000000000..85f4fbd4b2d
--- /dev/null
+++ b/modules/data.atmosphere/tests/testthat/test.check_met_file.R
@@ -0,0 +1,40 @@
+context("Check met input file correctly detects errors")
+
+test_that(
+  "Check met input correctly finds errors in bad met files",
+  {
+    urbana_daily_met <- system.file(
+      "tests/testthat/data/urbana_daily_test.nc",
+      package = "PEcAn.data.atmosphere"
+    )
+    urbana_daily_results <- check_met_input_file(urbana_daily_met)
+    expect_s3_class(urbana_daily_results, "data.frame")
+    expect_true(
+      all(c("correct dimensions", "required variable present", "variable has correct units") %in%
+            urbana_daily_results[["test_type"]])
+    )
+    expect_true(
+      all(urbana_daily_results %>%
+            dplyr::filter(test_type == "variable has correct units") %>%
+            dplyr::pull(test_passed))
+    )
+    expect_false(
+      all(urbana_daily_results %>%
+            dplyr::filter(target_variable %in% c("dimensions", "air_pressure", "eastward_wind")) %>%
+            dplyr::pull(test_passed))
+    )
+
+    urbana_subdaily_met <- system.file(
+      "tests/testthat/data/urbana_subdaily_test.nc",
+      package = "PEcAn.data.atmosphere"
+    )
+    urbana_subdaily_results <- check_met_input_file(urbana_subdaily_met)
+    urbana_subdaily_dims <- urbana_subdaily_results %>%
+      dplyr::filter(target_variable == "dimensions")
+    expect_false(urbana_subdaily_dims[["test_passed"]])
+    expect_match(
+      urbana_subdaily_dims[["test_error_message"]],
+      regexp = "length\\(dimensions\\) not equal to 3"
+    )
+  }
+)
diff --git a/modules/data.atmosphere/tests/testthat/test.download.CRUNCEP.R b/modules/data.atmosphere/tests/testthat/test.download.CRUNCEP.R
index 95d725cc6f7..6371af1365f 100644
--- a/modules/data.atmosphere/tests/testthat/test.download.CRUNCEP.R
+++ b/modules/data.atmosphere/tests/testthat/test.download.CRUNCEP.R
@@ -1,5 +1,8 @@
 context("Checking CRUNCEP download")
 
+tmpdir = tempfile(pattern="CRUNCEPtest")
+dir.create(tmpdir)
+teardown(unlink(tmpdir, recursive = TRUE))
 
 test_that("download works and returns a valid CF file", {
   # download is slow and was causing lots of Travis timeouts
@@ -7,9 +10,6 @@ test_that("download works and returns a valid CF file", {
 
   PEcAn.logger::logger.setLevel("WARN")
 
-  tmpdir <- tempdir()
-  on.exit(unlink(tmpdir, recursive = TRUE))
-
   result <- download.CRUNCEP(outfolder = tmpdir,
                              start_date = "2000-01-01",
                              end_date = "2000-12-31",
@@ -23,17 +23,14 @@ test_that("download works and returns a valid CF file", {
   # Expect that reference times are present and set to start date
   expect_equal(cf_units, "days since 2000-01-01T00:00:00Z")
 
-  # Expect that overwrite argument is respected
-  # The skip message comes fromPEcAn.logger::logger.error,
-  # which writes to stderr but does not use message().
-  # If it did, this test would reduce to expect_message(download.CRUNCEP(...), "foo")
-  msg <- capture.output(download.CRUNCEP(outfolder = tmpdir,
-                                         start_date = "2000-01-01",
-                                         end_date = "2000-12-31",
-                                         site_id = 753,
-                                         lat.in = 40,
-                                         lon.in = -88,
-                                         overwrite = FALSE),
-                        type = "message")
-  expect_match(paste(msg, collapse="\n"), "already exists. Skipping")
+  expect_log(
+    download.CRUNCEP(
+      outfolder = tmpdir,
+      start_date = "2000-01-01",
+      end_date = "2000-12-31",
+      site_id = 753,
+      lat.in = 40,
+      lon.in = -88,
+      overwrite = FALSE),
+    "already exists. Skipping")
 })
diff --git a/modules/data.atmosphere/tests/testthat/test.download.NARR.R b/modules/data.atmosphere/tests/testthat/test.download.NARR.R
new file mode 100644
index 00000000000..c3980c4ee3a
--- /dev/null
+++ b/modules/data.atmosphere/tests/testthat/test.download.NARR.R
@@ -0,0 +1,27 @@
+context("Download NARR via THREDDS")
+
+start_date <- "2012-02-20"
+end_date <- "2012-03-05"
+ntime <- as.numeric(difftime(end_date, start_date) + 1) * 24 / 3 + 1
+lat.in <- 43.3724
+lon.in <- -89.9071
+outfolder <- tempdir()
+
+r <- download.NARR_site(outfolder, start_date, end_date, lat.in, lon.in,
+                        progress = TRUE, parallel = TRUE)
+
+test_that(
+  "NARR download works as expected",
+  {
+    expect_equal(nrow(r), 1)
+    expect_true(file.exists(r$file[1]))
+    nc <- ncdf4::nc_open(r$file)
+    temp <- ncdf4::ncvar_get(nc, "air_temperature")
+    precip <- ncdf4::ncvar_get(nc, "precipitation_flux")
+    expect_true(all(!is.na(temp)), all(temp > 0), length(temp) == ntime)
+    expect_true(all(!is.na(precip)), length(precip) == ntime)
+    ncdf4::nc_close(nc)
+  }
+)
+
+unlink(outfolder, recursive = TRUE, force = TRUE)
diff --git a/modules/data.atmosphere/tests/testthat/test.load.cfmet.R b/modules/data.atmosphere/tests/testthat/test.load.cfmet.R
index 647d15ca7bb..9310c7a7e0c 100644
--- a/modules/data.atmosphere/tests/testthat/test.load.cfmet.R
+++ b/modules/data.atmosphere/tests/testthat/test.load.cfmet.R
@@ -1,6 +1,6 @@
 context("loading data from PEcAn-CF met drivers")
 
-PEcAn.logger::logger.setLevel("OFF")
+PEcAn.logger::logger.setLevel("DEBUG")
 
 daily_file <- "data/urbana_daily_test.nc"
 subdaily_file <- "data/urbana_subdaily_test.nc"
@@ -8,7 +8,7 @@ subdaily_file <- "data/urbana_subdaily_test.nc"
 daily.nc <- ncdf4::nc_open(daily_file)
 on.exit(ncdf4::nc_close(daily.nc))
 daily.cf <- load.cfmet(met.nc = daily.nc, lat = 39.75, lon = -87.25,
-                       start.date = "1951-01-01", end.date = "1951-06-01")
+                       start.date = "1951-01-02", end.date = "1951-05-31")
 subdaily.nc <- ncdf4::nc_open(subdaily_file)
 on.exit(ncdf4::nc_close(subdaily.nc), add=TRUE)
 
@@ -34,26 +34,24 @@ test_that("data extracted from test pecan-cf met files is valid",{
 })
 
 test_that("load.cfmet respects start/end date",{
-  skip("Broken test #1343")
-  expect_equal(strftime(min(daily.cf$date), "%F"), "1951-01-01")
-  expect_equal(strftime(max(daily.cf$date), "%F"), "1951-05-30")
+  expect_equal(strftime(min(daily.cf$date), "%F"), "1951-01-02")
+  expect_equal(strftime(max(daily.cf$date), "%F"), "1951-05-31")
   expect_equal(nrow(daily.cf), 150)
 })
 
 test_that("load.cfmet throws error if start/end date out of range",{
-
-  skip("Broken test #1343")
-
   expect_error(load.cfmet(met.nc = subdaily.nc, lat = 39, lon = -88,
-                          start.date = "9999-01-01", end.date = "9999-02-02"))
+                          start.date = "9999-01-01", end.date = "9999-02-02"),
+               "run end date .* after met data ends")
   expect_error(load.cfmet(met.nc = subdaily.nc, lat = 39, lon = -88,
-                          start.date = "0000-01-01", end.date = "0000-02-02"))
+                          start.date = "0000-01-01", end.date = "0000-02-02"),
+               "run start date .* before met data starts")
   expect_error(load.cfmet(met.nc = daily.nc, lat = 39, lon = -88,
                           start.date = "1950-12-31", end.date = "1951-12-31"),
                "run start date .* before met data starts")
   expect_error(load.cfmet(met.nc = daily.nc, lat = 39, lon = -88,
-                          start.date = "1951-01-01", end.date = "1952-01-01"),
-               "run start date .* after met data ends")
+                          start.date = "1951-01-02", end.date = "1952-01-01"),
+               "run end date .* after met data ends")
 })
 
 test_that("load.cfmet enforces lat/lon matching",{
diff --git a/modules/data.atmosphere/vignettes/compare_narr_cruncep_met.Rmd b/modules/data.atmosphere/vignettes/compare_narr_cruncep_met.Rmd
index 5704ca0ac64..23487a535ee 100644
--- a/modules/data.atmosphere/vignettes/compare_narr_cruncep_met.Rmd
+++ b/modules/data.atmosphere/vignettes/compare_narr_cruncep_met.Rmd
@@ -33,6 +33,7 @@ TODO: clean up figure titles, labels, write explanations
 ```{r loading-libraries}
 library(PEcAn.data.atmosphere)
 library(data.table)
+library(ggplot2)
 theme_set(theme_bw())
 data(narr_cruncep_ebifarm)
 
@@ -98,15 +99,14 @@ cruncep$source <- "cruncep"
 narr$source <- "narr"
 narr3h$source <- "narr3h"
 ebifarm$source <- "ebifarm"
+```
 
+```{r reorder-met}
 met <- rbind(cruncep[,list(source, date, temp = DailyTemp.C, RH, wind = WindSpeed, precip, solar = solarR)],
              narr[,list(source, date, temp = Temp, RH, wind = WS, precip, solar = SolarR)],
              narr3h[,list(source, date, temp = DailyTemp.C, RH, wind = WindSpeed, precip, solar = solarR)],
              ebifarm[,list(source, date, temp = Temp, RH = RH/100, wind, precip, solar = solar)])
 
-```
-
-```{r reorder-met}
 met$source <- factor(met$source,
          levels = c("ebifarm", "narr3h", "narr", "cruncep"))
 ```
diff --git a/modules/data.hydrology/DESCRIPTION b/modules/data.hydrology/DESCRIPTION
index 1e648facb8a..8ab9da10e23 100644
--- a/modules/data.hydrology/DESCRIPTION
+++ b/modules/data.hydrology/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.data.hydrology
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze, Carl
     Davidson, Rob Kooper
 Maintainer: David LeBauer <dlebauer@illinois.edu>
@@ -21,4 +21,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Collate:
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/data.land/DESCRIPTION b/modules/data.land/DESCRIPTION
index 897f706c0b1..ac9479d5676 100644
--- a/modules/data.land/DESCRIPTION
+++ b/modules/data.land/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.data.land
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze,
     Carl Davidson, Rob Kooper, Alexey Shiklomanov
 Maintainer: Mike Dietze <dietze@bu.edu>, David LeBauer <dlebauer@illinois.edu>
@@ -14,7 +14,10 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
 Depends:
     PEcAn.DB,
     PEcAn.utils,
-    dbplyr
+    dbplyr, 
+    redland,
+    datapack,
+    dataone,
 Imports:
     PEcAn.logger,
     PEcAn.remote,
@@ -35,4 +38,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/data.land/NAMESPACE b/modules/data.land/NAMESPACE
index 647eb45c0d6..5c3a779c4e2 100644
--- a/modules/data.land/NAMESPACE
+++ b/modules/data.land/NAMESPACE
@@ -5,10 +5,12 @@ export(InventoryGrowthFusion)
 export(InventoryGrowthFusionDiagnostics)
 export(Read_Tucson)
 export(buildJAGSdata_InventoryRings)
+export(cohort2pool)
 export(dataone_download)
 export(download_package_rm)
 export(extract.stringCode)
 export(extract_FIA)
+export(extract_soil_gssurgo)
 export(extract_soil_nc)
 export(extract_veg)
 export(fia.to.psscss)
@@ -16,6 +18,7 @@ export(find.land)
 export(format_identifier)
 export(from.Tag)
 export(from.TreeCode)
+export(gSSURGO.Query)
 export(get.attributes)
 export(get.soil)
 export(get_resource_map)
@@ -32,6 +35,7 @@ export(plot2AGB)
 export(pool_ic_list2netcdf)
 export(pool_ic_netcdf2list)
 export(prepare_pools)
+export(sample_ic)
 export(sclass)
 export(shp2kml)
 export(soil.units)
@@ -43,5 +47,6 @@ export(to.Tag)
 export(to.TreeCode)
 export(write_ic)
 export(write_veg)
+import(XML)
 importFrom(magrittr,"%>%")
 importFrom(ncdf4,ncvar_get)
diff --git a/modules/data.land/R/cohort2pool.R b/modules/data.land/R/cohort2pool.R
new file mode 100644
index 00000000000..8a4d73cfde9
--- /dev/null
+++ b/modules/data.land/R/cohort2pool.R
@@ -0,0 +1,56 @@
+##' cohort2pool function
+##'Calculates total biomass using veg cohort file. 
+##'
+##' @export
+##' @param veg_file path to standard cohort veg_file
+##' @param allom_param parameters for allometric equation, a and b. Based on base-10 log-log linear model (power law)
+##' @author Saloni Shah
+##' @examples
+##' \dontrun{
+##' veg_file <- "~/downloads/FFT_site_1-25665/FFT.2008.veg.rds"
+##' cohort2pool(veg_File = veg_file, allom_param = NULL)
+##' }
+
+cohort2pool <- function(veg_file, allom_param = NULL) {
+  
+  ## Building Site ID from past directories
+  path <- dirname(veg_file)
+  last_dir <- basename(path)
+  nums_id <- strsplit(last_dir,"[^[:digit:]]")
+  base_id <- nums_id[[1]][length(nums_id[[1]])]
+  suffix <- nums_id[[1]][(length(nums_id[[1]])-1)]
+  siteid = as.numeric(suffix)*1e9 + as.numeric(base_id)
+  
+  ## load data
+  
+  dat <- readRDS(veg_file)
+  
+  ## Grab DBH
+  dbh <- dat[[2]]$DBH
+  
+  ## Grab allometry
+  if(is.null(allom_param)){
+    a <- 2                        
+    b <- 0.3
+  } else {
+    print("user provided allometry parameters not yet supported")
+    return(NULL)
+  }
+  
+  #Calculate AGB
+  biomass = 10^(a + b*log10(dbh))
+  biomass[is.na(biomass)] <- 0
+  tot_biomass <- sum(biomass)
+  AGB <- tot_biomass
+  
+  #Prep Arguments for pool_ic function
+  dims <- list(time =1) #Time dimension may be irrelevant
+  variables <-list(AGB = tot_biomass)
+  input <- list(dims = dims,
+                vals = variables)
+  
+  # Execute pool_ic function
+  result <- PEcAn.data.land::pool_ic_list2netcdf(input = input, outdir = path, siteid = siteid)
+  
+  return(result)
+}
\ No newline at end of file
diff --git a/modules/data.land/R/dataone_download.R b/modules/data.land/R/dataone_download.R
index 4e574bd3c6c..1207c835f76 100644
--- a/modules/data.land/R/dataone_download.R
+++ b/modules/data.land/R/dataone_download.R
@@ -13,11 +13,12 @@
 #'
 
 #' @examples 
-#' /dontrun{
-#' dataone_download(id = "doi:10.6073/pasta/63ad7159306bc031520f09b2faefcf87", filepath = "/fs/data1/pecan.data/dbfiles/")
+
+#' \dontrun{
+#' dataone_download(id = "doi:10.6073/pasta/63ad7159306bc031520f09b2faefcf87", filepath = "/fs/data1/pecan.data/dbfiles")
 #' }
 
-dataone_download = function(id, filepath = "/fs/data1/pecan.data/dbfiles/", CNode = "PROD", lazyLoad = FALSE, quiet = F){ 
+dataone_download = function(id, filepath = "/fs/data1/pecan.data/dbfiles", CNode = "PROD", lazyLoad = FALSE, quiet = FALSE){ 
   ### Check for wget functionality
   test <- try(system2("wget", "--version", stderr = TRUE))
   if (class(test) == "try-error") {
@@ -27,23 +28,28 @@ dataone_download = function(id, filepath = "/fs/data1/pecan.data/dbfiles/", CNod
   ### automatically retrieve mnId
   cn <- dataone::CNode(CNode) 
   locations <- dataone::resolve(cn, pid = id) 
+    PEcAn.logger::logger.info("Connecting to Member Node")
   mnId <- locations$data[1,"nodeIdentifier"] 
   
   ### begin D1 download process
   d1c <- dataone::D1Client("PROD", mnId)
+    PEcAn.logger::logger.info("Resolving file locations. This may take a few minutes.")
   pkg <- dataone::getDataPackage(d1c, id = id, lazyLoad = lazyLoad, quiet = quiet, limit = "1GB") 
   files <- datapack::getValue(pkg, name="sysmeta@formatId")
   n <- length(files) # number of files
+    PEcAn.logger::logger.info("Files located.")
 
-  # make new directory within this directory
-  newdir <- file.path(filepath, paste0("DataOne_", gsub("/", "-", id)))
-  dir.create(newdir)
+  ### make new directory within this directory
+  newdir_D1 <<- file.path(filepath, paste0("DataOne_", gsub("/", "-", id)))
+  dir.create(newdir_D1)
   
-  # download the data with wget
+  ### download the data with wget 
+  # '--header='  spoofs the user agent so that we avoid authentication errors. DataONE is now actively preventing web scraping.
   for(i in 1:n){
-    system(paste("cd", newdir, "&&", "{", "wget", "--content-disposition", names(files)[i], "; cd -; }")) # cd to newdir, download files with wget, cd back
+    PEcAn.logger::logger.info(paste("Downloading", "file", i, "of", n, sep = " "))
+    system(paste("cd", newdir_D1, "&&", "{", "wget",  "--header='User-Agent: Mozilla/5.0 (Windows NT 5.1; rv:23.0) Gecko/20100101 Firefox/23.0'", "--content-disposition", names(files)[i], "; cd -; }")) # cd to newdir, download files with wget, cd back
   }
- 
+    PEcAn.logger::logger.info(paste(n, "files downloaded to", newdir_D1, sep = " "))
 }
 
 
diff --git a/modules/data.land/R/ens.veg.module.R b/modules/data.land/R/ens.veg.module.R
new file mode 100644
index 00000000000..a4ba6308ec5
--- /dev/null
+++ b/modules/data.land/R/ens.veg.module.R
@@ -0,0 +1,67 @@
+##' Sampling/ensemble module
+##' 
+##' @param getveg.id list, input.id and dbfile.id of the IC file in intermediate pecan standard
+##' @param dbparms list, settings$database info reqired for opening a connection to DB
+##' @param input_veg list, this is a sublist of settings$run$inputs that has info about source, id, metadata of the requested IC file
+##' @param outfolder path to where the processed files will be written
+##' @param machine data frame, DB info regarding localhost machine id/hostname etc.
+##' @param start_date date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$start.date, otherwise start_date of the IC file in DB
+##' @param end_date date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$end.date, otherwise end_date of the IC file in DB
+##' @param n.ensemble integer, ensemble member number
+##' @param new_site data frame, id/lat/lon/name info about the site
+##' @param host list, host info as in settings$host, host$name forced to be "localhost" upstream
+##' 
+##' @author Istem Fer
+ens_veg_module <- function(getveg.id, dbparms, 
+                            input_veg, 
+                            outfolder, 
+                            machine, 
+                            start_date, end_date,
+                            n.ensemble,
+                            new_site, 
+                            host){
+  
+  machine_host <- machine$hostname
+  
+  #--------------------------------------------------------------------------------------------------#
+  # Write model specific IC files
+  bety <- dplyr::src_postgres(dbname   = dbparms$bety$dbname, 
+                              host     = dbparms$bety$host, 
+                              user     = dbparms$bety$user, 
+                              password = dbparms$bety$password)
+  
+  con <- bety$con
+  on.exit(db.close(con))
+  
+  PEcAn.logger::logger.info("Begin IC sampling, ensemble member: ", n.ensemble)
+  
+  spp.file <- db.query(paste("SELECT * from dbfiles where container_id =", getveg.id), con)
+  
+  pkg  <- "PEcAn.data.land"
+  fcn  <- "sample_ic"
+  
+  ensveg.id <- convert.input(input.id = getveg.id,
+                             outfolder = paste0(outfolder, "/", input_veg$source, "_ens", n.ensemble, ".", lubridate::year(start_date)), 
+                             formatname = "spp.info", 
+                             mimetype = "application/rds",
+                             site.id = new_site$id, 
+                             start_date = start_date, end_date = end_date, 
+                             pkg = pkg, fcn = fcn, 
+                             con = con, host = host, browndog = NULL, 
+                             write = TRUE, 
+                             overwrite = FALSE, 
+                             pattern = paste0(input_veg$source, "_ens", n.ensemble),
+                             forecast = TRUE,
+                             ensemble = 1,
+                             # fcn specific args 
+                             in.path = spp.file$file_path, 
+                             in.name = spp.file$file_name,
+                             n.ensemble = n.ensemble,
+                             machine_host = machine_host,
+                             source = input_veg$source)
+  
+  
+  return(ensveg.id)
+  
+  
+}
diff --git a/modules/data.land/R/extract_soil_nc.R b/modules/data.land/R/extract_soil_nc.R
index d19cb88552f..302983f5254 100644
--- a/modules/data.land/R/extract_soil_nc.R
+++ b/modules/data.land/R/extract_soil_nc.R
@@ -1,3 +1,63 @@
+#' Extract soil data from gssurgo
+#'
+#' @param outdir Output directory for writing down the netcdf file
+#' @param lat Latitude 
+#' @param lon Longitude
+#'
+#' @return It returns the address for the generated soil netcdf file
+#' @export
+#'
+#' @examples
+#' outdir  <- "~/paleon/envTest"
+#' lat     <- 40
+#' lon     <- -80
+#' \dontrun{
+#'    PEcAn.data.land::extract_soil_gssurgo(outdir,lat,lon)
+#' }
+#' @author Hamze Dokoohaki
+
+extract_soil_gssurgo<-function(outdir,lat,lon){
+  #reading the mapunit based on latitude and longitude of the site
+  #the output is a gml file which need to be downloaded and read as a spatial file but I don't do that.
+  #I just read the file as a text and parse it out and try to find the mukey==mapunitkey
+  RCurl::getURL(paste0("https://sdmdataaccess.nrcs.usda.gov/Spatial/SDMWGS84Geographic.wfs?SERVICE=WFS&VERSION=1.1.0&REQUEST=GetFeature&TYPENAME=MapunitPoly&FILTER=<Filter><DWithin><PropertyName>Geometry</PropertyName><gml:Point>%20<gml:coordinates>",
+                lon ,",", lat,"</gml:coordinates></gml:Point><Distance%20units=%27m%27>0</Distance>%20</DWithin></Filter>"), ssl.verifyhost=FALSE, ssl.verifypeer=FALSE)->xmll
+  regexpr('<ms:mukey>', xmll)->startp
+  regexpr('</ms:mukey>', xmll)->stopp
+  #if you found the mapunit key
+  if (startp==-1 | stopp==-1) PEcAn.logger::logger.error("There was no mapunit keys found for this site.")
+    # caaling the query function sending the mapunit key
+    soilprop<-gSSURGO.Query(substr(xmll, startp%>%as.numeric+10, stopp%>%as.numeric-1))
+    #Filter based on the most abundant component in that mapunit key 
+    soilprop.new<-soilprop%>%
+      filter(comppct_r==max(soilprop$comppct_r, na.rm=T), hzdept_r>0)%>%
+      arrange(hzdept_r)%>%
+      select(-comppct_r, -chkey, -aws050wta)%>%
+      `colnames<-`( c("soil_cec", "fraction_of_sand_in_soil", "fraction_of_silt_in_soil", "fraction_of_clay_in_soil", "soilC" , "soil_depth" , "fraction_of_gravel_in_soil",
+                        "soil_bulk_density" , "soil_ph") )
+    #unit colnversion
+    soilprop.new [, c("fraction_of_sand_in_soil", "fraction_of_silt_in_soil" , "fraction_of_clay_in_soil" ,"fraction_of_gravel_in_soil" , "soil_depth")] <- soilprop.new [, c("fraction_of_sand_in_soil", "fraction_of_silt_in_soil" , "fraction_of_clay_in_soil" ,"fraction_of_gravel_in_soil" , "soil_depth")]/100
+    soilprop.new [, c("soilC")] <- soilprop.new [,c("soilC")]*0.69/100
+    soilprop.new$soil_bulk_density <- udunits2::ud.convert(soilprop.new$soil_bulk_density, "g cm-3", "kg m-3")
+    #converting it to list
+    names(soilprop.new) %>%
+      purrr::map(function(var){
+        soilprop.new[,var]
+      })%>% setNames(names(soilprop.new))->soil.data.gssurgo
+    # calc new filename
+    prefix <- "gSSURGO_soil"
+    new.file <- file.path(outdir, paste0(prefix,".nc"))
+    #sending it to the func where some new params will be added and then it will be written down as nc file.
+    soil2netcdf(soil.data.gssurgo, new.file)
+    
+    return(new.file)
+}
+
+
+
+
+
+
 #' Extract soil data
 #'
 #' @param in.file 
diff --git a/modules/data.land/R/gSSURGO_Query.R b/modules/data.land/R/gSSURGO_Query.R
new file mode 100644
index 00000000000..ba6ac10ed27
--- /dev/null
+++ b/modules/data.land/R/gSSURGO_Query.R
@@ -0,0 +1,80 @@
+############ Retrives soil data from gssurgo
+#' This function queries the gSSURGO database for a series of map unit keys
+#'
+#' @param mukeys map unit key from gssurgo
+#'
+#' @return a dataframe with soil properties. units can be looked up from database documentation
+#' @export
+#'
+#' @details 
+#' Full documention of available tables and their relationships can be found here \url{www.sdmdataaccess.nrcs.usda.gov/QueryHelp.aspx}
+#' There have been occasions where NRCS made some minor changes to the structure of the API which this code is where those changes need
+#' to be implemneted here.
+#' @import XML 
+gSSURGO.Query<-function(mukeys=2747727){
+  ######### Reteiv soil
+  headerFields =
+    c(Accept = "text/xml",
+      Accept = "multipart/*",
+      'Content-Type' = "text/xml; charset=utf-8",
+      SOAPAction = "http://SDMDataAccess.nrcs.usda.gov/Tabular/SDMTabularService.asmx/RunQuery")
+  
+  body = paste('<?xml version="1.0" encoding="utf-8"?>
+               <soap:Envelope xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/">
+               <soap:Body>
+               <RunQuery xmlns="http://SDMDataAccess.nrcs.usda.gov/Tabular/SDMTabularService.asmx">
+               <Query>
+               SELECT mapunit.mukey, mapunit.muname, component.cokey, component.mukey, component.comppct_r, chorizon.cec7_r,
+               chorizon.sandtotal_r,chorizon.silttotal_r,chorizon.claytotal_r,chorizon.om_r,chorizon.hzdept_r,chorizon.frag3to10_r,chorizon.dbovendry_r,
+               chorizon.ph1to1h2o_r,chorizon.cokey,chorizon.chkey,
+               muaggatt.aws050wta from mapunit
+               join muaggatt on mapunit.mukey=muaggatt.mukey
+               join component on mapunit.mukey=component.mukey
+               join chorizon on component.cokey=chorizon.cokey
+               where mapunit.mukey in (', paste(mukeys,collapse = ", "),');
+               </Query>
+               </RunQuery>
+               </soap:Body>
+               </soap:Envelope>')
+  reader <- RCurl::basicTextGatherer()
+  out<-RCurl::curlPerform(url = "https://SDMDataAccess.nrcs.usda.gov/Tabular/SDMTabularService.asmx",
+                          httpheader = headerFields,  postfields = body,
+                          writefunction = reader$update
+  )
+  suppressWarnings(
+    suppressMessages({
+      xml_doc <- xmlTreeParse(reader$value())
+      xmltop  <- xmlRoot(xml_doc)
+      tablesxml <- (xmltop[[1]]["RunQueryResponse"][[1]]["RunQueryResult"][[1]]["diffgram"][[1]]["NewDataSet"][[1]])
+    })
+  )
+  
+  #parsing the table  
+  tryCatch({
+    suppressMessages(
+      suppressWarnings({
+        tables<-getNodeSet(tablesxml,"//Table")
+        
+        ##### All datatables below newdataset
+        # This method leaves out the variables are all NAs  - so we can't have a fixed naming scheme for this df
+        dfs<-tables%>%
+          purrr::map_dfr(function(child){
+            xmlToList(child)[1:13]%>%
+              purrr::map(~ as.numeric( .x ))%>%
+              t%>%
+              as.data.frame()
+          })%>%
+          mutate_all(as.numeric)%>%
+          select(comppct_r:aws050wta)
+        
+      })
+    )
+    
+    
+    return(dfs)
+  },
+  error=function(cond) {
+    return(NULL)
+  })
+  
+}
diff --git a/modules/data.land/R/get.veg.module.R b/modules/data.land/R/get.veg.module.R
index 2f325e58c81..63be4ea6f1b 100644
--- a/modules/data.land/R/get.veg.module.R
+++ b/modules/data.land/R/get.veg.module.R
@@ -1,9 +1,22 @@
-.get.veg.module <- function(input_veg, 
+##' Load/extract + match species module
+##' 
+##' @param input_veg list, this is a sublist of settings$run$inputs that has info about source, id, metadata of the requested IC file
+##' @param outfolder path to where the processed files will be written
+##' @param start_date date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$start.date, otherwise start_date of the IC file in DB
+##' @param end_date date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$end.date, otherwise end_date of the IC file in DB
+##' @param dbparms list, settings$database info reqired for opening a connection to DB
+##' @param new_site data frame, id/lat/lon/name info about the site
+##' @param host list, host info as in settings$host, host$name forced to be "localhost" upstream
+##' @param machine_host local machine hostname, e.g. "pecan2.bu.edu"
+##' @param overwrite logical flag for convert.input
+##' 
+##' @author Istem Fer
+get_veg_module <- function(input_veg, 
                             outfolder,
                             start_date, end_date,
                             dbparms,
                             new_site, 
-                            host, machine_host,
+                            host, machine_host, 
                             overwrite){
 
   #--------------------------------------------------------------------------------------------------#
@@ -13,8 +26,7 @@
   lat       <- new_site$lat
   lon       <- new_site$lon
   site_id   <- new_site$id
-  site_name <- new_site$name   
-  
+  site_name <- new_site$name
   ## Prepare to call convert.inputs
   pkg  <- "PEcAn.data.land"
   bety <- dplyr::src_postgres(dbname   = dbparms$bety$dbname, 
@@ -28,7 +40,8 @@
     
     fcn <- "extract_veg"
     
-    getveg.id <- convert.input(input.id = NA,
+    
+  getveg.id <- convert.input(input.id = NA,
                                outfolder = outfolder, 
                                formatname = "spp.info", 
                                mimetype = "application/rds",
@@ -39,9 +52,9 @@
                                write = TRUE, 
                                overwrite = overwrite, 
                                # fcn specific args 
-                               new_site = new.site,
+                               new_site = new_site,
                                gridres = input_veg$gridres, dbparms = dbparms,
-                               machine_host = machine_host,
+                               machine_host = machine_host, input_veg = input, 
                                source = input_veg$source)
   
     
@@ -50,13 +63,11 @@
   }else{
     
     fcn <- "load_veg"
-    
-    if(!is.null(input_veg$source.id)){
-      source.id <- input_veg$source.id
+    if(!is.null(input_veg$id)){
+      source.id <- input_veg$id
     }else{
-      PEcAn.logger::logger.error("Must specify input source.id")
+      PEcAn.logger::logger.error("Must specify input id")
     }
-    
     getveg.id <- convert.input(input.id = NA,
                                outfolder = outfolder, 
                                formatname = "spp.info", 
@@ -68,21 +79,21 @@
                                write = TRUE, 
                                overwrite = overwrite, 
                                # fcn specific args 
-                               new_site = new_site,
+                               new_site = new.site,
                                source_id = source.id,
                                format_name = input_veg$match.format,
                                dbparms = dbparms,
                                machine_host = machine_host,
                                source = input_veg$source,
-                               ##  any meta data passed via settings to be used in the IC files (in veg2model)
+                               ##  any metadata passed via settings to be used in the IC files (in veg2model)
                                ##  if different than defaults, e.g.:
                                ##
-                               ##  <meta>
+                               ##  <metadata>
                                ##   <trk>2</trk>
                                ##   <age>70</age>
-                               ##  </meta>
+                               ##  </metadata>
                                ##
-                               icmeta = input_veg$meta)
+                               icmeta = input_veg$metadata)
     
 
     return(getveg.id)
diff --git a/modules/data.land/R/ic_process.R b/modules/data.land/R/ic_process.R
index a086773d45b..804e8a3c0be 100644
--- a/modules/data.land/R/ic_process.R
+++ b/modules/data.land/R/ic_process.R
@@ -25,14 +25,17 @@ ic_process <- function(settings, input, dir, overwrite = FALSE){
   # If overwrite is a plain boolean, fill in defaults for each module
   if (!is.list(overwrite)) {
     if (overwrite) {
-      overwrite <- list(getveg = TRUE,  putveg = TRUE)
+      overwrite <- list(getveg = TRUE,  ensveg = TRUE,  putveg = TRUE)
     } else {
-      overwrite <- list(getveg = FALSE, putveg = FALSE)
+      overwrite <- list(getveg = FALSE, ensveg = FALSE, putveg = FALSE)
     }
   } else {
     if (is.null(overwrite$getveg)) {
       overwrite$getveg <- FALSE
     }
+    if (is.null(overwrite$ensveg)) {
+      overwrite$ensveg <- FALSE
+    }
     if (is.null(overwrite$putveg)) {
       overwrite$putveg <- FALSE
     }
@@ -60,14 +63,12 @@ ic_process <- function(settings, input, dir, overwrite = FALSE){
     end_date   <- settings$run$end.date
   }else{
     
-    query      <- paste0("SELECT * FROM inputs where id = ", input$source.id)
-    input_file <- db.query(query, con = con)
-    start_date <- input_file$start_date
-    end_date   <- input_file$end_date
+   query      <- paste0("SELECT * FROM inputs where id = ", input$id)
+   input_file <- db.query(query, con = con) 
+   start_date <- input_file$start_date
+   end_date   <- input_file$end_date
     
   }
-  
-  
   # set up host information
   machine.host <- ifelse(host == "localhost" || host$name == "localhost", PEcAn.remote::fqdn(), host$name)
   machine <- db.query(paste0("SELECT * from machines where hostname = '", machine.host, "'"), con)
@@ -83,93 +84,172 @@ ic_process <- function(settings, input, dir, overwrite = FALSE){
                          lat = PEcAn.data.atmosphere::db.site.lat.lon(site$id, con = con)$lat, 
                          lon = PEcAn.data.atmosphere::db.site.lat.lon(site$id, con = con)$lon)
   new.site$name <- settings$run$site$name
+  
+
   str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
   
+  
   outfolder <- file.path(dir, paste0(input$source, "_site_", str_ns))
 
-  # veg or some other IC? Need to update later for other models
-  vegIC <- c("css", "pss", "site")
+   
   getveg.id <- putveg.id <- NULL
   
+  # this also needs to be in for-loop, n = 1 should be a special case
+  # but we might still want an ensemble from a single source, so need a check accordinly
+  # best pass a flag (<ensemble.source>TRUE<\ensemble.source>) if that's the case, omit the flag otherwise
+  # currently downloading/reading in different ensemble members is not implemented, 
+  # then we'll need to pass pattern, ensemble etc to convert.input
+  nsource <- ifelse(!is.null(input$ensemble.source) & !is.null(input$ensemble), as.numeric(input$ensemble), 1)
   
-  #--------------------------------------------------------------------------------------------------#
+#--------------------------------------------------------------------------------------------------#
   # Load/extract + match species module
   
-  if (is.null(getveg.id) & is.null(putveg.id) & input$output %in% vegIC) {
+  if (is.null(getveg.id) & is.null(putveg.id)) {
+
+    getveg.id <- list()
 
-    getveg.id <- .get.veg.module(input_veg = input, 
-                              outfolder = outfolder, 
-                              start_date = start_date, end_date = end_date,
-                              dbparms = dbparms,
-                              new_site = new.site,
-                              host = host, 
-                              machine_host = machine.host,
-                              overwrite = overwrite$getveg)
+    for(i in seq_len(nsource)){
+      getveg.id[[i]] <- get_veg_module(input_veg    = input, 
+                                       outfolder    = outfolder, 
+                                       start_date   = start_date, 
+                                       end_date     = end_date,
+                                       dbparms      = dbparms,
+                                       new_site     = new.site,
+                                       host         = host, 
+                                       machine_host = machine.host,
+                                       overwrite    = overwrite$getveg)
+    }
 
   }
   
-
-  #--------------------------------------------------------------------------------------------------#
+#--------------------------------------------------------------------------------------------------#
+  # Sampling/ensemble module
+  
+  if (!is.null(getveg.id) & !is.null(input$ensemble) & is.null(putveg.id)) { 
+    
+    ctr <- 1
+    
+    ensveg.id <- list()
+    for(i in seq_len(as.numeric(input$ensemble))){
+      
+      ctr <- ifelse(nsource == 1, 1, i)
+      ensveg.id[[i]] <- ens_veg_module(getveg.id    = getveg.id[[ctr]], 
+                                       dbparms      = dbparms,
+                                       input_veg    = input, 
+                                       outfolder    = outfolder, 
+                                       machine      = machine, 
+                                       start_date   = start_date, 
+                                       end_date     = end_date,
+                                       n.ensemble   = i,
+                                       new_site     = new.site,
+                                       host         = host)
+    }
+    getveg.id <- ensveg.id
+  }
+  
+#--------------------------------------------------------------------------------------------------#
   # Match species to PFTs + veg2model module
   
-  if (!is.null(getveg.id) & is.null(putveg.id) & input$output %in% vegIC) { # probably need a more sophisticated check here
+  if (!is.null(getveg.id) & is.null(putveg.id)) { # probably need a more sophisticated check here
     
-    putveg.id <- .put.veg.module(getveg.id = getveg.id, dbparms = dbparms,
-                                input_veg = input, pfts = settings$pfts,
-                                outfolder = outfolder, 
-                                dir = dir, machine = machine, model = model,
-                                start_date = start_date, end_date = end_date,
-                                new_site = new.site,
-                                host = host, overwrite = overwrite$putveg)
+    putveg.id <- list()
+    for(i in seq_along(getveg.id)){
+      putveg.id[[i]] <- put_veg_module(getveg.id  = getveg.id[[i]], 
+                                       dbparms    = dbparms,
+                                       input_veg  = input, 
+                                       pfts       = settings$pfts,
+                                       outfolder  = outfolder, 
+                                       n.ensemble = i,
+                                       dir        = dir, 
+                                       machine    = machine, 
+                                       model      = model,
+                                       start_date = start_date, 
+                                       end_date   = end_date,
+                                       new_site   = new.site,
+                                       host       = host, 
+                                       overwrite  = overwrite$putveg)
+    }
+
     
   }
 
   #--------------------------------------------------------------------------------------------------#
   # Fill settings
-  if (!is.null(putveg.id) & input$output %in% vegIC) {
+  if (!is.null(putveg.id)) {
     
+    # extend the inputs list for ensemble members
+    settings_inputs <- lapply(seq_along(settings$run$inputs), function(x) rep(settings$run$inputs[[x]], each = length((putveg.id))))
+
+    # make sure all sublists are grouped and renamed to have unique tags, e.g.:
+    # <id>
+    #   <id1>...</id1>
+    #        ...
+    #   <idN>...</idN>
+    # </id>
+    # <path>
+    #   <path1>...</path1>
+    #          ...
+    #   <pathN>...</pathN>
+    # </path>
+    settings_inputs <- lapply(seq_along(settings_inputs), function(x){
+      tmp.list <- settings_inputs[[x]]
+      sub_names <- names(settings$run$inputs[[x]])
+      names(settings_inputs[[x]]) <- paste0(names(settings_inputs[[x]]), rep(seq_along(putveg.id), length(settings$run$inputs[[x]])))
+      tmp.list  <- lapply(seq_along(sub_names), function(v) return(settings_inputs[[x]][names(tmp.list) == sub_names[v]]))
+      names(tmp.list) <- sub_names
+      if(is.null(tmp.list$path)) tmp.list$path <- list()
+      return(tmp.list)
+    })
     
-    model_file <- db.query(paste("SELECT * from dbfiles where container_id =", putveg.id), con)
-    
-    # now that we don't have multipasses, convert.input only inserts 1st filename
-    # do we want to change it in convert.inputs such that it loops over the dbfile.insert?
-    path_to_settings <- file.path(model_file[["file_path"]], model_file[["file_name"]])
-    settings$run$inputs[[input$output]][['path']] <- path_to_settings
+    names(settings_inputs) <- names(settings$run$inputs)
     
-    # NOTE : THIS BIT IS SENSITIVE TO THE ORDER OF TAGS IN PECAN.XML
-    # this took care of "css" only, others have the same prefix
-    if(input$output == "css"){
-      settings$run$inputs[["pss"]][['path']]  <- gsub("css","pss", path_to_settings)
-      settings$run$inputs[["site"]][['path']] <- gsub("css","site", path_to_settings)
+    for(i in seq_along(putveg.id)){
       
-      # IF: For now IC workflow is only working for ED and it's the only case for copying to remote
-      # but this copy to remote might need to go out of this if-block and change
+      model_file <- db.query(paste("SELECT * from dbfiles where container_id =", putveg.id[[i]], "and machine_id =", machine$id), con)
       
-      # Copy to remote, update DB and change paths if needed
-      if (settings$host$name != "localhost") {
-        
-        remote_dir <- file.path(settings$host$folder, paste0(input$source, "_site_", str_ns))
+      # now that we don't have multipasses, convert.input only inserts 1st filename
+      # do we want to change it in convert.inputs such that it loops over the dbfile.insert?
+      path_to_settings <- file.path(model_file[["file_path"]], model_file[["file_name"]])
+      settings_inputs[[input$output]][['path']][[paste0('path', i)]] <- path_to_settings
+      
+      # NOTE : THIS BIT IS SENSITIVE TO THE ORDER OF TAGS IN PECAN.XML
+      # this took care of "css" only, others have the same prefix
+      if(input$output == "css"){  
+        settings_inputs[["pss"]][['path']][[paste0('path', i)]]  <- gsub("css","pss", path_to_settings)
+        settings_inputs[["site"]][['path']][[paste0('path', i)]] <- gsub("css","site", path_to_settings)
         
-        # copies css
-        css_file <- basename(settings$run$inputs[["css"]][['path']])
-        PEcAn.remote::remote.copy.update(putveg.id, remote_dir, remote_file_name = css_file, settings$host, con)
-        settings$run$inputs[["css"]][['path']] <- file.path(remote_dir, css_file)
+        # IF: For now IC workflow is only working for ED and it's the only case for copying to remote
+        # but this copy to remote might need to go out of this if-block and change
         
-        # pss 
-        pss_file <-  basename(settings$run$inputs[["pss"]][['path']])
-        PEcAn.remote::remote.copy.update(putveg.id, remote_dir, remote_file_name = pss_file, settings$host, con)
-        settings$run$inputs[["pss"]][['path']] <- file.path(remote_dir, pss_file)
+        # Copy to remote, update DB and change paths if needed
+        if (settings$host$name != "localhost") {
           
-        # site
-        site_file <- basename(settings$run$inputs[["site"]][['path']])
-        PEcAn.remote::remote.copy.update(putveg.id, remote_dir, remote_file_name = site_file, settings$host, con)
-        settings$run$inputs[["site"]][['path']] <- file.path(remote_dir, site_file)
-        
+          folder_dir <- paste0(input$source, "_site_", str_ns, "/", input$source, "_ens", i, ".", lubridate::year(start_date))
+          remote_dir <- file.path(settings$host$folder, folder_dir)
+          
+          # copies css
+          css_file <- settings_inputs[["css"]][['path']][[paste0('path', i)]]
+          PEcAn.remote::remote.copy.update(putveg.id[[i]], remote_dir, local_file_path = css_file, host = settings$host, con = con)
+          settings_inputs[["css"]][['path']][[paste0('path', i)]] <- file.path(remote_dir, basename(css_file))
+          
+          # pss 
+          pss_file <- settings_inputs[["pss"]][['path']][[paste0('path', i)]]
+          PEcAn.remote::remote.copy.update(putveg.id[[i]], remote_dir, local_file_path = pss_file, host = settings$host, con = con)
+          settings_inputs[["pss"]][['path']][[paste0('path', i)]] <- file.path(remote_dir, basename(pss_file))
+          
+          # site
+          site_file <- settings_inputs[["site"]][['path']][[paste0('path', i)]]
+          PEcAn.remote::remote.copy.update(putveg.id[[i]], remote_dir, local_file_path = site_file, host = settings$host, con = con)
+          settings_inputs[["site"]][['path']][[paste0('path', i)]] <- file.path(remote_dir, basename(site_file))
+          
+        }
       }
     }
-    
+
+    settings$run$inputs <- settings_inputs
   }
   
+  PEcAn.logger::logger.info("Finished IC for vegetation.")
   
   return(settings)
 } # ic_process
diff --git a/modules/data.land/R/load_veg.R b/modules/data.land/R/load_veg.R
index 04f5ec02e0c..d27455d67be 100644
--- a/modules/data.land/R/load_veg.R
+++ b/modules/data.land/R/load_veg.R
@@ -7,8 +7,7 @@ load_veg <- function(new_site, start_date, end_date,
                      source_id, source, icmeta = NULL, format_name = NULL, 
                      machine_host, dbparms, outfolder, overwrite = FALSE, ...){
   
-  
-  bety <- dplyr::src_postgres(dbname   = dbparms$bety$dbname, 
+   bety <- dplyr::src_postgres(dbname   = dbparms$bety$dbname, 
                               host     = dbparms$bety$host, 
                               user     = dbparms$bety$user, 
                               password = dbparms$bety$password)
@@ -17,7 +16,7 @@ load_veg <- function(new_site, start_date, end_date,
   # Load data : this step requires DB connections 
   
   # get machine id
-  machine_id <- get.id(table = "machines", colnames = "hostname", 
+  machine_id <- PEcAn.DB::get.id(table = "machines", colnames = "hostname", 
                        values = machine_host, con = bety$con)
   
   # query data.path from source id [input id in BETY]
@@ -25,7 +24,8 @@ load_veg <- function(new_site, start_date, end_date,
                        "AND machine_id=", machine_id)
   
   input_file <- PEcAn.DB::db.query(query, con = bety$con)
-  data_path  <- file.path(input_file[["file_path"]], input_file[["file_name"]])
+  data_path  <- file.path(input_file[["file_path"]], input_file[["file_name"]]) #File path and file name of source file from bety
+
   
   # query format info
   format     <- PEcAn.DB::query.format.vars(bety = bety, input.id = source_id)
@@ -33,6 +33,7 @@ load_veg <- function(new_site, start_date, end_date,
   # load_data{benchmark}
   obs        <- PEcAn.benchmark::load_data(data.path = data_path, format, site = new_site)
   
+  
   #--------------------------------------------------------------------------------------------------#
   # Match species : this step requires DB connections 
   
@@ -42,6 +43,7 @@ load_veg <- function(new_site, start_date, end_date,
   }else if("latin_name" %in% format$vars$bety_name){
     # not encountered an actual case yet, put here as a reminder
     code.col <- "latin_name"
+    format_name <- "latin_name" 
     # might indicate a custom format, should be passed to function
     if(is.null(format_name)){
       PEcAn.logger::logger.severe("Can't match code to species. Please provide 'match.format' via settings.")
@@ -49,13 +51,10 @@ load_veg <- function(new_site, start_date, end_date,
   }else{
     PEcAn.logger::logger.severe("Can't match code to species. No valid format found.")
   } 
-  
   # match code to species ID
   # no lower case
   obs[[code.col]] <- toupper(obs[[code.col]])
-  
   spp.info <- match_species_id(input_codes = obs[[code.col]], format_name = format_name, bety = bety)
-  
   # merge with data
   tmp <- spp.info[ , colnames(spp.info) != "input_code"]
   
@@ -66,19 +65,25 @@ load_veg <- function(new_site, start_date, end_date,
     # the first sublist can be for the metadata maybe?
     # to be handled by veg2model later
     veg_info[[1]] <- icmeta
+    if(is.null(icmeta$area)){
+      # this might not be needed for all models but let's put a warning here before it's too late
+      PEcAn.logger::logger.warn("IMPORTANT : No area info passed via metadata, 
+                                if your model needs plot area in IC calculations please provide it under 'settings$run$inputs$css$metadata$area'.")
+    }
   }else{
     veg_info[[1]] <- NULL 
+    # this might not be needed for all models but let's put a warning here before it's too late
+    PEcAn.logger::logger.warn("IMPORTANT : No area info passed via metadata, 
+                              if your model needs plot area in IC calculations please provide it under 'settings$run$inputs$css$metadata$area'.")
   }
   
   veg_info[[2]] <- cbind(obs, tmp)
   
-  
   #--------------------------------------------------------------------------------------------------#
   # Write vegettion data as rds, return results to convert.input
   
   # need check for overwrite
   sppfilename <- write_veg(outfolder, start_date, veg_info = veg_info, source)
-  
   # Build results dataframe for convert.input
   results <- data.frame(file = sppfilename, 
                         host = machine_host, 
@@ -88,7 +93,6 @@ load_veg <- function(new_site, start_date, end_date,
                         enddate = end_date, 
                         dbfile.name = basename(sppfilename), 
                         stringsAsFactors = FALSE)
-  
   ### return for convert.inputs
   return(invisible(results))  
   
diff --git a/modules/data.land/R/match_pft.R b/modules/data.land/R/match_pft.R
index d14bb596894..5cfe24bc93c 100644
--- a/modules/data.land/R/match_pft.R
+++ b/modules/data.land/R/match_pft.R
@@ -37,7 +37,7 @@ match_pft <- function(bety_species_id, pfts, query = NULL, con = NULL, allow_mis
       bety_pft <- traits::betydb_query(name = pft$name, table = 'pfts', user = 'bety', pwd = 'bety')
       # query species id
       bety_species <- traits::betydb_query(pft_id = bety_pft$id, table = 'pfts_species', user = 'bety', pwd = 'bety')
-      bety_list[[pft$name]] <- bety_species$pfts_species.specie_id
+      bety_list[[pft$name]] <- bety_species$specie_id
     }
     tmp <- lapply(seq_along(bety_list), function(x){
         data.frame(pft = rep(names(bety_list)[x], length(bety_list[[x]])),
diff --git a/modules/data.land/R/match_species_id.R b/modules/data.land/R/match_species_id.R
index 64b3ba4efc2..27f6821858a 100644
--- a/modules/data.land/R/match_species_id.R
+++ b/modules/data.land/R/match_species_id.R
@@ -36,82 +36,78 @@
 #' @importFrom magrittr %>%
 #' @export
 match_species_id <- function(input_codes, format_name = 'custom', bety = NULL, translation_table = NULL, ...) {
-    # Relate format names to BETY columns
-    formats_dict <- c('usda' = 'Symbol',
-                      'fia' = 'spcd',
-                      'latin_name' = 'scientificname',
-                      'custom' = 'custom')
-    if (!format_name %in% names(formats_dict)) {
-        PEcAn.logger::logger.severe('format_name "', format_name, '" not found. ',
-                                   'Please use one of the following: ',
-                                   paste(names(formats_dict), collapse = ', '))
-    }
-    if (!is.null(translation_table)) {
-        msg2 <- c('Found the following columns: ',
-                  paste(colnames(translation_table), collapse = ', '))
-        if (!'input_code' %in% colnames(translation_table)) {
-            PEcAn.logger::logger.severe('Custom translation table must have column "input_code". ', msg2)
-        } else if (!'bety_species_id' %in% colnames(translation_table)) {
-            PEcAn.logger::logger.severe('Custom translation table must have column "bety_species_id". ', msg2)
-        } else {
-            if (any(grepl('^(genus|species)$', colnames(translation_table)))) {
-                PEcAn.logger::logger.warn('"genus" or "species" columns found in translation table. ',
-                                         'Because these also match the BETY table, ',
-                                         'they will be ignored by the merge, but their names will ',
-                                         'be appended with ".translation_table" for disambiguation')
-            }
-            bety_species <- dplyr::tbl(bety, 'species') %>%
-                dplyr::filter_(~id %in% translation_table[['bety_species_id']]) %>%
-                dplyr::select_('bety_species_id' = 'id', 'genus', 'species') %>%
-                dplyr::collect()
-            translation <- dplyr::left_join(translation_table, bety_species,
-                                            by = 'bety_species_id',
-                                            suffix = c('.translation_table', ''))
-        }
-    } else {
-      column <- formats_dict[format_name]
-      if(!is.null(bety)){
-        # query BETY
-        filter_cri <- lazyeval::interp(~ col %in% codes,
-                                       col = as.name(column),
-                                       codes = input_codes)
-        translation <- dplyr::tbl(bety, 'species') %>%
-          dplyr::filter_(filter_cri) %>%
-          dplyr::select_('bety_species_id' = 'id', 'genus', 'species',
-                         'input_code' = column) %>%
-          dplyr::collect()
-
-      }else{
-        # use traits package
-
-        # can call traits::betydb_query one at a time?
-        # reduce the number of calls
-        translation <- data.frame(input_code = unique(input_codes),
-                           bety_species_id  = rep(NA, length(unique(input_codes))),
-                           genus            = rep(NA, length(unique(input_codes))),
-                           species          = rep(NA, length(unique(input_codes))),
-                           stringsAsFactors = FALSE)
-
-        for(i in 1:nrow(unique.tmp)){
-          foo <- eval(parse(text =paste0("traits::betydb_query(",
-                                  column, "='", unique.tmp$input_code[i], "', table = 'species', user = 'bety', pwd = 'bety')")))
-          translation$bety_species_id[i] <- foo$id
-          translation$genus[i]           <- foo$genus
-          translation$species[i]         <- foo$species
-        }
 
+  # Relate format names to BETY columns
+  formats_dict <- c('usda' = 'Symbol',
+                    'fia' = 'spcd',
+                    'latin_name' = 'scientificname',
+                    'custom' = 'custom')
+  if (!format_name %in% names(formats_dict)) {
+    PEcAn.logger::logger.severe('format_name "', format_name, '" not found. ',
+                                'Please use one of the following: ',
+                                paste(names(formats_dict), collapse = ', '))
+  }
+  if (!is.null(translation_table)) {
+    msg2 <- c('Found the following columns: ',
+              paste(colnames(translation_table), collapse = ', '))
+    if (!'input_code' %in% colnames(translation_table)) {
+      PEcAn.logger::logger.severe('Custom translation table must have column "input_code". ', msg2)
+    } else if (!'bety_species_id' %in% colnames(translation_table)) {
+      PEcAn.logger::logger.severe('Custom translation table must have column "bety_species_id". ', msg2)
+    } else {
+      if (any(grepl('^(genus|species)$', colnames(translation_table)))) {
+        PEcAn.logger::logger.warn('"genus" or "species" columns found in translation table. ',
+                                  'Because these also match the BETY table, ',
+                                  'they will be ignored by the merge, but their names will ',
+                                  'be appended with ".translation_table" for disambiguation')
       }
-
+      bety_species <- dplyr::tbl(bety, 'species') %>%
+        dplyr::filter_(~id %in% translation_table[['bety_species_id']]) %>%
+        dplyr::select_('bety_species_id' = 'id', 'genus', 'species') %>%
+        dplyr::collect()
+      translation <- dplyr::left_join(translation_table, bety_species,
+                                      by = 'bety_species_id',
+                                      suffix = c('.translation_table', ''))
     }
-    input_table <- data.frame(input_code = input_codes, stringsAsFactors = FALSE)
-    # preserving the order is important for downstream
-    merge_table <- dplyr::left_join(input_table, translation)
-
-    if(sum(is.na(merge_table$bety_species_id)) > 0){
-      bad <- unique(merge_table$input_code[is.na(merge_table$bety_species_id)])
-      PEcAn.logger::logger.error(paste0("Species for the following code(s) not found : ", paste(bad, collapse = ", ")))
+  } else {
+    column <- formats_dict[format_name]
+    if(!is.null(bety)){
+      # query BETY for species, id, genus, and latin name
+      translation <- dplyr::tbl(bety, 'species') %>%
+        dplyr::select_('bety_species_id' = 'id', 'genus', 'species',
+                       'input_code' = column) %>%
+        dplyr::collect()
+       translation<- translation %>% dplyr::mutate(input_code = toupper(input_code)) #match_species_id is case-sensitive, to match species names in obs to translation, 'input_codes' needs to be upper-case since 'latin_names' in obs are upper-case
+      colnames(translation) <- c('bety_species_id', 'genus', 'species',"input_codes") #semi_join requires that the column name within the tables being matched have the same name
+      translation <- dplyr::semi_join(translation, as.data.frame(input_codes), by = "input_codes" )  #Keep rows in translation table that have the same 'latin_name' within obs
+    }else{
+      # use traits package
+      
+      # can call traits::betydb_query one at a time?
+      # reduce the number of calls
+      translation <- data.frame(bety_species_id  = rep(NA, length(unique(input_codes))),
+                                genus            = rep(NA, length(unique(input_codes))),
+                                species          = rep(NA, length(unique(input_codes))),
+                                input_code = unique(input_codes),
+                                stringsAsFactors = FALSE)
+      for(i in 1:nrow(translation)){
+        foo <- eval(parse(text =paste0("traits::betydb_query(",
+                                       column, "='", translation$input_code[i], "', table = 'species', user = 'bety', pwd = 'bety')")))
+        translation$bety_species_id[i] <- foo$id
+        translation$genus[i]           <- foo$genus
+        translation$species[i]         <- foo$species
+      }
+      
     }
-
-    return(merge_table)
+    
+  }
+  input_table <- data.frame(input_code = input_codes, stringsAsFactors = FALSE)
+  # preserving the order is important for downstream
+  colnames(translation)<- c('bety_species_id', 'genus', 'species',"input_code") #changed 'latin_name' back to 'input_codes' to enable 'left_join' since columns being matched must have same name, also changed 'id' back to 'bety_species_id' so species id can be checked in bety database  
+  merge_table <- dplyr::left_join(input_table, translation)
+  if(sum(is.na(merge_table$bety_species_id)) > 0){
+    bad <- unique(merge_table$input_code[is.na(merge_table$bety_species_id)])
+    PEcAn.logger::logger.error(paste0("Species for the following code(s) not found : ", paste(bad, collapse = ", ")))
+  }
+  return(merge_table)
 } # match_species_id
-
diff --git a/modules/data.land/R/put.veg.module.R b/modules/data.land/R/put.veg.module.R
index e402bcc72b0..feaf37a5e82 100644
--- a/modules/data.land/R/put.veg.module.R
+++ b/modules/data.land/R/put.veg.module.R
@@ -1,6 +1,24 @@
-.put.veg.module <- function(getveg.id, dbparms, 
+##' Match species to PFTs + veg2model module
+##' 
+##' @param getveg.id list, input.id and dbfile.id of the IC file in intermediate pecan standard
+##' @param dbparms list, settings$database info reqired for opening a connection to DB
+##' @param input_veg list, this is a sublist of settings$run$inputs that has info about source, id, metadata of the requested IC file
+##' @param pfts list, same as settings$pfts
+##' @param outfolder path to where the processed files will be written
+##' @param n.ensemble integer, ensemble member number
+##' @param dir dir path to dbfiles on local machine
+##' @param machine data frame, DB info regarding localhost machine id/hostname etc.
+##' @param model model name, e.g. "ED2"
+##' @param start_date date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$start.date, otherwise start_date of the IC file in DB
+##' @param end_date date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$end.date, otherwise end_date of the IC file in DB
+##' @param new_site data frame, id/lat/lon/name info about the site
+##' @param host list, host info as in settings$host, host$name forced to be "localhost" upstream
+##' @param overwrite logical flag for convert.input
+##' 
+##' @author Istem Fer
+put_veg_module <- function(getveg.id, dbparms, 
                             input_veg, pfts,
-                            outfolder, 
+                            outfolder, n.ensemble,
                             dir, machine, model,
                             start_date, end_date,
                             new_site, 
@@ -16,6 +34,7 @@
                               password = dbparms$bety$password)
   
   con <- bety$con
+  on.exit(db.close(con))
   
   # Determine IC file format name and mimetype
   model_info <- db.query(paste0("SELECT f.name, f.id, mt.type_string from modeltypes as m", " join modeltypes_formats as mf on m.id = mf.modeltype_id", 
@@ -27,14 +46,14 @@
   formatname <- model_info[1]
   mimetype   <- model_info[3]
   
-  spp.file <- db.query(paste("SELECT * from dbfiles where container_id =", getveg.id), con)
-  
+  # spp.file <- db.query(paste("SELECT * from dbfiles where container_id =", getveg.id), con)
+  spp.file <- PEcAn.DB::db.query(paste0("SELECT * from dbfiles where id = ", getveg.id$dbfile.id), con)
   
   pkg  <- "PEcAn.data.land"
   fcn  <- "write_ic"
   
   putveg.id <- convert.input(input.id = getveg.id,
-                             outfolder = outfolder, 
+                             outfolder = spp.file$file_path, 
                              formatname = formatname, 
                              mimetype = mimetype,
                              site.id = new_site$id, 
diff --git a/modules/data.land/R/sample_ic.R b/modules/data.land/R/sample_ic.R
new file mode 100644
index 00000000000..c7cffb9a78a
--- /dev/null
+++ b/modules/data.land/R/sample_ic.R
@@ -0,0 +1,101 @@
+##' @name sample_ic
+##' @title sample_ic
+##' 
+##' @param in.path path to folder of the file to be sampled
+##' @param in.name file name of the file to be sampled
+##' @param start_date date in "YYYY-MM-DD" format
+##' @param end_date date in "YYYY-MM-DD" format
+##' @param outfolder dir path, whete to write the file
+##' @param n.ensemble integer, ensemble member number
+##' @param machine_host localhost name, e.g. "pecan2.bu.edu"
+##' @param source string to appear in file names, e.g. "PalEON"
+##' 
+##' @export
+##' @author Istem Fer
+sample_ic <- function(in.path, in.name, start_date, end_date, outfolder,
+                      n.ensemble, machine_host, source, ...){
+  
+  
+  #--------------------------------------------------------------------------------------------------#
+  # Read
+  rds_file <- file.path(in.path, in.name)
+  veg_info <- readRDS(rds_file) 
+  
+  #--------------------------------------------------------------------------------------------------#
+  # Prepare for sampling
+  # NOTE: This function might call different functions in the future, e.g. : sample_cohort, sample_pool, or both
+  # Then, the rest of the script would change, this is cohort-based only
+  
+  # 1st sublist is either NULL or has metadata (e.g. age, area), in the future we might want to sample over that too
+  obs <- as.data.frame(veg_info[[2]], stringsAsFactors = FALSE)
+  
+  year <- lubridate::year(start_date)
+  
+  # subset samples for the year 
+  samples <- obs[obs$year == year, ]
+  
+  # remove rows with NAs (we don't want DBH to be NA but do we want to allow missing taxa?)
+  samples <- samples[complete.cases(samples), ]
+  
+  # if there are subplots, sample within each subplot instead of pooling all together, maybe pass down a flag if we want to pool anyway
+  if(!is.null(samples$Subplot)){
+    n.subplot <- length(unique(samples$Subplot))
+  }else{
+    n.subplot <- 1
+    samples$Subplot <- 1
+  }
+  
+  #--------------------------------------------------------------------------------------------------#
+  # Sampling 
+  
+  sub.list <- list()
+  for(np in seq_len(n.subplot)){
+    samples_sub <- samples[samples$Subplot == np,] 
+    
+    ############################################
+    #  
+    #  samples_sub is in this format (there are other columns):
+    # 
+    #   DBH  MCMC_iteration ... Tree_number ...
+    #    36               1 ...           1 ...
+    #  16.1               1 ...           2 ...
+    #    24               1 ...           3 ...
+    #   ...             ... ...         ... ...
+    #  36.5               2 ...           1 ...
+    #  16.2               2 ...           2 ...
+    #   ...             ... ...         ... ...
+    #  35.9            1000 ...           1 ...
+    #    16            1000 ...           2 ...
+    #   ...             ... ...         ... ...
+    #   6.8            1000 ...         170 ...   
+    #
+    #  we can use Tree_number as the index for tapply and sample 1 from MCMC samples
+    samp_ind    <- tapply(seq_along(samples_sub$Tree_number), samples_sub$Tree_number, sample, 1)
+    sub_samp    <- samples_sub[samp_ind,]
+      
+    sub.list[[np]]  <- sub_samp
+  }
+    
+  veg_info[[2]] <- do.call("rbind", sub.list)
+  
+  #--------------------------------------------------------------------------------------------------#
+  # Write vegettion data as rds, return results to convert.input
+  
+  # write with ensemble number
+  sppfilename <- write_veg(outfolder, start_date, veg_info = veg_info, paste0(source, "_ens", n.ensemble))
+  
+  # Build results dataframe for convert.input
+  results <- data.frame(file = sppfilename, 
+                        host = machine_host, 
+                        mimetype = "application/rds", 
+                        formatname = "spp.info", 
+                        startdate = start_date, 
+                        enddate = end_date, 
+                        dbfile.name = basename(sppfilename), 
+                        stringsAsFactors = FALSE)
+  
+  ### return for convert.inputs
+  return(invisible(results))  
+  
+  
+} # sample_ic
diff --git a/modules/data.land/R/soil2netcdf.R b/modules/data.land/R/soil2netcdf.R
index cc8e7518445..6dc16c6b0f6 100644
--- a/modules/data.land/R/soil2netcdf.R
+++ b/modules/data.land/R/soil2netcdf.R
@@ -27,7 +27,7 @@
 #' }
 soil2netcdf <- function(soil.data,new.file){
   soil.data <- as.list(soil.data)
-  
+
   ## convert soil type to parameters via look-up-table / equations
   mysoil <- PEcAn.data.land::soil_params(sand=soil.data$fraction_of_sand_in_soil,
                                          silt=soil.data$fraction_of_silt_in_soil,
@@ -54,7 +54,7 @@ soil2netcdf <- function(soil.data,new.file){
   ncvar <- list()
   good_vars <- 0
   for(n in seq_along(soil.data)){
-    if(is.null(soil.data[[n]])|is.na(soil.data[[n]])) next
+    if(all(is.null(soil.data[[n]])) | all(is.na(soil.data[[n]]))) next
     varname <- names(soil.data)[n]
     if(length(soil.data[[n]])>1){
       ## if vector, save by depth
diff --git a/modules/data.land/R/soil_process.R b/modules/data.land/R/soil_process.R
index 5f1fd22181c..59ff97eb25e 100644
--- a/modules/data.land/R/soil_process.R
+++ b/modules/data.land/R/soil_process.R
@@ -11,23 +11,20 @@
 #' @examples
 soil_process <- function(settings, input, dbfiles, overwrite = FALSE,run.local=TRUE){
   
-  if(is.null(input$id)){
+  if(input$soil$source=="PalEON_soil" && is.null(input$id)){
     PEcAn.logger::logger.severe("currently soil_process requires an input ID to be specified")
     return(NULL)
   }
   
-  if(is.null(input$source)){
-    input$source <- "PalEON_soil"  ## temporarily hardcoding in the only source
+  if(is.null(input$soil$source)){
+    input$soil$source <- "PalEON_soil"  ## temporarily hardcoding in the only source
                                    ## in the future this should throw an error
   }
-  
-  #--------------------------------------------------------------------------------------------------#
   # Extract info from settings and setup
   site       <- settings$run$site
   model      <- settings$model$type
   host       <- settings$host
   dbparms    <- settings$database
-  
   # set up bety connection
   bety <- dplyr::src_postgres(dbname   = dbparms$bety$dbname, 
                               host     = dbparms$bety$host, 
@@ -35,7 +32,22 @@ soil_process <- function(settings, input, dbfiles, overwrite = FALSE,run.local=T
                               password = dbparms$bety$password)
   con <- bety$con
   on.exit(PEcAn.DB::db.close(con))
-  
+  # get site info
+  latlon <- PEcAn.data.atmosphere::db.site.lat.lon(site$id, con = con)
+  new.site <- data.frame(id = as.numeric(site$id), 
+                         lat = latlon$lat, 
+                         lon = latlon$lon)
+  str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
+  outfolder <- file.path(dbfiles, paste0(input$soil$source, "_site_", str_ns))
+  if(!dir.exists(outfolder)) dir.create(outfolder)
+  #--------------------------------------------------------------------------------------------------#   
+  # if we are reading from gSSURGO
+  if (input$soil$source=="gSSURGO"){
+    newfile<-extract_soil_gssurgo(outfolder,lat = latlon$lat,lon=latlon$lon)
+    return(newfile)
+  }
+  #--------------------------------------------------------------------------------------------------# 
+  # if we are reading  PalEON_soil
   # get existing input info
   source.input <- PEcAn.DB::db.query(paste0("SELECT * from Inputs where id =",input$id),con)
   if(run.local){
@@ -52,15 +64,8 @@ soil_process <- function(settings, input, dbfiles, overwrite = FALSE,run.local=T
       return(source.file)    
     }
   }  ## otherwise continue to process soil
-  
-  # get site info
-  latlon <- PEcAn.data.atmosphere::db.site.lat.lon(site$id, con = con)
-  new.site <- data.frame(id = as.numeric(site$id), 
-                         lat = latlon$lat, 
-                         lon = latlon$lon)
-  str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09)
-  
-  # set up host information
+
+    # set up host information
   machine.host <- ifelse(host == "localhost" || host$name == "localhost" || run.local,
                          PEcAn.remote::fqdn(), host$name)
   machine <- PEcAn.DB::db.query(paste0("SELECT * from machines where hostname = '", machine.host, "'"), con)
@@ -71,9 +76,6 @@ soil_process <- function(settings, input, dbfiles, overwrite = FALSE,run.local=T
     model <- db.query(paste0("SELECT name FROM modeltypes where id = '", modeltype_id, "'"), con)[[1]]
   }
   
-  outfolder <- file.path(dbfiles, paste0(input$source, "_site_", str_ns))
-  if(!dir.exists(outfolder)) dir.create(outfolder)
-  
   newfile <- PEcAn.data.land::extract_soil_nc(source.file,outfolder,lat = latlon$lat,lon=latlon$lon)
   
   return(newfile)
diff --git a/modules/data.land/R/soil_utils.R b/modules/data.land/R/soil_utils.R
index cc5bf2d7f79..53c1adca5d8 100644
--- a/modules/data.land/R/soil_utils.R
+++ b/modules/data.land/R/soil_utils.R
@@ -24,11 +24,10 @@
 #' clay <- c(0.3,0.3,0.3)
 #' soil_params(sand=sand,clay=clay)
 soil_params <- function(soil_type,sand,silt,clay,bulk){
-
   ## load soil parameters
   load(system.file("data/soil_class.RData",package = "PEcAn.data.land"))
   mysoil <- list()
-  
+
   #---------------------------------------------------------------------------------------#
   #     Find soil class and sand, silt, and clay fractions.                               #
   #---------------------------------------------------------------------------------------#
@@ -50,7 +49,9 @@ soil_params <- function(soil_type,sand,silt,clay,bulk){
       clay <- 1-sand-silt
     } else {
       #not missing anything else, normalize
+
       stot <- sand+silt+clay
+
       if(any(stot > 2)) stot <- stot*100 ## assume values reported in % not proportion
       sand <- sand/stot
       silt <- silt/stot
@@ -124,7 +125,7 @@ soil_params <- function(soil_type,sand,silt,clay,bulk){
   #---------------------------------------------------------------------------------------#
   #      Calculate the derived properties in case this is not bedrock.                    #
   #---------------------------------------------------------------------------------------#
-  mysoil$slpotcp = mysoil$volume_fraction_of_condensed_water_in_dry_soil = mysoil$slpotwp = olume_fraction_of_condensed_water_in_soil_at_wilting_point = 0.0
+  mysoil$slpotcp = mysoil$volume_fraction_of_condensed_water_in_dry_soil = mysoil$slpotwp = mysoil$volume_fraction_of_condensed_water_in_soil_at_wilting_point = 0.0
   for(z in which(!(mysoil$soil_n == 13))){
     # Dry soil capacity (at -3.1MPa) [ m^3/m^3 ]
     mysoil$slpotcp[z]   <- - soilcp.MPa * 1000. / grav
diff --git a/modules/data.land/R/write_ic.R b/modules/data.land/R/write_ic.R
index 9d3f146773b..aa47336b6a1 100644
--- a/modules/data.land/R/write_ic.R
+++ b/modules/data.land/R/write_ic.R
@@ -52,9 +52,7 @@ write_ic <- function(in.path, in.name, start_date, end_date,
                         stringsAsFactors = FALSE)
   
   ### return for convert.inputs
-  return(invisible(results))  
-  
+  return(invisible(results))
+
   
 } # write_ic
-
-
diff --git a/modules/data.land/contrib/FIA/README.txt b/modules/data.land/contrib/FIA/README.txt
old mode 100755
new mode 100644
diff --git a/modules/data.land/contrib/FIA/html2text.py b/modules/data.land/contrib/FIA/html2text.py
old mode 100755
new mode 100644
diff --git a/modules/data.land/contrib/FIA/mirror.sh b/modules/data.land/contrib/FIA/mirror.sh
old mode 100755
new mode 100644
diff --git a/modules/data.land/inst/FIA_allometry/allometry.r b/modules/data.land/inst/FIA_allometry/allometry.r
old mode 100755
new mode 100644
diff --git a/modules/data.land/inst/FIA_allometry/biomass.r b/modules/data.land/inst/FIA_allometry/biomass.r
old mode 100755
new mode 100644
diff --git a/modules/data.land/man/InventoryGrowthFusion.Rd b/modules/data.land/man/InventoryGrowthFusion.Rd
index 13e99ba6558..92aadc13530 100644
--- a/modules/data.land/man/InventoryGrowthFusion.Rd
+++ b/modules/data.land/man/InventoryGrowthFusion.Rd
@@ -6,8 +6,9 @@
 \usage{
 InventoryGrowthFusion(data, cov.data = NULL, time_data = NULL,
   n.iter = 5000, n.chunk = n.iter, n.burn = min(n.chunk, 2000),
-  random = NULL, fixed = NULL, time_varying = NULL, burnin_plot = FALSE,
-  save.jags = "IGF.txt", z0 = NULL, save.state = TRUE, restart = NULL)
+  random = NULL, fixed = NULL, time_varying = NULL,
+  burnin_plot = FALSE, save.jags = "IGF.txt", z0 = NULL,
+  save.state = TRUE, restart = NULL)
 }
 \arguments{
 \item{data}{list of data inputs}
diff --git a/modules/data.land/man/InventoryGrowthFusionDiagnostics.Rd b/modules/data.land/man/InventoryGrowthFusionDiagnostics.Rd
index 83b022ae864..63e316e7be9 100644
--- a/modules/data.land/man/InventoryGrowthFusionDiagnostics.Rd
+++ b/modules/data.land/man/InventoryGrowthFusionDiagnostics.Rd
@@ -11,6 +11,9 @@ InventoryGrowthFusionDiagnostics(jags.out, combined = NULL)
 
 \item{combined}{data output from matchInventoryRings}
 }
+\description{
+InventoryGrowthFusionDiagnostics
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/data.land/man/cohort2pool.Rd b/modules/data.land/man/cohort2pool.Rd
new file mode 100644
index 00000000000..8ea59ee68f3
--- /dev/null
+++ b/modules/data.land/man/cohort2pool.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cohort2pool.R
+\name{cohort2pool}
+\alias{cohort2pool}
+\title{cohort2pool function
+Calculates total biomass using veg cohort file.}
+\usage{
+cohort2pool(veg_file, allom_param = NULL)
+}
+\arguments{
+\item{veg_file}{path to standard cohort veg_file}
+
+\item{allom_param}{parameters for allometric equation, a and b. Based on base-10 log-log linear model (power law)}
+}
+\description{
+cohort2pool function
+Calculates total biomass using veg cohort file.
+}
+\examples{
+\dontrun{
+veg_file <- "~/downloads/FFT_site_1-25665/FFT.2008.veg.rds"
+cohort2pool(veg_File = veg_file, allom_param = NULL)
+}
+}
+\author{
+Saloni Shah
+}
diff --git a/modules/data.land/man/dataone_download.Rd b/modules/data.land/man/dataone_download.Rd
index be7195ee8e5..8b008d763dc 100644
--- a/modules/data.land/man/dataone_download.Rd
+++ b/modules/data.land/man/dataone_download.Rd
@@ -4,8 +4,8 @@
 \alias{dataone_download}
 \title{DataONE download}
 \usage{
-dataone_download(id, filepath = "/fs/data1/pecan.data/dbfiles/",
-  CNode = "PROD", lazyLoad = FALSE, quiet = F)
+dataone_download(id, filepath = "/fs/data1/pecan.data/dbfiles",
+  CNode = "PROD", lazyLoad = FALSE, quiet = FALSE)
 }
 \arguments{
 \item{id}{"The identifier of a package, package metadata or other package member" -- dataone r}
@@ -22,8 +22,8 @@ dataone_download(id, filepath = "/fs/data1/pecan.data/dbfiles/",
 Adapts the dataone::getDataPackage workflow to allow users to download data from the DataONE federation by simply entering the doi or associated package id
 }
 \examples{
-/dontrun{
-dataone_download(id = "doi:10.6073/pasta/63ad7159306bc031520f09b2faefcf87", filepath = "/fs/data1/pecan.data/dbfiles/")
+\dontrun{
+dataone_download(id = "doi:10.6073/pasta/63ad7159306bc031520f09b2faefcf87", filepath = "/fs/data1/pecan.data/dbfiles")
 }
 }
 \author{
diff --git a/modules/data.land/man/download_package_rm.Rd b/modules/data.land/man/download_package_rm.Rd
index 895927451fd..b9dc7ab3cf6 100644
--- a/modules/data.land/man/download_package_rm.Rd
+++ b/modules/data.land/man/download_package_rm.Rd
@@ -5,7 +5,8 @@
 \title{download_packages}
 \usage{
 download_package_rm(resource_map, directory, CNode = "PROD",
-  download_format = "application/bagit-097", overwrite_directory = TRUE)
+  download_format = "application/bagit-097",
+  overwrite_directory = TRUE)
 }
 \arguments{
 \item{resource_map}{the resource map that corresponds to the given data package}
diff --git a/modules/data.land/man/ens_veg_module.Rd b/modules/data.land/man/ens_veg_module.Rd
new file mode 100644
index 00000000000..68dce462385
--- /dev/null
+++ b/modules/data.land/man/ens_veg_module.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ens.veg.module.R
+\name{ens_veg_module}
+\alias{ens_veg_module}
+\title{Sampling/ensemble module}
+\usage{
+ens_veg_module(getveg.id, dbparms, input_veg, outfolder, machine,
+  start_date, end_date, n.ensemble, new_site, host)
+}
+\arguments{
+\item{getveg.id}{list, input.id and dbfile.id of the IC file in intermediate pecan standard}
+
+\item{dbparms}{list, settings$database info reqired for opening a connection to DB}
+
+\item{input_veg}{list, this is a sublist of settings$run$inputs that has info about source, id, metadata of the requested IC file}
+
+\item{outfolder}{path to where the processed files will be written}
+
+\item{machine}{data frame, DB info regarding localhost machine id/hostname etc.}
+
+\item{start_date}{date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$start.date, otherwise start_date of the IC file in DB}
+
+\item{end_date}{date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$end.date, otherwise end_date of the IC file in DB}
+
+\item{n.ensemble}{integer, ensemble member number}
+
+\item{new_site}{data frame, id/lat/lon/name info about the site}
+
+\item{host}{list, host info as in settings$host, host$name forced to be "localhost" upstream}
+}
+\description{
+Sampling/ensemble module
+}
+\author{
+Istem Fer
+}
diff --git a/modules/data.land/man/extract.stringCode.Rd b/modules/data.land/man/extract.stringCode.Rd
index 0ff343bcf04..417a742f944 100644
--- a/modules/data.land/man/extract.stringCode.Rd
+++ b/modules/data.land/man/extract.stringCode.Rd
@@ -6,3 +6,6 @@
 \usage{
 extract.stringCode(x, extractor = from.TreeCode)
 }
+\description{
+extract.string.code
+}
diff --git a/modules/data.land/man/extract_FIA.Rd b/modules/data.land/man/extract_FIA.Rd
index 661c53f9353..c582cfd87a8 100644
--- a/modules/data.land/man/extract_FIA.Rd
+++ b/modules/data.land/man/extract_FIA.Rd
@@ -6,6 +6,9 @@
 \usage{
 extract_FIA(lon, lat, start_date, end_date, gridres = 0.075, dbparms)
 }
+\description{
+extract_FIA
+}
 \author{
 Istem Fer
 }
diff --git a/modules/data.land/man/extract_soil_gssurgo.Rd b/modules/data.land/man/extract_soil_gssurgo.Rd
new file mode 100644
index 00000000000..765678cf00b
--- /dev/null
+++ b/modules/data.land/man/extract_soil_gssurgo.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/extract_soil_nc.R
+\name{extract_soil_gssurgo}
+\alias{extract_soil_gssurgo}
+\title{Extract soil data from gssurgo}
+\usage{
+extract_soil_gssurgo(outdir, lat, lon)
+}
+\arguments{
+\item{outdir}{Output directory for writing down the netcdf file}
+
+\item{lat}{Latitude}
+
+\item{lon}{Longitude}
+}
+\value{
+It returns the address for the generated soil netcdf file
+}
+\description{
+Extract soil data from gssurgo
+}
+\examples{
+outdir  <- "~/paleon/envTest"
+lat     <- 40
+lon     <- -80
+\dontrun{
+   PEcAn.data.land::extract_soil_gssurgo(outdir,lat,lon)
+}
+}
+\author{
+Hamze Dokoohaki
+}
diff --git a/modules/data.land/man/extract_veg.Rd b/modules/data.land/man/extract_veg.Rd
index ce053e982f2..b4d2e9d3d1b 100644
--- a/modules/data.land/man/extract_veg.Rd
+++ b/modules/data.land/man/extract_veg.Rd
@@ -5,8 +5,8 @@
 \title{load_veg}
 \usage{
 extract_veg(new_site, start_date, end_date, source, gridres,
-  format_name = NULL, machine_host, dbparms, outfolder, overwrite = FALSE,
-  ...)
+  format_name = NULL, machine_host, dbparms, outfolder,
+  overwrite = FALSE, ...)
 }
 \description{
 Function queries a DB to extract veg info downstream
diff --git a/modules/data.land/man/from.Tag.Rd b/modules/data.land/man/from.Tag.Rd
index 3d207438db1..b08861fcb0c 100644
--- a/modules/data.land/man/from.Tag.Rd
+++ b/modules/data.land/man/from.Tag.Rd
@@ -6,3 +6,6 @@
 \usage{
 from.Tag(x)
 }
+\description{
+from.Tag
+}
diff --git a/modules/data.land/man/from.TreeCode.Rd b/modules/data.land/man/from.TreeCode.Rd
index 83e85653e0c..fa4db29ca63 100644
--- a/modules/data.land/man/from.TreeCode.Rd
+++ b/modules/data.land/man/from.TreeCode.Rd
@@ -6,3 +6,6 @@
 \usage{
 from.TreeCode(x)
 }
+\description{
+from.TreeCode
+}
diff --git a/modules/data.land/man/gSSURGO.Query.Rd b/modules/data.land/man/gSSURGO.Query.Rd
new file mode 100644
index 00000000000..20b97aa3988
--- /dev/null
+++ b/modules/data.land/man/gSSURGO.Query.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gSSURGO_Query.R
+\name{gSSURGO.Query}
+\alias{gSSURGO.Query}
+\title{This function queries the gSSURGO database for a series of map unit keys}
+\usage{
+gSSURGO.Query(mukeys = 2747727)
+}
+\arguments{
+\item{mukeys}{map unit key from gssurgo}
+}
+\value{
+a dataframe with soil properties. units can be looked up from database documentation
+}
+\description{
+This function queries the gSSURGO database for a series of map unit keys
+}
+\details{
+Full documention of available tables and their relationships can be found here \url{www.sdmdataaccess.nrcs.usda.gov/QueryHelp.aspx}
+There have been occasions where NRCS made some minor changes to the structure of the API which this code is where those changes need
+to be implemneted here.
+}
diff --git a/modules/data.land/man/get_veg_module.Rd b/modules/data.land/man/get_veg_module.Rd
new file mode 100644
index 00000000000..400f5e53175
--- /dev/null
+++ b/modules/data.land/man/get_veg_module.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get.veg.module.R
+\name{get_veg_module}
+\alias{get_veg_module}
+\title{Load/extract + match species module}
+\usage{
+get_veg_module(input_veg, outfolder, start_date, end_date, dbparms,
+  new_site, host, machine_host, overwrite)
+}
+\arguments{
+\item{input_veg}{list, this is a sublist of settings$run$inputs that has info about source, id, metadata of the requested IC file}
+
+\item{outfolder}{path to where the processed files will be written}
+
+\item{start_date}{date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$start.date, otherwise start_date of the IC file in DB}
+
+\item{end_date}{date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$end.date, otherwise end_date of the IC file in DB}
+
+\item{dbparms}{list, settings$database info reqired for opening a connection to DB}
+
+\item{new_site}{data frame, id/lat/lon/name info about the site}
+
+\item{host}{list, host info as in settings$host, host$name forced to be "localhost" upstream}
+
+\item{machine_host}{local machine hostname, e.g. "pecan2.bu.edu"}
+
+\item{overwrite}{logical flag for convert.input}
+}
+\description{
+Load/extract + match species module
+}
+\author{
+Istem Fer
+}
diff --git a/modules/data.land/man/ic_process.Rd b/modules/data.land/man/ic_process.Rd
index b7386265340..dcaea86fae7 100644
--- a/modules/data.land/man/ic_process.Rd
+++ b/modules/data.land/man/ic_process.Rd
@@ -13,6 +13,9 @@ ic_process(settings, input, dir, overwrite = FALSE)
 
 \item{dbfiles}{where to write files}
 }
+\description{
+ic_process
+}
 \author{
 Istem Fer
 }
diff --git a/modules/data.land/man/load_veg.Rd b/modules/data.land/man/load_veg.Rd
index 4a5186b05f8..6f04359155d 100644
--- a/modules/data.land/man/load_veg.Rd
+++ b/modules/data.land/man/load_veg.Rd
@@ -4,9 +4,9 @@
 \alias{load_veg}
 \title{load_veg}
 \usage{
-load_veg(new_site, start_date, end_date, source_id, source, icmeta = NULL,
-  format_name = NULL, machine_host, dbparms, outfolder, overwrite = FALSE,
-  ...)
+load_veg(new_site, start_date, end_date, source_id, source,
+  icmeta = NULL, format_name = NULL, machine_host, dbparms, outfolder,
+  overwrite = FALSE, ...)
 }
 \description{
 Function uses load_data{benchmark} to get veg data
diff --git a/modules/data.land/man/matchInventoryRings.Rd b/modules/data.land/man/matchInventoryRings.Rd
index a07c466adbf..13d3e8feafd 100644
--- a/modules/data.land/man/matchInventoryRings.Rd
+++ b/modules/data.land/man/matchInventoryRings.Rd
@@ -7,3 +7,6 @@
 matchInventoryRings(trees, rings, extractor = "TreeCode", nyears = 30,
   coredOnly = TRUE)
 }
+\description{
+matchInventoryRings
+}
diff --git a/modules/data.land/man/parse.MatrixNames.Rd b/modules/data.land/man/parse.MatrixNames.Rd
index 0f75382b8ab..8beaca28979 100644
--- a/modules/data.land/man/parse.MatrixNames.Rd
+++ b/modules/data.land/man/parse.MatrixNames.Rd
@@ -16,6 +16,9 @@ parse.MatrixNames(w, pre = "x", numeric = FALSE)
 \value{
 matrix
 }
+\description{
+parse.MatrixNames
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/data.land/man/put_veg_module.Rd b/modules/data.land/man/put_veg_module.Rd
new file mode 100644
index 00000000000..62bdde250ca
--- /dev/null
+++ b/modules/data.land/man/put_veg_module.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/put.veg.module.R
+\name{put_veg_module}
+\alias{put_veg_module}
+\title{Match species to PFTs + veg2model module}
+\usage{
+put_veg_module(getveg.id, dbparms, input_veg, pfts, outfolder, n.ensemble,
+  dir, machine, model, start_date, end_date, new_site, host, overwrite)
+}
+\arguments{
+\item{getveg.id}{list, input.id and dbfile.id of the IC file in intermediate pecan standard}
+
+\item{dbparms}{list, settings$database info reqired for opening a connection to DB}
+
+\item{input_veg}{list, this is a sublist of settings$run$inputs that has info about source, id, metadata of the requested IC file}
+
+\item{pfts}{list, same as settings$pfts}
+
+\item{outfolder}{path to where the processed files will be written}
+
+\item{n.ensemble}{integer, ensemble member number}
+
+\item{dir}{dir path to dbfiles on local machine}
+
+\item{machine}{data frame, DB info regarding localhost machine id/hostname etc.}
+
+\item{model}{model name, e.g. "ED2"}
+
+\item{start_date}{date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$start.date, otherwise start_date of the IC file in DB}
+
+\item{end_date}{date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$end.date, otherwise end_date of the IC file in DB}
+
+\item{new_site}{data frame, id/lat/lon/name info about the site}
+
+\item{host}{list, host info as in settings$host, host$name forced to be "localhost" upstream}
+
+\item{overwrite}{logical flag for convert.input}
+}
+\description{
+Match species to PFTs + veg2model module
+}
+\author{
+Istem Fer
+}
diff --git a/modules/data.land/man/sample_ic.Rd b/modules/data.land/man/sample_ic.Rd
new file mode 100644
index 00000000000..f5c77391fac
--- /dev/null
+++ b/modules/data.land/man/sample_ic.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sample_ic.R
+\name{sample_ic}
+\alias{sample_ic}
+\title{sample_ic}
+\usage{
+sample_ic(in.path, in.name, start_date, end_date, outfolder, n.ensemble,
+  machine_host, source, ...)
+}
+\arguments{
+\item{in.path}{path to folder of the file to be sampled}
+
+\item{in.name}{file name of the file to be sampled}
+
+\item{start_date}{date in "YYYY-MM-DD" format}
+
+\item{end_date}{date in "YYYY-MM-DD" format}
+
+\item{outfolder}{dir path, whete to write the file}
+
+\item{n.ensemble}{integer, ensemble member number}
+
+\item{machine_host}{localhost name, e.g. "pecan2.bu.edu"}
+
+\item{source}{string to appear in file names, e.g. "PalEON"}
+}
+\description{
+sample_ic
+}
+\author{
+Istem Fer
+}
diff --git a/modules/data.land/man/soil_process.Rd b/modules/data.land/man/soil_process.Rd
index db7b568d5ce..43c657884f0 100644
--- a/modules/data.land/man/soil_process.Rd
+++ b/modules/data.land/man/soil_process.Rd
@@ -4,7 +4,8 @@
 \alias{soil_process}
 \title{Module for managing soil texture extraction}
 \usage{
-soil_process(settings, input, dbfiles, overwrite = FALSE, run.local = TRUE)
+soil_process(settings, input, dbfiles, overwrite = FALSE,
+  run.local = TRUE)
 }
 \arguments{
 \item{settings}{PEcAn settings list}
diff --git a/modules/data.land/man/to.Tag.Rd b/modules/data.land/man/to.Tag.Rd
index 0349b5544f0..d215a1c6141 100644
--- a/modules/data.land/man/to.Tag.Rd
+++ b/modules/data.land/man/to.Tag.Rd
@@ -6,3 +6,6 @@
 \usage{
 to.Tag(SITE, PLOT, SUBPLOT, TAG = NULL)
 }
+\description{
+to.Tag
+}
diff --git a/modules/data.land/man/to.TreeCode.Rd b/modules/data.land/man/to.TreeCode.Rd
index 048982ead14..4ae4614939d 100644
--- a/modules/data.land/man/to.TreeCode.Rd
+++ b/modules/data.land/man/to.TreeCode.Rd
@@ -6,3 +6,6 @@
 \usage{
 to.TreeCode(SITE, PLOT, SUBPLOT, TAG = NULL)
 }
+\description{
+to.TreeCode
+}
diff --git a/modules/data.land/man/write_ic.Rd b/modules/data.land/man/write_ic.Rd
index 50b28752333..00837f4455d 100644
--- a/modules/data.land/man/write_ic.Rd
+++ b/modules/data.land/man/write_ic.Rd
@@ -4,8 +4,11 @@
 \alias{write_ic}
 \title{write_ic}
 \usage{
-write_ic(in.path, in.name, start_date, end_date, outfolder, model, new_site,
-  pfts, source = input_veg$source, overwrite = FALSE, ...)
+write_ic(in.path, in.name, start_date, end_date, outfolder, model,
+  new_site, pfts, source = input_veg$source, overwrite = FALSE, ...)
+}
+\description{
+write_ic
 }
 \author{
 Istem Fer
diff --git a/modules/data.land/tests/testthat/test.match_species_id.R b/modules/data.land/tests/testthat/test.match_species_id.R
index 6fe75dba3a0..0ddb3f3e1ce 100644
--- a/modules/data.land/tests/testthat/test.match_species_id.R
+++ b/modules/data.land/tests/testthat/test.match_species_id.R
@@ -1,34 +1,37 @@
-library(PEcAn.data.land)
-library(testthat)
 
-test_merge <- function(input_codes, format_name, bety, ...) {
-    dat_merge <- match_species_id(input_codes = input_codes, 
-                                  format_name = format_name,
-                                  bety = bety,
-                                  ...)
-    test_that(paste0('Species match works for format: ', format_name),
-              {
-                  expect_equal(dat_merge[1, 'genus'], 'Acer')
-                  expect_equal(dat_merge[1, 'species'], 'rubrum')
-                  expect_equal(dat_merge[2, 'genus'], 'Tsuga')
-                  expect_equal(dat_merge[2, 'species'], 'canadensis')
-                  expect_equal(nrow(dat_merge), length(input_codes))
-                  expect_false(any(is.na(dat_merge$bety_species_id)))
-                  expect_false(any(duplicated(dat_merge)))
-              })
-    return(dat_merge)
-}
+context("Species matching")
 
-bety <- dplyr::src_postgres(dbname = 'bety',
-                              user = 'bety',
-                              password = 'bety')
+test_that("Species matching works", {
+  skip("Failing test (#1959); please fix and re-enable")
+  test_merge <- function(input_codes, format_name, bety, ...) {
+      dat_merge <- match_species_id(input_codes = input_codes,
+                                    format_name = format_name,
+                                    bety = bety,
+                                    ...)
+      test_that(paste0('Species match works for format: ', format_name),
+                {
+                    expect_equal(dat_merge[1, 'genus'], 'Acer')
+                    expect_equal(dat_merge[1, 'species'], 'rubrum')
+                    expect_equal(dat_merge[2, 'genus'], 'Tsuga')
+                    expect_equal(dat_merge[2, 'species'], 'canadensis')
+                    expect_equal(nrow(dat_merge), length(input_codes))
+                    expect_false(any(is.na(dat_merge$bety_species_id)))
+                    expect_false(any(duplicated(dat_merge)))
+                })
+      return(dat_merge)
+  }
 
-test_merge(c('ACRU', 'TSCA'), 'usda', bety)
-test_merge(c(316, 261), 'fia', bety)
-test_merge(c('Acer rubrum', 'Tsuga canadensis'), 'latin_name', bety)
+  bety <- dplyr::src_postgres(dbname = 'bety',
+                                user = 'bety',
+                                password = 'bety')
 
-test_table <- data.frame(bety_species_id = c(30, 1419),
-                         input_code = c('AceRub', 'TsuCan'))
+  test_merge(c('ACRU', 'TSCA'), 'usda', bety)
+  test_merge(c(316, 261), 'fia', bety)
+  test_merge(c('Acer rubrum', 'Tsuga canadensis'), 'latin_name', bety)
 
-test_merge(input_codes = test_table$input_code, format_name = 'custom', bety = bety,
-           translation_table = test_table)
+  test_table <- data.frame(bety_species_id = c(30, 1419),
+                           input_code = c('AceRub', 'TsuCan'))
+
+  test_merge(input_codes = test_table$input_code, format_name = 'custom', bety = bety,
+             translation_table = test_table)
+})
diff --git a/modules/data.mining/DESCRIPTION b/modules/data.mining/DESCRIPTION
index 0da86845364..393b3e0db35 100644
--- a/modules/data.mining/DESCRIPTION
+++ b/modules/data.mining/DESCRIPTION
@@ -2,8 +2,8 @@ Package: PEcAn.data.mining
 Type: Package
 Title: PEcAn functions used for exploring model residuals and structures
 Description: (Temporary description) PEcAn functions used for exploring model residuals and structures
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Depends:
@@ -18,4 +18,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Collate:
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/data.remote/DESCRIPTION b/modules/data.remote/DESCRIPTION
index 6f867d389a2..f5785352afb 100644
--- a/modules/data.remote/DESCRIPTION
+++ b/modules/data.remote/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.data.remote
 Type: Package
 Title: PEcAn functions used for remote sensing
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: PEcAn module for processing remote data
@@ -16,4 +16,5 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/data.remote/man/call_MODIS.Rd b/modules/data.remote/man/call_MODIS.Rd
index 2641a50ce3a..e3ae1f1e69c 100644
--- a/modules/data.remote/man/call_MODIS.Rd
+++ b/modules/data.remote/man/call_MODIS.Rd
@@ -4,9 +4,9 @@
 \alias{call_MODIS}
 \title{call_MODIS}
 \usage{
-call_MODIS(outfolder = ".", fname = "m_data.nc", start_date, end_date, lat,
-  lon, size = 0, product = "MOD15A2", band = "Lai_1km", qc_band = NA,
-  sd_band = NA, verbose = TRUE)
+call_MODIS(outfolder = ".", fname = "m_data.nc", start_date, end_date,
+  lat, lon, size = 0, product = "MOD15A2", band = "Lai_1km",
+  qc_band = NA, sd_band = NA, verbose = TRUE)
 }
 \arguments{
 \item{outfolder}{where the output file will be stored}
diff --git a/modules/data.remote/man/extract_NLCD.Rd b/modules/data.remote/man/extract_NLCD.Rd
index 95036a6db4d..34c85c46c9b 100644
--- a/modules/data.remote/man/extract_NLCD.Rd
+++ b/modules/data.remote/man/extract_NLCD.Rd
@@ -4,7 +4,8 @@
 \alias{extract_NLCD}
 \title{extract.NLCD}
 \usage{
-extract_NLCD(buffer, coords, data_dir = NULL, con = NULL, year = 2011)
+extract_NLCD(buffer, coords, data_dir = NULL, con = NULL,
+  year = 2011)
 }
 \arguments{
 \item{buffer}{search radius (meters)}
diff --git a/modules/emulator/DESCRIPTION b/modules/emulator/DESCRIPTION
index 8c4fe4e43ab..c70ef6c689a 100644
--- a/modules/emulator/DESCRIPTION
+++ b/modules/emulator/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.emulator
 Type: Package
 Title: Gausian Process emulator
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Michael Dietze
 Maintainer: Michael Dietze <dietze@bu.edu>
 Depends:
@@ -17,4 +17,5 @@ Description: Implementation of a Gaussian Process model (both likelihood and
     bayesian approaches) for kriging and model emulation.  Includes functions
     for sampling design and prediction.
 License: FreeBSD + file LICENSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/emulator/R/minimize.GP.R b/modules/emulator/R/minimize.GP.R
index 276173aef8c..71ce65ede3b 100644
--- a/modules/emulator/R/minimize.GP.R
+++ b/modules/emulator/R/minimize.GP.R
@@ -215,12 +215,12 @@ mcmc.GP <- function(gp, x0, nmcmc, rng, format = "lin", mix = "joint", splinefcn
   
   
   currllp <- pda.calc.llik.par(settings, n.of.obs, currSS, hyper.pars)
-  LLpar  <- unlist(sapply(currllp, `[[` , "par"))
+  pcurr   <- unlist(sapply(currllp, `[[` , "par"))
   
   xcurr <- x0
   dim   <- length(x0)
   samp  <- matrix(NA, nmcmc, dim)
-  par   <- matrix(NA, nmcmc, length(LLpar), dimnames = list(NULL, names(LLpar))) # note: length(LLpar) can be 0
+  par   <- matrix(NA, nmcmc, length(pcurr), dimnames = list(NULL, names(pcurr))) # note: length(pcurr) can be 0
   
   
   if (run.block) {
@@ -275,7 +275,7 @@ mcmc.GP <- function(gp, x0, nmcmc, rng, format = "lin", mix = "joint", splinefcn
       
       
       newSS  <- get_ss(gp, xnew, pos.check)
-      if(newSS != -Inf){
+      if(all(newSS != -Inf)){
         
         newllp <- pda.calc.llik.par(settings, n.of.obs, newSS, hyper.pars)
         ynew   <- get_y(newSS, xnew, llik.fn, priors, newllp)
diff --git a/modules/emulator/man/GaussProcess.Rd b/modules/emulator/man/GaussProcess.Rd
index cbc3348d2a7..4755cf455ba 100644
--- a/modules/emulator/man/GaussProcess.Rd
+++ b/modules/emulator/man/GaussProcess.Rd
@@ -18,6 +18,9 @@ GaussProcess(x, y, isotropic = TRUE, nugget = TRUE, method = "bayes",
 
 \item{exclude}{}
 }
+\description{
+GaussProcess
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/bounded.Rd b/modules/emulator/man/bounded.Rd
index cbe72fff6b3..bf00246d813 100644
--- a/modules/emulator/man/bounded.Rd
+++ b/modules/emulator/man/bounded.Rd
@@ -6,3 +6,6 @@
 \usage{
 bounded(xnew, rng)
 }
+\description{
+bounded
+}
diff --git a/modules/emulator/man/calcSpatialCov.Rd b/modules/emulator/man/calcSpatialCov.Rd
index ad65f8a8ba8..742c27e75d0 100644
--- a/modules/emulator/man/calcSpatialCov.Rd
+++ b/modules/emulator/man/calcSpatialCov.Rd
@@ -6,6 +6,9 @@
 \usage{
 calcSpatialCov(x, ...)
 }
+\description{
+calcSpatialCov
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/calculate.prior.Rd b/modules/emulator/man/calculate.prior.Rd
index dd1488f8245..fd4f82717ad 100644
--- a/modules/emulator/man/calculate.prior.Rd
+++ b/modules/emulator/man/calculate.prior.Rd
@@ -6,3 +6,6 @@
 \usage{
 calculate.prior(samples, priors)
 }
+\description{
+calculate.prior
+}
diff --git a/modules/emulator/man/ddist.Rd b/modules/emulator/man/ddist.Rd
index 96d046af601..e7132eaeaf7 100644
--- a/modules/emulator/man/ddist.Rd
+++ b/modules/emulator/man/ddist.Rd
@@ -6,3 +6,6 @@
 \usage{
 ddist(x, prior)
 }
+\description{
+ddist
+}
diff --git a/modules/emulator/man/distance.Rd b/modules/emulator/man/distance.Rd
index ab1aef7b350..aebf4473b8a 100644
--- a/modules/emulator/man/distance.Rd
+++ b/modules/emulator/man/distance.Rd
@@ -12,6 +12,9 @@ distance(x, power = 1)
 \value{
 dst
 }
+\description{
+distance
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/distance.martix.Rd b/modules/emulator/man/distance.martix.Rd
index 06f534c6de3..c3cbe3b45f1 100644
--- a/modules/emulator/man/distance.martix.Rd
+++ b/modules/emulator/man/distance.martix.Rd
@@ -13,6 +13,9 @@ distance.matrix(x, power = 1, dim = 2)
 \value{
 d
 }
+\description{
+distance.matrix
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/distance12.martix.Rd b/modules/emulator/man/distance12.martix.Rd
index 8b0ef125bf7..28de9e0cd6b 100644
--- a/modules/emulator/man/distance12.martix.Rd
+++ b/modules/emulator/man/distance12.martix.Rd
@@ -13,6 +13,9 @@ distance12.matrix(x, n1, power = 1)
 \value{
 d
 }
+\description{
+distance12.matrix
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/get_ss.Rd b/modules/emulator/man/get_ss.Rd
index beb06006055..5d771a7bb2c 100644
--- a/modules/emulator/man/get_ss.Rd
+++ b/modules/emulator/man/get_ss.Rd
@@ -6,3 +6,6 @@
 \usage{
 get_ss(gp, xnew, pos.check)
 }
+\description{
+get_ss
+}
diff --git a/modules/emulator/man/get_y.Rd b/modules/emulator/man/get_y.Rd
index a19fbeae4b8..06913850cc6 100644
--- a/modules/emulator/man/get_y.Rd
+++ b/modules/emulator/man/get_y.Rd
@@ -6,3 +6,6 @@
 \usage{
 get_y(SSnew, xnew, llik.fn, priors, llik.par)
 }
+\description{
+get_y
+}
diff --git a/modules/emulator/man/gp_mle.Rd b/modules/emulator/man/gp_mle.Rd
index b6295ef3794..180a289ce69 100644
--- a/modules/emulator/man/gp_mle.Rd
+++ b/modules/emulator/man/gp_mle.Rd
@@ -12,6 +12,9 @@ gp_mle(theta, d, nugget, myY, maxval = Inf)
 \value{
 val
 }
+\description{
+gp_mle
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/groupid.Rd b/modules/emulator/man/groupid.Rd
index 4ebbe7a5eb2..e20bba56969 100644
--- a/modules/emulator/man/groupid.Rd
+++ b/modules/emulator/man/groupid.Rd
@@ -6,6 +6,9 @@
 \usage{
 groupid(x)
 }
+\description{
+groupid
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/is.accepted.Rd b/modules/emulator/man/is.accepted.Rd
index 170c1a8b548..68498f17ca6 100644
--- a/modules/emulator/man/is.accepted.Rd
+++ b/modules/emulator/man/is.accepted.Rd
@@ -6,3 +6,6 @@
 \usage{
 is.accepted(ycurr, ynew, format = "lin")
 }
+\description{
+is.accepted
+}
diff --git a/modules/emulator/man/jump.Rd b/modules/emulator/man/jump.Rd
index 3ae1cd55a3c..7e5f349416c 100644
--- a/modules/emulator/man/jump.Rd
+++ b/modules/emulator/man/jump.Rd
@@ -2,7 +2,6 @@
 % Please edit documentation in R/jump.R, R/zzz.R
 \name{jump}
 \alias{jump}
-\alias{jump}
 \title{jump}
 \usage{
 jump(ic = 0, rate = 0.4, ...)
@@ -10,6 +9,11 @@ jump(ic = 0, rate = 0.4, ...)
 \arguments{
 \item{rate}{}
 }
+\description{
+jump
+
+setClass jump
+}
 \author{
 Michael Dietze
 
diff --git a/modules/emulator/man/mcmc.GP.Rd b/modules/emulator/man/mcmc.GP.Rd
index 0e63c413c71..f16c8726a16 100644
--- a/modules/emulator/man/mcmc.GP.Rd
+++ b/modules/emulator/man/mcmc.GP.Rd
@@ -5,9 +5,9 @@
 \title{mcmc.GP}
 \usage{
 mcmc.GP(gp, x0, nmcmc, rng, format = "lin", mix = "joint",
-  splinefcns = NULL, jmp0 = 0.35 * (rng[, 2] - rng[, 1]), ar.target = 0.5,
-  priors = NA, settings, run.block = TRUE, n.of.obs, llik.fn, hyper.pars,
-  resume.list = NULL)
+  splinefcns = NULL, jmp0 = 0.35 * (rng[, 2] - rng[, 1]),
+  ar.target = 0.5, priors = NA, settings, run.block = TRUE, n.of.obs,
+  llik.fn, hyper.pars, resume.list = NULL)
 }
 \arguments{
 \item{x0}{}
diff --git a/modules/emulator/man/minimize.GP.Rd b/modules/emulator/man/minimize.GP.Rd
index 0e1d98f1297..91572bb0261 100644
--- a/modules/emulator/man/minimize.GP.Rd
+++ b/modules/emulator/man/minimize.GP.Rd
@@ -11,6 +11,9 @@ minimize.GP(gp, rng, x0, splinefuns = NULL)
 
 \item{splinefuns}{}
 }
+\description{
+minimize.GP
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/mvjump.Rd b/modules/emulator/man/mvjump.Rd
index acf80dc343f..b8c81c08bbe 100644
--- a/modules/emulator/man/mvjump.Rd
+++ b/modules/emulator/man/mvjump.Rd
@@ -2,7 +2,6 @@
 % Please edit documentation in R/jump.R, R/zzz.R
 \name{mvjump}
 \alias{mvjump}
-\alias{mvjump}
 \title{mvjump}
 \usage{
 mvjump(ic = 0, rate = 0.4, nc = 2, ...)
diff --git a/modules/emulator/man/nderiv.Rd b/modules/emulator/man/nderiv.Rd
index c4cb9e8709f..dad68699940 100644
--- a/modules/emulator/man/nderiv.Rd
+++ b/modules/emulator/man/nderiv.Rd
@@ -9,6 +9,9 @@ nderiv(x, y)
 \value{
 der
 }
+\description{
+nderiv
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/p.Rd b/modules/emulator/man/p.Rd
index da8ec499bd8..73996251ea2 100644
--- a/modules/emulator/man/p.Rd
+++ b/modules/emulator/man/p.Rd
@@ -6,3 +6,6 @@
 \usage{
 p(x, ...)
 }
+\description{
+p
+}
diff --git a/modules/emulator/man/p.jump.Rd b/modules/emulator/man/p.jump.Rd
index 6f757f956d3..81f62fe20d3 100644
--- a/modules/emulator/man/p.jump.Rd
+++ b/modules/emulator/man/p.jump.Rd
@@ -9,6 +9,9 @@
 \arguments{
 \item{jmp}{jump parameter}
 }
+\description{
+p.jump
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/p.mvjump.Rd b/modules/emulator/man/p.mvjump.Rd
index ba904d05683..045da503822 100644
--- a/modules/emulator/man/p.mvjump.Rd
+++ b/modules/emulator/man/p.mvjump.Rd
@@ -9,3 +9,6 @@
 \arguments{
 \item{jmp}{jump parameter}
 }
+\description{
+p.mvjump
+}
diff --git a/modules/emulator/man/plot.jump.Rd b/modules/emulator/man/plot.jump.Rd
index 2c3327f997c..648561b8e4c 100644
--- a/modules/emulator/man/plot.jump.Rd
+++ b/modules/emulator/man/plot.jump.Rd
@@ -9,6 +9,9 @@
 \arguments{
 \item{jmp}{jump parameter}
 }
+\description{
+plot.jump
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/plot.mvjump.Rd b/modules/emulator/man/plot.mvjump.Rd
index 6db3056b86d..5d71a07499d 100644
--- a/modules/emulator/man/plot.mvjump.Rd
+++ b/modules/emulator/man/plot.mvjump.Rd
@@ -9,6 +9,9 @@
 \arguments{
 \item{jmp}{}
 }
+\description{
+plot.mvjump
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/predict.GP.Rd b/modules/emulator/man/predict.GP.Rd
index ca0a51b6ea8..7ac8630fb7a 100644
--- a/modules/emulator/man/predict.GP.Rd
+++ b/modules/emulator/man/predict.GP.Rd
@@ -4,13 +4,17 @@
 \alias{predict.GP}
 \title{predict.GP}
 \usage{
-\method{predict}{GP}(gp, xpred, cI = NULL, pI = NULL, splinefcns = NULL)
+\method{predict}{GP}(gp, xpred, cI = NULL, pI = NULL,
+  splinefcns = NULL)
 }
 \arguments{
 \item{cI}{credible interval}
 
 \item{pI}{prediction interval}
 }
+\description{
+predict.GP
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/summarize.GP.Rd b/modules/emulator/man/summarize.GP.Rd
index 55c705b92d1..c57e772cf94 100644
--- a/modules/emulator/man/summarize.GP.Rd
+++ b/modules/emulator/man/summarize.GP.Rd
@@ -9,6 +9,9 @@ summarize.GP(gp, pdf_file = NULL, txt_file = NULL)
 \arguments{
 \item{txt_file}{}
 }
+\description{
+summarize.GP
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/update.jump.Rd b/modules/emulator/man/update.jump.Rd
index 546b656254e..56dcb077ffa 100644
--- a/modules/emulator/man/update.jump.Rd
+++ b/modules/emulator/man/update.jump.Rd
@@ -14,6 +14,9 @@
 \value{
 jmp updated jump parameter
 }
+\description{
+update.jump
+}
 \author{
 Michael Dietze
 }
diff --git a/modules/emulator/man/update.mvjump.Rd b/modules/emulator/man/update.mvjump.Rd
index 489a85916fc..e99e1b81ec0 100644
--- a/modules/emulator/man/update.mvjump.Rd
+++ b/modules/emulator/man/update.mvjump.Rd
@@ -6,3 +6,6 @@
 \usage{
 \method{update}{mvjump}(jmp, chain)
 }
+\description{
+update.mvjump
+}
diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION
index adab17dbceb..007e2050d27 100644
--- a/modules/meta.analysis/DESCRIPTION
+++ b/modules/meta.analysis/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.MA
 Type: Package
 Title: PEcAn functions used for meta-analysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze, Carl
     Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <dlebauer@illinois.edu>
@@ -19,8 +19,9 @@ Depends:
     PEcAn.utils,
     PEcAn.DB
 Imports:
+    coda (>= 0.18),
     PEcAn.logger,
-    coda (>= 0.18)
+    PEcAn.settings
 Suggests:
     rjags,
     testthat (>= 1.0.2),
@@ -28,6 +29,6 @@ Suggests:
 SystemRequirements: JAGS
 License: FreeBSD + file LICENSE
 Copyright: Authors
-LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/meta.analysis/R/meta.analysis.summary.R b/modules/meta.analysis/R/meta.analysis.summary.R
index b69f9f5cd46..a9505e8cc69 100644
--- a/modules/meta.analysis/R/meta.analysis.summary.R
+++ b/modules/meta.analysis/R/meta.analysis.summary.R
@@ -7,19 +7,23 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 
+##' Generate summary statistics and diagnostics for PEcAn meta.analysis
 ##'
-##' @name pecan.ma.summary
-##' @title Generate summary statitics and diagnostics for PEcAn meta.analysis
 ##' @param mcmc.object JAGS mcmc output from \code{\link{pecan.ma}}
 ##' @param pft plant functional type
 ##' @param outdir output directory
 ##' @param threshold Gelman-Rubin convergence diagnostic (MGPRF)
 ##' default = 1.2 following Bolker 2008 Ecological Models and Data in R
+##' @param gg produce extra diagnostic plots using the "ggmcmc" package? Caution: very slow!
 ##' @export
 ##'
 ##' @examples
 ##' \dontrun{
-##' summary <- pecan.ma.summary(trait.mcmc,settings$pfts$pft,settings$outdir,settings$meta.analysis$threshold)
+##' summary <- pecan.ma.summary(
+##'  trait.mcmc,
+##'  settings$pfts$pft,
+##'  settings$outdir,
+##'  settings$meta.analysis$threshold)
 ##' }
 ##' @author David LeBauer, Shawn Serbin
 pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FALSE) {
diff --git a/modules/meta.analysis/R/run.meta.analysis.R b/modules/meta.analysis/R/run.meta.analysis.R
index 4c3b3c603aa..f3acd8911e4 100644
--- a/modules/meta.analysis/R/run.meta.analysis.R
+++ b/modules/meta.analysis/R/run.meta.analysis.R
@@ -157,9 +157,11 @@ run.meta.analysis.pft <- function(pft, iterations, random = TRUE, threshold = 1.
 ##' @param random should random effects be used?
 ##' @param dbfiles location where previous results are found
 ##' @param database database connection parameters
+##' @param threshold Gelman-Rubin convergence diagnostic, passed on to
+##'   \code{\link{pecan.ma.summary}}
 ##' @return nothing, as side effect saves \code{trait.mcmc} created by
 ##' \code{\link{pecan.ma}} and post.distns created by
-##' \code{\link{approx.posterior(trait.mcmc, ...)}}  to trait.mcmc.Rdata \
+##' \code{\link{approx.posterior}(trait.mcmc, ...)}  to trait.mcmc.Rdata \
 ##' and post.distns.Rdata, respectively
 ##' @export
 ##' @author Shawn Serbin, David LeBauer
diff --git a/modules/meta.analysis/R/zzz.R b/modules/meta.analysis/R/zzz.R
new file mode 100644
index 00000000000..c9394eef533
--- /dev/null
+++ b/modules/meta.analysis/R/zzz.R
@@ -0,0 +1,19 @@
+# A special function always executed at package load time
+#
+# Used here to load the `coda` namespace.
+# This is necessary because `coda` defines S3 methods for mcmc.list that we
+# need when calling base generics (in particular, it provides
+# as.matrix.mcmc.list) but it does not export them, so we can't use @importFrom
+# to pull in only the subset we need.
+# 
+# @param libname,pkgname Not used; present for historical reasons
+# @return nothing
+#
+.onLoad <- function(libname, pkgname) {
+	if(!requireNamespace("coda", quietly = TRUE)){
+		PEcAn.logger::logger.severe(
+			"coda is not installed, but is needed by PEcAn.MA.",
+			"Try running `install.packages('coda')`")
+	}
+	invisible()
+}
diff --git a/modules/meta.analysis/man/pecan.ma.Rd b/modules/meta.analysis/man/pecan.ma.Rd
index a6186299378..408efd50e9e 100644
--- a/modules/meta.analysis/man/pecan.ma.Rd
+++ b/modules/meta.analysis/man/pecan.ma.Rd
@@ -4,8 +4,8 @@
 \alias{pecan.ma}
 \title{Trait Meta-analysis}
 \usage{
-pecan.ma(trait.data, prior.distns, taupriors, j.iter, outdir, random = FALSE,
-  overdispersed = TRUE)
+pecan.ma(trait.data, prior.distns, taupriors, j.iter, outdir,
+  random = FALSE, overdispersed = TRUE)
 }
 \arguments{
 \item{trait.data}{list of dataframes, one per trait for which data is available, generated by call to query.traits()}
diff --git a/modules/meta.analysis/man/pecan.ma.summary.Rd b/modules/meta.analysis/man/pecan.ma.summary.Rd
index 2f74a94bd13..827bcc43913 100644
--- a/modules/meta.analysis/man/pecan.ma.summary.Rd
+++ b/modules/meta.analysis/man/pecan.ma.summary.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/meta.analysis.summary.R
 \name{pecan.ma.summary}
 \alias{pecan.ma.summary}
-\title{Generate summary statitics and diagnostics for PEcAn meta.analysis}
+\title{Generate summary statistics and diagnostics for PEcAn meta.analysis}
 \usage{
 pecan.ma.summary(mcmc.object, pft, outdir, threshold = 1.2, gg = FALSE)
 }
@@ -15,10 +15,19 @@ pecan.ma.summary(mcmc.object, pft, outdir, threshold = 1.2, gg = FALSE)
 
 \item{threshold}{Gelman-Rubin convergence diagnostic (MGPRF)
 default = 1.2 following Bolker 2008 Ecological Models and Data in R}
+
+\item{gg}{produce extra diagnostic plots using the "ggmcmc" package? Caution: very slow!}
+}
+\description{
+Generate summary statistics and diagnostics for PEcAn meta.analysis
 }
 \examples{
 \dontrun{
-summary <- pecan.ma.summary(trait.mcmc,settings$pfts$pft,settings$outdir,settings$meta.analysis$threshold)
+summary <- pecan.ma.summary(
+ trait.mcmc,
+ settings$pfts$pft,
+ settings$outdir,
+ settings$meta.analysis$threshold)
 }
 }
 \author{
diff --git a/modules/meta.analysis/man/run.meta.analysis.Rd b/modules/meta.analysis/man/run.meta.analysis.Rd
index 50c912991a4..aad32335b44 100644
--- a/modules/meta.analysis/man/run.meta.analysis.Rd
+++ b/modules/meta.analysis/man/run.meta.analysis.Rd
@@ -9,8 +9,8 @@ This will use the following items from setings:
 - settings$database$dbfiles
 - settings$meta.analysis$update}
 \usage{
-run.meta.analysis(pfts, iterations, random = TRUE, threshold = 1.2, dbfiles,
-  database)
+run.meta.analysis(pfts, iterations, random = TRUE, threshold = 1.2,
+  dbfiles, database)
 }
 \arguments{
 \item{pfts}{the list of pfts to get traits for}
@@ -19,6 +19,9 @@ run.meta.analysis(pfts, iterations, random = TRUE, threshold = 1.2, dbfiles,
 
 \item{random}{should random effects be used?}
 
+\item{threshold}{Gelman-Rubin convergence diagnostic, passed on to
+\code{\link{pecan.ma.summary}}}
+
 \item{dbfiles}{location where previous results are found}
 
 \item{database}{database connection parameters}
@@ -26,7 +29,7 @@ run.meta.analysis(pfts, iterations, random = TRUE, threshold = 1.2, dbfiles,
 \value{
 nothing, as side effect saves \code{trait.mcmc} created by
 \code{\link{pecan.ma}} and post.distns created by
-\code{\link{approx.posterior(trait.mcmc, ...)}}  to trait.mcmc.Rdata \
+\code{\link{approx.posterior}(trait.mcmc, ...)}  to trait.mcmc.Rdata \
 and post.distns.Rdata, respectively
 }
 \description{
diff --git a/modules/meta.analysis/man/write.ma.model.Rd b/modules/meta.analysis/man/write.ma.model.Rd
index c0600fe20d3..3769f618cb3 100644
--- a/modules/meta.analysis/man/write.ma.model.Rd
+++ b/modules/meta.analysis/man/write.ma.model.Rd
@@ -4,8 +4,8 @@
 \alias{write.ma.model}
 \title{write.ma.model}
 \usage{
-write.ma.model(modelfile, outfile, reg.model, pr.dist, pr.param.a, pr.param.b,
-  n, trt.n, site.n, ghs.n, tauA, tauB)
+write.ma.model(modelfile, outfile, reg.model, pr.dist, pr.param.a,
+  pr.param.b, n, trt.n, site.n, ghs.n, tauA, tauB)
 }
 \arguments{
 \item{modelfile}{model template file (ma.model.template.R)}
diff --git a/modules/meta.analysis/tests/testthat.R b/modules/meta.analysis/tests/testthat.R
index b8f45fe201f..c2dcd0f0512 100644
--- a/modules/meta.analysis/tests/testthat.R
+++ b/modules/meta.analysis/tests/testthat.R
@@ -7,7 +7,7 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 library(testthat)
-library(PEcAn.utils)
+library(PEcAn.MA)
 
 PEcAn.logger::logger.setQuitOnSevere(FALSE)
 test_check("PEcAn.MA")
diff --git a/modules/meta.analysis/tests/testthat/test.run.meta.analysis.R b/modules/meta.analysis/tests/testthat/test.run.meta.analysis.R
index 5e6e13da199..2d174d948e1 100644
--- a/modules/meta.analysis/tests/testthat/test.run.meta.analysis.R
+++ b/modules/meta.analysis/tests/testthat/test.run.meta.analysis.R
@@ -6,6 +6,9 @@
 # which accompanies this distribution, and is available at
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
+
+context("run.meta.analysis")
+
 test_that("p.point.in.prior function is functional",{
   prior <- list(distn = "norm", parama = 0, paramb = 1)
   expect_equal(p.point.in.prior(point = 3, prior = prior),
diff --git a/modules/photosynthesis/DESCRIPTION b/modules/photosynthesis/DESCRIPTION
index 779a9f52972..41ca54a8deb 100644
--- a/modules/photosynthesis/DESCRIPTION
+++ b/modules/photosynthesis/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.photosynthesis
 Type: Package
 Title: PEcAn functions used for leaf-level photosynthesis calculations
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Mike Dietze, Xiaohui Feng, Shawn Serbin
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
@@ -26,4 +26,5 @@ Collate:
     fitA.R
     Licor.QC.R
     plots.R
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/photosynthesis/man/Licor_QC.Rd b/modules/photosynthesis/man/Licor_QC.Rd
index ff09f0e9e2a..7a7b1ebfa43 100644
--- a/modules/photosynthesis/man/Licor_QC.Rd
+++ b/modules/photosynthesis/man/Licor_QC.Rd
@@ -13,6 +13,9 @@ Licor_QC(dat, curve = c("ACi", "AQ"), tol = 0.05)
 
 \item{tol}{Code automatically tries to separate ACi and AQ curves in the same dataset by detecting the 'reference' condition for light and CO2 respectively. This is the relative error around the mode in that detection.}
 }
+\description{
+Licor_QC
+}
 \author{
 Mike Dietze
 }
diff --git a/modules/photosynthesis/man/ciEnvelope.Rd b/modules/photosynthesis/man/ciEnvelope.Rd
index a8afeb208cb..b1e8d6f80e3 100644
--- a/modules/photosynthesis/man/ciEnvelope.Rd
+++ b/modules/photosynthesis/man/ciEnvelope.Rd
@@ -6,6 +6,9 @@
 \usage{
 ciEnvelope(x, ylo, yhi, col = "lightgrey", ...)
 }
+\description{
+shaded confidence interval
+}
 \author{
 Mike Dietze
 }
diff --git a/modules/photosynthesis/man/estimate_mode.Rd b/modules/photosynthesis/man/estimate_mode.Rd
index cb44c487c5e..d33553b60c9 100644
--- a/modules/photosynthesis/man/estimate_mode.Rd
+++ b/modules/photosynthesis/man/estimate_mode.Rd
@@ -6,6 +6,9 @@
 \usage{
 estimate_mode(x, adjust = 0.1)
 }
+\description{
+estimate_mode
+}
 \author{
 Mike Dietze
 
diff --git a/modules/photosynthesis/man/fitA.Rd b/modules/photosynthesis/man/fitA.Rd
index 0e8b476cb70..ccc806738cd 100644
--- a/modules/photosynthesis/man/fitA.Rd
+++ b/modules/photosynthesis/man/fitA.Rd
@@ -15,6 +15,9 @@ fitA(flux.data, cov.data = NULL, model = NULL)
 
 Right now the fixed effects are specified as a string using the standard R lm formula syntax, but without the LHS variable (e.g. '~ SLA + chl + SLA:chl'). The tilde is optional. For random effects, the two options right now are just 'leaf' for leaf-level random effects and NULL. 'model' has a default that sets all effects to NULL (fit one curve to all data) and n.iter=1000.}
 }
+\description{
+fitA
+}
 \author{
 Mike Dietze
 
diff --git a/modules/photosynthesis/man/plot_photo.Rd b/modules/photosynthesis/man/plot_photo.Rd
index b9b8174680d..8513b5642ea 100644
--- a/modules/photosynthesis/man/plot_photo.Rd
+++ b/modules/photosynthesis/man/plot_photo.Rd
@@ -4,7 +4,11 @@
 \alias{plot_photo}
 \title{plot_photo}
 \usage{
-plot_photo(data, out, curve = c("ACi", "AQ"), tol = 0.05, byLeaf = TRUE)
+plot_photo(data, out, curve = c("ACi", "AQ"), tol = 0.05,
+  byLeaf = TRUE)
+}
+\description{
+plot_photo
 }
 \author{
 Mike Dietze
diff --git a/modules/photosynthesis/man/read_Licor.Rd b/modules/photosynthesis/man/read_Licor.Rd
index a08c89385d9..dcef9674bf8 100644
--- a/modules/photosynthesis/man/read_Licor.Rd
+++ b/modules/photosynthesis/man/read_Licor.Rd
@@ -13,6 +13,9 @@ read_Licor(filename, sep = "\\t", ...)
 
 \item{...}{optional arguements forwarded to read.table}
 }
+\description{
+read_Licor
+}
 \author{
 Mike Dietze
 }
diff --git a/modules/priors/DESCRIPTION b/modules/priors/DESCRIPTION
index cc55713158d..512cdd28109 100644
--- a/modules/priors/DESCRIPTION
+++ b/modules/priors/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAn.priors
 Type: Package
 Title: PEcAn functions used to estimate priors from data
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer
 Maintainer: David LeBauer <dlebauer@illinois.edu>
 Description: Functions to estimate priors from data.
@@ -17,4 +17,5 @@ Imports:
     ggplot2
 Suggests:
     testthat
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/priors/man/create.density.df.Rd b/modules/priors/man/create.density.df.Rd
index 4bd80016a30..019e94588d5 100644
--- a/modules/priors/man/create.density.df.Rd
+++ b/modules/priors/man/create.density.df.Rd
@@ -4,8 +4,8 @@
 \alias{create.density.df}
 \title{Create Density Data Frame from Sample}
 \usage{
-create.density.df(samps = NULL, zero.bounded = FALSE, distribution = NULL,
-  n = 1000, ...)
+create.density.df(samps = NULL, zero.bounded = FALSE,
+  distribution = NULL, n = 1000, ...)
 }
 \arguments{
 \item{samps}{a vector of samples from a distribution}
diff --git a/modules/priors/man/plot.trait.Rd b/modules/priors/man/plot.trait.Rd
index d8acdfbf836..ba36d3ae116 100644
--- a/modules/priors/man/plot.trait.Rd
+++ b/modules/priors/man/plot.trait.Rd
@@ -5,8 +5,8 @@
 \title{Plot trait density}
 \usage{
 \method{plot}{trait}(trait, prior = NULL, posterior.sample = NULL,
-  trait.df = NULL, fontsize = list(title = 18, axis = 14), x.lim = NULL,
-  y.lim = NULL, logx = FALSE)
+  trait.df = NULL, fontsize = list(title = 18, axis = 14),
+  x.lim = NULL, y.lim = NULL, logx = FALSE)
 }
 \arguments{
 \item{trait}{character, name of trait to be plotted}
diff --git a/modules/priors/man/priorfig.Rd b/modules/priors/man/priorfig.Rd
index 2d88fc1e331..0f703484cba 100644
--- a/modules/priors/man/priorfig.Rd
+++ b/modules/priors/man/priorfig.Rd
@@ -4,8 +4,8 @@
 \alias{priorfig}
 \title{Prior Figure}
 \usage{
-priorfig(priordata = NA, priordensity = NA, trait = "", xlim = "auto",
-  fontsize = 18)
+priorfig(priordata = NA, priordensity = NA, trait = "",
+  xlim = "auto", fontsize = 18)
 }
 \arguments{
 \item{priordata}{observations to be plotted as points}
diff --git a/modules/rtm/DESCRIPTION b/modules/rtm/DESCRIPTION
index 1eb482c39a2..42ba180705e 100644
--- a/modules/rtm/DESCRIPTION
+++ b/modules/rtm/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: PEcAnRTM
 Type: Package
 Title: PEcAn functions used for radiative transfer modeling
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: Alexey Shiklomanov, Shawn Serbin, Mike Dietze
 Maintainer: Alexey Shiklomanov <ashiklom@bu.edu>
 Description: This package contains functions for performing forward runs and
@@ -30,6 +30,7 @@ License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
+Encoding: UTF-8
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
diff --git a/modules/rtm/NAMESPACE b/modules/rtm/NAMESPACE
index a8de1676778..18c94f5efad 100644
--- a/modules/rtm/NAMESPACE
+++ b/modules/rtm/NAMESPACE
@@ -15,15 +15,14 @@ S3method(resample,matrix)
 S3method(resample,spectra)
 S3method(str,spectra)
 export(EDR)
-export(EDR.preprocess.ed2in)
 export(EDR.preprocess.history)
-export(EDR.prospect)
 export(burnin.thin)
 export(check.convergence)
 export(default.settings.prospect)
 export(defparam)
 export(dtnorm)
 export(fortran_data_module)
+export(foursail)
 export(generalized_plate_model)
 export(generate.noise)
 export(get.EDR.output)
@@ -40,6 +39,7 @@ export(neff)
 export(params.prospect4)
 export(params.prospect5)
 export(params.prospect5b)
+export(params2edr)
 export(print_results_summary)
 export(prior.defaultvals.prospect)
 export(priorfunc.prospect)
@@ -51,6 +51,7 @@ export(resample)
 export(rtnorm)
 export(sensor.list)
 export(sensor.proper)
+export(setup_edr)
 export(spectra)
 export(spectral.response)
 export(summary_mvnorm)
diff --git a/modules/rtm/R/bayestools.R b/modules/rtm/R/bayestools.R
index 9362d809638..974f3e33da6 100644
--- a/modules/rtm/R/bayestools.R
+++ b/modules/rtm/R/bayestools.R
@@ -117,13 +117,16 @@ prospect_bt_prior <- function(version, custom_prior = list()) {
 #'      - `verbose_loglike` -- Diagnostic messages in log likelihood output. Default is TRUE.
 #'
 #' See the BayesianTools sampler documentation for what can go in the `BayesianTools` settings lists.
-#' @param observed Vector of observations
+#' @param observed Vector of observations. Ignored if `loglike` is not `NULL`.
 #' @param model Function called by log-likelihood. Must be `function(params)`
-#' and return a vector equal to `length(observed)` or `nrow(observed)`.
+#' and return a vector equal to `length(observed)` or `nrow(observed)`. Ignored 
+#' if `loglike` is not `NULL`.
 #' @param prior BayesianTools prior object.
 #' @param custom_settings Nested settings list. See Details.
+#' @param loglike Custom log likelihood function. If `NULL`, use [rtm_loglike] 
+#' with provided `observed` and `model`.
 #' @export
-invert_bt <- function(observed, model, prior, custom_settings = list()) {
+invert_bt <- function(observed, model, prior, custom_settings = list(), loglike = NULL) {
 
   default_settings <- list(
     common = list(),
@@ -171,15 +174,23 @@ invert_bt <- function(observed, model, prior, custom_settings = list()) {
   stopifnot('prior' %in% class(prior))
   test_samp <- prior$sampler()
   param_names <- names(test_samp)
+  if (is.null(param_names)) {
+    warning("Parameters are not named! Unable to check validity.")
+  } else {
+    if (!("residual" %in% param_names)) {
+      stop("One of the parameters must be `residual`.")
+    }
+  }
   nparams <- length(test_samp[param_names != 'residual'])
-  loglike <- rtm_loglike(
-    nparams = nparams,
-    model = model,
-    observed = observed,
-    lag.max = lag.max,
-    verbose = verbose_loglike
-  )
-
+  if (is.null(loglike)) {
+    loglike <- rtm_loglike(
+      nparams = nparams,
+      model = model,
+      observed = observed,
+      lag.max = lag.max,
+      verbose = verbose_loglike
+    )
+  }
 
   setup <- BayesianTools::createBayesianSetup(
     likelihood = loglike,
diff --git a/modules/rtm/R/edr.wrapper.R b/modules/rtm/R/edr.wrapper.R
index 91feb34bba9..68965c01dfe 100644
--- a/modules/rtm/R/edr.wrapper.R
+++ b/modules/rtm/R/edr.wrapper.R
@@ -1,19 +1,11 @@
-#' @title ED radiative transfer module (EDR) wrapper function
+#' ED radiative transfer module (EDR) wrapper function
 #' 
 #' This function provides a convenient way to call the ED 
 #' radiative transfer module (EDR, which simulates full spectral return of an 
 #' ED patch for a given point in time) directly from R.
-#' 
-#' @param paths List of relevant paths. Must contain the following:
-#'  * `ed2in` -- Path to ED2IN file for the original ED run. If this is `NA`, the 
-#'  function assumes that the ED2IN file in `output.path` is already up-to-date 
-#'  and skips the analysis step.
-#'  * `history` -- Path and prefix for history file for the run of interest;
-#'  * `edr.exe` -- Path to EDR executable
-#'  * `soil_reflect` -- Path to soil reflectance. If NULL or unset, use 
-#'  reflectance in package. If NA, skip (assume data already in directory).
-#'  * `wood_reflect` -- Path to wood reflectance. If NULL or unset, use 
-#'  reflectance in package. If NA, skip (assume data already in directory).
+#'
+#' @param img_path Path to Singularity container (usually a `.simg` file)
+#' @param ed2in_path Path to ED2IN file.
 #' @param spectra_list List of spectral data matrices. Names must exactly match 
 #' the PFTs given in `trait.values`. Each item must be a matrix of
 #' reflectance (labeled 'R' or 'reflectance') and transmittance (labeled 'T' or 
@@ -21,167 +13,167 @@
 #' [spectra()]), it must also have a column of wavelength values (labeled 
 #' 'wl'). Such a matrix is returned by default by all versions of PROSPECT in 
 #' this package.
-#' @param par.wl Vector of wavelengths defining PAR region
-#' @param nir.wl Vector of wavelengths defining NIR region
-#' @param datetime POSIXlt object defining the date and at which the run will 
-#' take place. N datetime POSIXlt object defining the date and at which the run 
-#' will take place. Note that runs at night and during the winter can give poor 
-#' results.
 #' @param trait.values Named, hierarchical list of trait values for generating 
 #' config.xml file. Names must be PFTs, and must exactly match names of 
 #' `spectra_list`.
-#' @param settings PEcAn settings list. Default is model$revision = 'git', model$config.header = NULL.
-#' @param history.prefix Prefix in histroy file name. Will be appended to 
-#' history path.
-#' @param edr.exe.name Name of EDR executable. Default = 'ed_2.1-opt'
-#' @param change.history.time Logical. If `TRUE`, rename the history file to 
-#' the time specified in `datetime`. Default = TRUE.
-#' @param output.path Path to store all output files. Default is current 
-#' working directory.
+#' @param soil_reflect_path Path to soil reflectance file (defaults to spectra 
+#' in package `extdata`)
+#' @param wood_reflect_path Path to wood reflectance file (defaults to spectra 
+#' in package `extdata`)
+#' @param par.wl Vector of wavelengths defining PAR region
+#' @param nir.wl Vector of wavelengths defining NIR region
+#' @param edr_exe_path If `img_path` is `NULL`, a full path to the EDR 
+#' executable. Ignored otherwise.
+#' @param output.path Directory in which to execute the run. Defaults to 
+#' `dirname(ed2in_path)`.
+#' @param settings PEcAn settings list. Default is `list(model = list(revision 
+#' = "git", config.header = NULL))`.
+#' @param singularity_args Additional arguments to be passed to `singularity run` (before)
 #' @param clean Logical. If `TRUE`, remove all files generated by this function 
 #' (e.g. cloned history file, ED2IN, output HDF files).
+#' @param stderr Logical. If `TRUE` (default), internalize `system2` results as 
+#' R character vector. `TRUE` is recommended because it allows EDR to check its 
+#' execution and to run more quietly.
+#' @param verbose_error Logical. If `TRUE` (default), spit out the full ED 
+#' if EDR execution fails.
+#' @param ... Additional arguments to `system2`
 #' 
+#' @author Alexey Shiklomanov
 #' @export
-EDR <- function(paths,
+EDR <- function(img_path,
+                ed2in_path,
                 spectra_list,
-                par.wl,
-                nir.wl,
-                datetime,
                 trait.values,
-                settings = list(model = list(revision = "git",
-                                             config.header = NULL)),
-                history.prefix = 'history',
-                edr.exe.name = 'ed_2.1-opt',
-                change.history.time = TRUE,
-                output.path = getwd(),
-                clean = FALSE) {
+                soil_reflect_path = system.file("extdata", "soil_reflect_par.dat", package = "PEcAnRTM"),
+                wood_reflect_path = system.file("extdata", "wood_reflect_par.dat", package = "PEcAnRTM"),
+                par.wl = 400:2499,
+                nir.wl = 2500,
+                edr_exe_path = NULL,
+                output.path = dirname(normalizePath(ed2in_path, mustWork = TRUE)),
+                settings = list(model = list(revision = "git", config.header = NULL)),
+                singularity_args = list(),
+                clean = FALSE,
+                stderr = TRUE,
+                verbose_error = TRUE,
+                ...) {
 
-  # Extract paths
-  # TODO: Provide option to just a results path with implied file structure
-  # (ED2IN, config.xml, history)
-  ed2in.path <- ifelse(is.na(paths$ed2in), NA, normalizePath(paths$ed2in))
-  history.path <- normalizePath(paths$history)
-  output.path <- normalizePath(output.path)
-  
-  # Process datetime
-  if (!any(grepl("POSIX", class(datetime)))) {
-    stop("datetime is not POSIX")
-  }
-  
-  # Preprocess history file
-  if (change.history.time) {
-    history.full.prefix <- EDR.preprocess.history(history.path, output.path, datetime, history.prefix)
-  } else {
-    history.full.prefix <- file.path(history.path, history.prefix)
-  }
-  # TODO: Read old config file as template
-  # This ensures that all PFTs and previous default trait values that were in the
-  # run are loaded.
-  # Pseudocode:
-  # xml.old <- XML::xmlToList(XML::xmlParse(old.config.path))
-  # defaults.old <- xml.old$defaults
-  # settings.old <- xml.old$settings
-  # trait.values.old <- xml.old$trait.values
+  ed2in_path <- normalizePath(ed2in_path, mustWork = TRUE)
   
   # Write ED2 config.xml file
-  defaults <- list() 
-  xml <- PEcAn.ED2::write.config.xml.ED2(defaults = defaults,
-                                         settings = settings,
-                                         trait.values = trait.values)
+  defaults <- list()
+  xml <- PEcAn.ED2::write.config.xml.ED2(
+    defaults = defaults,
+    settings = settings,
+    trait.values = trait.values
+  )
   
   new.config.path <- file.path(output.path, "config.xml")
   PREFIX_XML <- '<?xml version="1.0"?>\n<!DOCTYPE config SYSTEM "ed.dtd">\n'
   XML::saveXML(xml, file = new.config.path, indent=TRUE, prefix = PREFIX_XML)
   
-  # Preprocess ED2IN Otherwise, skip this step
-  if (!is.na(ed2in.path)) {
-    EDR.preprocess.ed2in(ed2in.path, output.path, new.config.path, datetime, history.full.prefix)
-  }
-  
   # Generate input files
-  files_list <- file.path(output.path, 
-                          c('lengths.dat', 'reflect_par.dat', 'reflect_nir.dat',
-                            'trans_par.dat', 'trans_nir.dat'))
-  names(files_list) <- c('lengths', 'reflect_par', 'reflect_nir', 
-                         'trans_par', 'trans_nir')
+  files_list <- file.path(
+    output.path,
+    c("lengths.dat",
+      "reflect_par.dat", "reflect_nir.dat",
+      "trans_par.dat", "trans_nir.dat")
+  )
+  names(files_list) <- c("lengths", "reflect_par", "reflect_nir",
+                         "trans_par", "trans_nir")
   file.create(files_list)
 
   write_dat <- function(value, file) {
-    cat(value, file = file, sep = ' ', append = TRUE) 
-    cat('\n', file = file, append = TRUE)
+    cat(value, file = file, sep = " ", append = TRUE)
+    cat("\n", file = file, append = TRUE)
   }
   
   par.nir.lengths <- c(length(par.wl), length(nir.wl))
-  write_dat(par.nir.lengths, files_list['lengths'])
+  write_dat(par.nir.lengths, files_list["lengths"])
 
   if (is_spectra(spectra_list[[1]])) {
     wl <- wavelengths(spectra_list[[1]])
   } else {
-    wl <- spectra_list[[1]][,'wl']
+    wl <- spectra_list[[1]][, "wl"]
   }
   par.ind <- which(wl %in% par.wl)
   nir.ind <- which(wl %in% nir.wl)
 
   # Set up soil and wood reflectance files
-  soil_fname <- "soil_reflect_par.dat"
-  soil_reflect_path <- paths$soil_reflect
-  if (is.null(soil_reflect_path)) {
-    soil_reflect_path <- system.file('extdata', soil_fname, package = 'PEcAnRTM')
-  }
-
   if (!is.na(soil_reflect_path)) {
-    file.copy(soil_reflect_path, file.path(output.path, soil_fname),
-              overwrite = TRUE)
-  }
-
-  wood_fname <- "wood_reflect_par.dat"
-  wood_reflect_path <- paths$wood_reflect
-  if (is.null(wood_reflect_path)) {
-    wood_reflect_path <- system.file('extdata', wood_fname, package = 'PEcAnRTM')
+    file.copy(
+      soil_reflect_path,
+      file.path(output.path, "soil_reflect_par.dat"),
+      overwrite = TRUE
+    )
   }
 
   if (!is.na(wood_reflect_path)) {
-    file.copy(wood_reflect_path, file.path(output.path, wood_fname),
-              overwrite = TRUE)
+    file.copy(
+      wood_reflect_path,
+      file.path(output.path, "wood_reflect_par.dat"),
+      overwrite = TRUE
+    )
   }
 
   # Multi-PFT settings
-  if (length(trait.values) > 0) {
-    if (length(spectra_list) != length(trait.values)) {
-      stop('Spectral data and trait.values do not have same length.\n',
-           'Spectral data length: ', length(spectra_list), '\n',
-           'trait.values length: ', length(trait.values))
-    }
-    pft_names <- names(trait.values)
-    if (any(sort(names(spectra_list)) != sort(pft_names))) {
-      stop('Spectral data and trait.values do not have same PFT names.\n',
-           'Spectral data names: ', names(spectra_list), '\n',
-           'trait.values names: ', pft_names)
-    }
-    data(pftmapping, package = 'PEcAn.ED2')
-    npft <- length(pft_names)
-    write_dat(npft, files_list['lengths'])
-    pft_numbers <- numeric(npft)
-    for (i in seq_len(npft)) {
-      pft_numbers[i] <- pftmapping[pftmapping$PEcAn == pft_names[i], 'ED']
-      write_dat(pft_numbers[i], files_list['lengths'])
-      spectra_list_pft <- spectra_list[[pft_names[i]]]
-      rind <- which(colnames(spectra_list_pft) %in% c('R', 'reflectance'))
-      tind <- which(colnames(spectra_list_pft) %in% c('T', 'transmittance'))
-      write_dat(spectra_list_pft[par.ind, rind], files_list['reflect_par'])
-      write_dat(spectra_list_pft[nir.ind, rind], files_list['reflect_nir'])
-      write_dat(spectra_list_pft[par.ind, tind], files_list['trans_par'])
-      write_dat(spectra_list_pft[nir.ind, tind], files_list['trans_nir'])
-    }
+  if (length(spectra_list) != length(trait.values)) {
+    stop("Spectral data and trait.values do not have same length. ",
+         "Spectral data length: ", length(spectra_list),
+         "trait.values length: ", length(trait.values))
+  }
+  pft_names <- names(trait.values)
+  if (any(!names(spectra_list) %in% pft_names)) {
+    stop("Spectral data and trait.values do not have same PFT names. ",
+         "Spectral data names: ", names(spectra_list),
+         "trait.values names: ", pft_names)
+  }
+  data(pftmapping, package = "PEcAn.ED2")
+  npft <- length(pft_names)
+  write_dat(npft, files_list["lengths"])
+  pft_numbers <- numeric(npft)
+  for (i in seq_len(npft)) {
+    pft_numbers[i] <- pftmapping[pftmapping$PEcAn == pft_names[i], "ED"]
+    write_dat(pft_numbers[i], files_list["lengths"])
+    spectra_list_pft <- spectra_list[[pft_names[i]]]
+    rind <- which(colnames(spectra_list_pft) %in% c("R", "reflectance"))
+    tind <- which(colnames(spectra_list_pft) %in% c("T", "transmittance"))
+    write_dat(spectra_list_pft[par.ind, rind], files_list["reflect_par"])
+    write_dat(spectra_list_pft[nir.ind, rind], files_list["reflect_nir"])
+    write_dat(spectra_list_pft[par.ind, tind], files_list["trans_par"])
+    write_dat(spectra_list_pft[nir.ind, tind], files_list["trans_nir"])
   }
-  
+
+  oldwd <- getwd()
+  setwd(output.path)
+  on.exit(setwd(oldwd))
+
+  if (!is.null(img_path)) {
+    ex <- PEcAn.ED2::run_ed_singularity(
+      img_path, ed2in_path,
+      app = "EDR",
+      singularity_args = singularity_args,
+      stderr = stderr,
+      stdout = stderr,
+      ...
+    )
+  } else {
+    ex <- system2(
+      edr_exe_path,
+      args = c("-f", ed2in_path),
+      stderr = stderr,
+      stdout = stderr,
+      ...
+    )
+  }
+
   # Call EDR -- NOTE that this requires that the ED2IN
-  exec.command <- sprintf("(cd %s; ./%s)", output.path, edr.exe.name)
-  ex <- system(exec.command, intern = TRUE)
-  if (any(grepl("fatal error", ex, ignore.case = TRUE))) {
-    print(ex)
-    stop("Error executing EDR")
+  if (stderr && any(grepl("fatal error|fortran runtime error", ex, ignore.case = TRUE))) {
+    if (verbose_error) {
+      print(ex)
+    }
+    stop("Error executing EDR.")
   }
+
   # Analyze output
   albedo <- get.EDR.output(output.path)
   # Optionally, clean up all generated files
@@ -195,47 +187,8 @@ EDR <- function(paths,
   return(albedo)
 } # EDR
 
-
-#' @title ED RTM coupled to PROSPECT leaf RTM
-#' 
-#' @name EDR.prospect
-#' @param prospect.param Vector of PROSPECT parameters
-#' @param prospect.version Version of PROSPECT to use. Default = 5
-#' @param paths List of paths required by EDR
-#' @param par.wl Vector of wavelengths constituting PAR.
-#' @param nir.wl Vector of wavelengtsh constituting NIR.
-#' @param datetime POSIX datetime object for EDR run
-#' @param ... Other arguments to EDR
-#' @examples
-#' \dontrun{
-#'   ed2in.path <- '/projectnb/dietzelab/pecan.data/output/ashiklom/1000001295/run/1000336885/ED2IN' # Note that the file itself is pointed to
-#'   history.path <- '/projectnb/dietzelab/pecan.data/output/ashiklom/1000001295/out/1000336885/'    # Note that the prefix is NOT included -- only the directory path
-#'   paths <- list(ed2in.path = ed2in.path, history.path = history.path)
-#'   par.wl <- 400:750
-#'   nir.wl <- 751:2500
-#'   prospect.param <- c(1.4, 40, 5, 0.01, 0.01)
-#'   prospect.version <- 5
-#'   datetime <- ISOdatetime(2004, 07, 01, 12, 00, 00)
-#'   albedo <- EDR.prospect(prospect.param = prospect.param,
-#'                          prospect.version = prospect.version,
-#'                          paths=paths, 
-#'                          par.wl = par.wl, nir.wl = nir.wl,
-#'                          datetime = datetime, 
-#'                          history.prefix = 'history', change.history.time = TRUE,
-#'                          output.path = getwd())
-#'   plot(albedo, type='l')
-#' }
-#' @export
-EDR.prospect <- function(prospect.param, prospect.version = 5, paths, par.wl, nir.wl, datetime, ...) {
-  stop('This function is currently deprecated. Use `EDR(...)` instead.')
-  RT.matrix <- prospect(prospect.param, prospect.version)
-  albedo <- EDR(paths, RT.matrix, par.wl, nir.wl, datetime, ...)
-  return(albedo)
-}  # EDR.prospect
-
-#' @title Read EDR output
+#' Read EDR output
 #' 
-#' @name get.EDR.output
 #' @param path Path to directory containing `albedo_par/nir.dat` files
 #' @export
 get.EDR.output <- function(path = getwd()) {
@@ -245,11 +198,10 @@ get.EDR.output <- function(path = getwd()) {
   return(albedo)
 }
 
-#' @title Preprocess history file for EDR
+#' Preprocess history file for EDR
 #' 
-#' @name EDR.preprocess.history
-#' @description Locate history file based on path and prefix, copy to specified 
-#' output directory, and rename to correct time.
+#' Locate history file based on path and prefix, copy to specified output 
+#' directory, and rename to correct time.
 #' @param history.path Path to directory containing history file.
 #' @param history.prefix String describing the history file prefix in 
 #' `history.path`. Default = 'history'
@@ -257,16 +209,16 @@ get.EDR.output <- function(path = getwd()) {
 #' @export
 EDR.preprocess.history <- function(history.path, output.path, datetime, history.prefix = "history") {
   # Check inputs
-  stopifnot(is.character(history.path))
-  stopifnot(is.character(history.prefix))
-  if (!any(grepl("POSIX", class(datetime)))) {
-    stop("datetime is not POSIX")
-  }
+  stopifnot(
+    is.character(history.path),
+    is.character(history.prefix)
+  )
+
   # Extract date and time
-  day          <- strftime(datetime, "%d")
-  month        <- strftime(datetime, "%m")
-  year         <- strftime(datetime, "%Y")
-  time.history <- strftime(datetime, "%H%M%S")
+  day          <- strftime(datetime, "%d", tz = "UTC")
+  month        <- strftime(datetime, "%m", tz = "UTC")
+  year         <- strftime(datetime, "%Y", tz = "UTC")
+  time.history <- strftime(datetime, "%H%M%S", tz = "UTC")
   # Locate history file
   history.search <- sprintf("%1$s-S-%2$s-%3$s-%4$s",
                             history.prefix, year, month, day)
@@ -292,100 +244,3 @@ EDR.preprocess.history <- function(history.path, output.path, datetime, history.
   history.full.prefix <- file.path(output.path, history.prefix)
   return(history.full.prefix)
 } # EDR.preprocess.history
-
-
-#' @title Preprocess ED2IN file for EDR
-#' 
-#' @name EDR.preprocess.ed2in
-#' @description Copy ED2IN to `output.path` and modify for EDR specifications
-#' @param ed2in.path Path to original ED2IN file.
-#' @param output.path Path to directory for new ED2IN file (and where analysis 
-#' is performed)
-#' @param datetime POSIX datetime object defining the time at which to run EDR
-#' @param history.full.prefix Full path and prefix for history file
-#' @export
-EDR.preprocess.ed2in <- function (ed2in.path, output.path, config.path, datetime, 
-                                  history.full.prefix) {
-  # Process datetime
-  day        <- strftime(datetime, "%d")
-  month      <- strftime(datetime, "%m")
-  year       <- strftime(datetime, "%Y")
-  starttime  <- "0000"  # Not the RTM time, but the 'model' time (shouldn't matter)
-  nextdate   <- as.Date(datetime) + 1  # For 'terminating' the run -- set to next day (shouldn't matter)
-  nextday    <- strftime(nextdate, "%d")
-  nextmonth  <- strftime(nextdate, "%m")
-  nextyear   <- strftime(nextdate, "%Y")
-  nexttime   <- "0000"  # Not the RTM time, but the 'model' time -- shouldn't matter
-  time.ed2in <- strftime(datetime, "%H%M")
-  # Copy ED2IN to output.path
-  ed2in.copy <- file.copy(ed2in.path, output.path) # Copy ED2IN to local directory -- returns logical
-  if(!ed2in.copy) {
-    warning("Could not copy ED2IN with overwrite=FALSE. Attempting with overwrite=TRUE")
-    ed2in.copy <- file.copy(ed2in.path, output.path, overwrite=TRUE)
-    if(!ed2in.copy) {
-      stop('Unable to copy ED2IN file, even with overwrite=TRUE. Check permissions on both input and output directories.')
-    }
-  }
-  # Modify ED2IN
-  ed2in.local.path <- file.path(output.path, "ED2IN")
-  ed2in <- readLines(ed2in.local.path)
-  ed2in <- gsub("(NL%RUNTYPE).*", 
-                sprintf("\\1 = '%s'  !! MODIFIED BY R WRAPPER", "HISTORY"), 
-                ed2in)
-  # Start day and time
-  ed2in <- gsub("(NL%IMONTHA).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", month), 
-                ed2in)
-  ed2in <- gsub("(NL%IDATEA).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", day), 
-                ed2in)
-  ed2in <- gsub("(NL%IYEARA).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", year),
-                ed2in)
-  ed2in <- gsub("(NL%ITIMEA).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", starttime), 
-                ed2in)
-  # End date and time
-  ed2in <- gsub("(NL%IMONTHZ).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", nextmonth), 
-                ed2in)
-  ed2in <- gsub("(NL%IDATEZ).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", nextday), 
-                ed2in)
-  ed2in <- gsub("(NL%IYEARZ).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", nextyear),
-                ed2in)
-  ed2in <- gsub("(NL%ITIMEZ).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", nexttime),
-                ed2in)
-  # Output file location
-  ed2in <- gsub("(NL%FFILOUT).*", 
-                sprintf("\\1 = '%s/analysis'  !! MODIFIED BY R WRAPPER", output.path), 
-                ed2in)
-  ed2in <- gsub("(NL%SFILOUT).*",
-                sprintf("\\1 = '%s/history'  !! MODIFIED BY R WRAPPER", output.path),
-                ed2in)
-  # Input (history) file location
-  ed2in <- gsub("(NL%SFILIN).*", 
-                sprintf("\\1 = '%s'  !! MODIFIED BY R WRAPPER", history.full.prefix),
-                ed2in)
-  # History file information
-  ed2in <- gsub("(NL%ITIMEH).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", time.ed2in), 
-                ed2in)
-  ed2in <- gsub("(NL%IDATEH).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", day), 
-                ed2in)
-  ed2in <- gsub("(NL%IMONTHH).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", month), 
-                ed2in)
-  ed2in <- gsub("(NL%IYEARH).*", 
-                sprintf("\\1 = %s  !! MODIFIED BY R WRAPPER", year),
-                ed2in)
-  # config.xml file
-  ed2in <- gsub("(NL%IEDCNFGF).*", 
-                sprintf("\\1 = '%s'  !! MODIFIED BY R WRAPPER", config.path), 
-                ed2in)
-  # Write resulting ED2IN to file
-  write(ed2in, file = ed2in.local.path)
-} # EDR.preprocess.ed2in
diff --git a/modules/rtm/R/params2edr.R b/modules/rtm/R/params2edr.R
new file mode 100644
index 00000000000..46204576c28
--- /dev/null
+++ b/modules/rtm/R/params2edr.R
@@ -0,0 +1,62 @@
+#' Convert named parameter vector to EDR-compatible inputs
+#'
+#' Creates a nested list whose components are suitable for passing to EDR.
+#'
+#' If `prospect = TRUE`, parameters prefixed with `prospect_` are passed to 
+#' [prospect] with the specified `version`, and other parameters are passed to 
+#' `trait.values`.
+#'
+#' The regular expression defining the separation is greedy, i.e. 
+#' `temperate.Early_Hardwood.SLA` will separate into `temperate.Early_Hardwood` 
+#' and `SLA` (assuming the default `sep = "."`). Therefore, it is crucial that 
+#' trait names not contain any `sep` characters (neither ED nor PROSPECT 
+#' parameters should anyway). If this is a problem, use an alternate separator 
+#' (e.g. `|`).
+#'
+#' Note that using `sep = "."` allows this function to directly invert the 
+#' default behavior of `unlist`. That is, calling 
+#' `unlist(params2edr(params, prospect = FALSE)$trait.values)` will return the input vector of 
+#' trait values. This makes `unlist` a convenient way to go from a 
+#' `trait.values` list to a properly formatted `params` vector.
+#'
+#' Because unused ED parameters in the `config.xml` are ignored, the PROSPECT 
+#' parameters are saved in the `trait.values` object as well, which may be 
+#' useful for debugging.
+#'
+#' @param params Named parameter vector
+#' @param sep Separator between PFT name and trait name. Must be a single 
+#' character (default = ".").
+#' @param prospect Logical. If `TRUE` (default), scan for PROSPECT traits and 
+#' pass them to PROSPECT.
+#' @param version PROSPECT version
+#' @return List containing `spectra_list` and `trait.values`, both objects needed by [EDR].
+#' @author Alexey Shiklomanov
+#' @export
+params2edr <- function(params, sep = ".", prospect = TRUE, version = 5) {
+  stopifnot(
+    !is.null(names(params)),
+    all(grepl(sep, names(params)))
+  )
+  params <- params[names(params) != "residual"]
+  split_regex <- paste0("(.*)[", sep, "](.*)")
+  pfts <- gsub(split_regex, "\\1", names(params))
+  traits <- gsub(split_regex, "\\2", names(params))
+  distinct_pfts <- unique(pfts)
+  result <- list(trait.values = vector("list", length(distinct_pfts)))
+  names(result$trait.values) <- distinct_pfts
+  if (prospect) {
+    result$spectra_list <- result$trait.values
+
+  }
+  for (pft in distinct_pfts) {
+    pft_ind <- pfts == pft
+    pft_traits <- params[pft_ind]
+    names(pft_traits) <- traits[pft_ind]
+    if (prospect) {
+      prospect_traits <- grepl("prospect_", names(pft_traits))
+      result$spectra_list[[pft]] <- prospect(pft_traits[prospect_traits], version)
+    }
+    result$trait.values[[pft]] <- pft_traits
+  }
+  result
+}
diff --git a/modules/rtm/R/sail.R b/modules/rtm/R/sail.R
new file mode 100644
index 00000000000..6a8f56a31de
--- /dev/null
+++ b/modules/rtm/R/sail.R
@@ -0,0 +1,47 @@
+#' SAIL model
+#'
+#' R wrapper for 4SAIL model
+#' @author Shawn Serbin
+#' @author Alexey Shiklomanov
+#' 
+#' @param refl input leaf reflectance from 400-2500nm (can be measured or modeled)
+#' @param tran input leaf transmittance from 400-2500nm (can be measured or modeled)
+#' @param rsoil input soil reflectance spectra from 400-2500nm (can be measured or modeled)
+#' @param param Vector of SAIL parameter values:
+#'      * LIDFa: Leaf angle distribution function - parameter a
+#'      * LIDFb: Leaf angle distribution function - parameter b
+#'      * TypeLIDF: Leaf angle distribution function type (1 or 2)
+#'      * LAI: Leaf area index
+#'      * q: Hot spot effect parameter
+#'      * tts: Solar zenith angle
+#'      * tto: Observer zenith angle
+#'      * psi: Sun-sensor azimuth angle
+#' 
+#' @return Spectra matrix (see [spectra()]) (2101 x 4) of reflectance factors 
+#' for wavelengths 400 to 2500nm:
+#'      * bi-hemispherical reflectance (rddt)
+#'      * hemispherical directional (rsdt)
+#'      * directional hemispherical (rdot)
+#'      * bi-directional (rsot)
+#' @export
+foursail <- function(refl, tran, rsoil, param) {
+  rho <- as.vector(refl)
+  tau <- as.vector(tran)
+  rsoil <- as.vector(rsoil)
+  plist <- c(list(rho), list(tau), as.list(param), list(rsoil))
+  nw    <- 2101
+  plist$rddt <- numeric(nw)
+  plist$rsdt <- numeric(nw)
+  plist$rdot <- numeric(nw)
+  plist$rsot <- numeric(nw)
+  inputs     <- c("foursail", plist)
+  outlist <- do.call(.Fortran, inputs)
+  lo      <- length(outlist)
+  canopy_refl    <- do.call(cbind, outlist[(lo - 3):lo])
+  reflspec <- spectra(canopy_refl, 400:2500)
+  colnames(reflspec) <- c("bi-hemispherical", "hemispherical_directional",
+                          "directional_hemispherical", "bi-directional")
+  reflspec
+} # sail
+
+
diff --git a/modules/rtm/R/setup_edr.R b/modules/rtm/R/setup_edr.R
new file mode 100644
index 00000000000..d3f50ef65cd
--- /dev/null
+++ b/modules/rtm/R/setup_edr.R
@@ -0,0 +1,56 @@
+#' Setup EDR run
+#'
+#' Using an existing ED2IN file as a template, create a new ED2IN and history 
+#' file configured for running EDR.
+#'
+#' @param ed2in ED2IN list object (see [PEcAn.ED2::read_ed2in]).
+#' @param output_dir Directory in which run files will be stored
+#' @param datetime Date time object (or compliant string) at which to run EDR. 
+#' Defaults to 12 noon on start date in ED2IN.
+#' @return Path to EDR-configured ED2IN file.
+#' @author Alexey Shiklomanov
+#' @export
+setup_edr <- function(ed2in, output_dir,
+                      datetime = ISOdatetime(ed2in[["IYEARA"]],
+                                             ed2in[["IMONTHA"]],
+                                             ed2in[["IDATEA"]],
+                                             12, 00, 00, tz = "UTC"),
+                      ...) {
+
+  hour <- as.numeric(strftime(datetime, "%H", tz = "UTC"))
+  if (hour < 8 | hour > 17) {
+    PEcAn.logger::logger.warn(
+      "Starting hour ", hour,
+      " is not between 8am and 5pm. ",
+      "It is generally a good idea to run EDR during the day to get good results."
+    )
+  }
+
+  dir.create(output_dir, showWarnings = FALSE)
+  nextday <- as.POSIXct(datetime, tz = "UTC") + 86400   # Add one day
+
+  history_prefix <- EDR.preprocess.history(
+    history.path = dirname(ed2in$SFILOUT),
+    history.prefix = basename(ed2in$SFILOUT),
+    datetime = datetime,
+    output.path = output_dir
+  )
+
+  ed2in_edr <- PEcAn.ED2::modify_ed2in(
+    ed2in,
+    start_date = datetime,
+    end_date = nextday,
+    output_dir = output_dir,
+    run_dir = output_dir,
+    runtype = "HISTORY",
+    SFILIN = history_prefix,
+    ...
+  )
+
+  PEcAn.ED2::check_ed2in(ed2in_edr)
+
+  ed2in_edr_path <- file.path(output_dir, "ED2IN")
+  PEcAn.ED2::write_ed2in(ed2in_edr, ed2in_edr_path)
+
+  ed2in_edr_path
+}
diff --git a/modules/rtm/man/EDR.Rd b/modules/rtm/man/EDR.Rd
index 68b56365556..68d65608f36 100644
--- a/modules/rtm/man/EDR.Rd
+++ b/modules/rtm/man/EDR.Rd
@@ -2,30 +2,22 @@
 % Please edit documentation in R/edr.wrapper.R
 \name{EDR}
 \alias{EDR}
-\title{ED radiative transfer module (EDR) wrapper function
-
-This function provides a convenient way to call the ED
-radiative transfer module (EDR, which simulates full spectral return of an
-ED patch for a given point in time) directly from R.}
+\title{ED radiative transfer module (EDR) wrapper function}
 \usage{
-EDR(paths, spectra_list, par.wl, nir.wl, datetime, trait.values,
+EDR(img_path, ed2in_path, spectra_list, trait.values,
+  soil_reflect_path = system.file("extdata", "soil_reflect_par.dat",
+  package = "PEcAnRTM"), wood_reflect_path = system.file("extdata",
+  "wood_reflect_par.dat", package = "PEcAnRTM"), par.wl = 400:2499,
+  nir.wl = 2500, edr_exe_path = NULL,
+  output.path = dirname(normalizePath(ed2in_path, mustWork = TRUE)),
   settings = list(model = list(revision = "git", config.header = NULL)),
-  history.prefix = "history", edr.exe.name = "ed_2.1-opt",
-  change.history.time = TRUE, output.path = getwd(), clean = FALSE)
+  singularity_args = list(), clean = FALSE, stderr = TRUE,
+  verbose_error = TRUE, ...)
 }
 \arguments{
-\item{paths}{List of relevant paths. Must contain the following:
-\itemize{
-\item \code{ed2in} -- Path to ED2IN file for the original ED run. If this is \code{NA}, the
-function assumes that the ED2IN file in \code{output.path} is already up-to-date
-and skips the analysis step.
-\item \code{history} -- Path and prefix for history file for the run of interest;
-\item \code{edr.exe} -- Path to EDR executable
-\item \code{soil_reflect} -- Path to soil reflectance. If NULL or unset, use
-reflectance in package. If NA, skip (assume data already in directory).
-\item \code{wood_reflect} -- Path to wood reflectance. If NULL or unset, use
-reflectance in package. If NA, skip (assume data already in directory).
-}}
+\item{img_path}{Path to Singularity container (usually a \code{.simg} file)}
+
+\item{ed2in_path}{Path to ED2IN file.}
 
 \item{spectra_list}{List of spectral data matrices. Names must exactly match
 the PFTs given in \code{trait.values}. Each item must be a matrix of
@@ -35,32 +27,47 @@ reflectance (labeled 'R' or 'reflectance') and transmittance (labeled 'T' or
 'wl'). Such a matrix is returned by default by all versions of PROSPECT in
 this package.}
 
-\item{par.wl}{Vector of wavelengths defining PAR region}
-
-\item{nir.wl}{Vector of wavelengths defining NIR region}
-
-\item{datetime}{POSIXlt object defining the date and at which the run will
-take place. N datetime POSIXlt object defining the date and at which the run
-will take place. Note that runs at night and during the winter can give poor
-results.}
-
 \item{trait.values}{Named, hierarchical list of trait values for generating
 config.xml file. Names must be PFTs, and must exactly match names of
 \code{spectra_list}.}
 
-\item{settings}{PEcAn settings list. Default is model$revision = 'git', model$config.header = NULL.}
+\item{soil_reflect_path}{Path to soil reflectance file (defaults to spectra
+in package \code{extdata})}
 
-\item{history.prefix}{Prefix in histroy file name. Will be appended to
-history path.}
+\item{wood_reflect_path}{Path to wood reflectance file (defaults to spectra
+in package \code{extdata})}
 
-\item{edr.exe.name}{Name of EDR executable. Default = 'ed_2.1-opt'}
+\item{par.wl}{Vector of wavelengths defining PAR region}
 
-\item{change.history.time}{Logical. If \code{TRUE}, rename the history file to
-the time specified in \code{datetime}. Default = TRUE.}
+\item{nir.wl}{Vector of wavelengths defining NIR region}
 
-\item{output.path}{Path to store all output files. Default is current
-working directory.}
+\item{edr_exe_path}{If \code{img_path} is \code{NULL}, a full path to the EDR
+executable. Ignored otherwise.}
+
+\item{output.path}{Directory in which to execute the run. Defaults to
+\code{dirname(ed2in_path)}.}
+
+\item{settings}{PEcAn settings list. Default is \code{list(model = list(revision = "git", config.header = NULL))}.}
+
+\item{singularity_args}{Additional arguments to be passed to \code{singularity run} (before)}
 
 \item{clean}{Logical. If \code{TRUE}, remove all files generated by this function
 (e.g. cloned history file, ED2IN, output HDF files).}
+
+\item{stderr}{Logical. If \code{TRUE} (default), internalize \code{system2} results as
+R character vector. \code{TRUE} is recommended because it allows EDR to check its
+execution and to run more quietly.}
+
+\item{verbose_error}{Logical. If \code{TRUE} (default), spit out the full ED
+if EDR execution fails.}
+
+\item{...}{Additional arguments to \code{system2}}
+}
+\description{
+This function provides a convenient way to call the ED
+radiative transfer module (EDR, which simulates full spectral return of an
+ED patch for a given point in time) directly from R.
+}
+\author{
+Alexey Shiklomanov
 }
diff --git a/modules/rtm/man/EDR.preprocess.ed2in.Rd b/modules/rtm/man/EDR.preprocess.ed2in.Rd
deleted file mode 100644
index 1c2d090f5fc..00000000000
--- a/modules/rtm/man/EDR.preprocess.ed2in.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/edr.wrapper.R
-\name{EDR.preprocess.ed2in}
-\alias{EDR.preprocess.ed2in}
-\title{Preprocess ED2IN file for EDR}
-\usage{
-EDR.preprocess.ed2in(ed2in.path, output.path, config.path, datetime,
-  history.full.prefix)
-}
-\arguments{
-\item{ed2in.path}{Path to original ED2IN file.}
-
-\item{output.path}{Path to directory for new ED2IN file (and where analysis
-is performed)}
-
-\item{datetime}{POSIX datetime object defining the time at which to run EDR}
-
-\item{history.full.prefix}{Full path and prefix for history file}
-}
-\description{
-Copy ED2IN to \code{output.path} and modify for EDR specifications
-}
diff --git a/modules/rtm/man/EDR.preprocess.history.Rd b/modules/rtm/man/EDR.preprocess.history.Rd
index 756f0daa741..d8514993eee 100644
--- a/modules/rtm/man/EDR.preprocess.history.Rd
+++ b/modules/rtm/man/EDR.preprocess.history.Rd
@@ -16,6 +16,6 @@ EDR.preprocess.history(history.path, output.path, datetime,
 \code{history.path}. Default = 'history'}
 }
 \description{
-Locate history file based on path and prefix, copy to specified
-output directory, and rename to correct time.
+Locate history file based on path and prefix, copy to specified output
+directory, and rename to correct time.
 }
diff --git a/modules/rtm/man/EDR.prospect.Rd b/modules/rtm/man/EDR.prospect.Rd
deleted file mode 100644
index 4c871639bc9..00000000000
--- a/modules/rtm/man/EDR.prospect.Rd
+++ /dev/null
@@ -1,44 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/edr.wrapper.R
-\name{EDR.prospect}
-\alias{EDR.prospect}
-\title{ED RTM coupled to PROSPECT leaf RTM}
-\usage{
-EDR.prospect(prospect.param, prospect.version = 5, paths, par.wl, nir.wl,
-  datetime, ...)
-}
-\arguments{
-\item{prospect.param}{Vector of PROSPECT parameters}
-
-\item{prospect.version}{Version of PROSPECT to use. Default = 5}
-
-\item{paths}{List of paths required by EDR}
-
-\item{par.wl}{Vector of wavelengths constituting PAR.}
-
-\item{nir.wl}{Vector of wavelengtsh constituting NIR.}
-
-\item{datetime}{POSIX datetime object for EDR run}
-
-\item{...}{Other arguments to EDR}
-}
-\examples{
-\dontrun{
-  ed2in.path <- '/projectnb/dietzelab/pecan.data/output/ashiklom/1000001295/run/1000336885/ED2IN' # Note that the file itself is pointed to
-  history.path <- '/projectnb/dietzelab/pecan.data/output/ashiklom/1000001295/out/1000336885/'    # Note that the prefix is NOT included -- only the directory path
-  paths <- list(ed2in.path = ed2in.path, history.path = history.path)
-  par.wl <- 400:750
-  nir.wl <- 751:2500
-  prospect.param <- c(1.4, 40, 5, 0.01, 0.01)
-  prospect.version <- 5
-  datetime <- ISOdatetime(2004, 07, 01, 12, 00, 00)
-  albedo <- EDR.prospect(prospect.param = prospect.param,
-                         prospect.version = prospect.version,
-                         paths=paths, 
-                         par.wl = par.wl, nir.wl = nir.wl,
-                         datetime = datetime, 
-                         history.prefix = 'history', change.history.time = TRUE,
-                         output.path = getwd())
-  plot(albedo, type='l')
-}
-}
diff --git a/modules/rtm/man/foursail.Rd b/modules/rtm/man/foursail.Rd
new file mode 100644
index 00000000000..dd206b2ef60
--- /dev/null
+++ b/modules/rtm/man/foursail.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sail.R
+\name{foursail}
+\alias{foursail}
+\title{SAIL model}
+\usage{
+foursail(refl, tran, rsoil, param)
+}
+\arguments{
+\item{refl}{input leaf reflectance from 400-2500nm (can be measured or modeled)}
+
+\item{tran}{input leaf transmittance from 400-2500nm (can be measured or modeled)}
+
+\item{rsoil}{input soil reflectance spectra from 400-2500nm (can be measured or modeled)}
+
+\item{param}{Vector of SAIL parameter values:
+* LIDFa: Leaf angle distribution function - parameter a
+* LIDFb: Leaf angle distribution function - parameter b
+* TypeLIDF: Leaf angle distribution function type (1 or 2)
+* LAI: Leaf area index
+* q: Hot spot effect parameter
+* tts: Solar zenith angle
+* tto: Observer zenith angle
+* psi: Sun-sensor azimuth angle}
+}
+\value{
+Spectra matrix (see \code{\link[=spectra]{spectra()}}) (2101 x 4) of reflectance factors
+for wavelengths 400 to 2500nm:
+* bi-hemispherical reflectance (rddt)
+* hemispherical directional (rsdt)
+* directional hemispherical (rdot)
+* bi-directional (rsot)
+}
+\description{
+R wrapper for 4SAIL model
+}
+\author{
+Shawn Serbin
+
+Alexey Shiklomanov
+}
diff --git a/modules/rtm/man/get.EDR.output.Rd b/modules/rtm/man/get.EDR.output.Rd
index 44df363712e..06ec5c49cb1 100644
--- a/modules/rtm/man/get.EDR.output.Rd
+++ b/modules/rtm/man/get.EDR.output.Rd
@@ -9,3 +9,6 @@ get.EDR.output(path = getwd())
 \arguments{
 \item{path}{Path to directory containing \code{albedo_par/nir.dat} files}
 }
+\description{
+Read EDR output
+}
diff --git a/modules/rtm/man/invert_bt.Rd b/modules/rtm/man/invert_bt.Rd
index b1ef06619b4..d2d79e7cfef 100644
--- a/modules/rtm/man/invert_bt.Rd
+++ b/modules/rtm/man/invert_bt.Rd
@@ -4,17 +4,22 @@
 \alias{invert_bt}
 \title{Perform Bayesian inversion using BayesianTools package}
 \usage{
-invert_bt(observed, model, prior, custom_settings = list())
+invert_bt(observed, model, prior, custom_settings = list(),
+  loglike = NULL)
 }
 \arguments{
-\item{observed}{Vector of observations}
+\item{observed}{Vector of observations. Ignored if \code{loglike} is not \code{NULL}.}
 
 \item{model}{Function called by log-likelihood. Must be \code{function(params)}
-and return a vector equal to \code{length(observed)} or \code{nrow(observed)}.}
+and return a vector equal to \code{length(observed)} or \code{nrow(observed)}. Ignored
+if \code{loglike} is not \code{NULL}.}
 
 \item{prior}{BayesianTools prior object.}
 
 \item{custom_settings}{Nested settings list. See Details.}
+
+\item{loglike}{Custom log likelihood function. If \code{NULL}, use \link{rtm_loglike}
+with provided \code{observed} and \code{model}.}
 }
 \description{
 Use samplers from the BayesianTools package to fit models to data. Like
diff --git a/modules/rtm/man/params.prospect5.Rd b/modules/rtm/man/params.prospect5.Rd
index adb2729a4a0..7a785216060 100644
--- a/modules/rtm/man/params.prospect5.Rd
+++ b/modules/rtm/man/params.prospect5.Rd
@@ -8,4 +8,7 @@
 \usage{
 params.prospect5
 }
+\description{
+PROSPECT 5 parameters
+}
 \keyword{datasets}
diff --git a/modules/rtm/man/params.prospect5b.Rd b/modules/rtm/man/params.prospect5b.Rd
index b95229833cd..7af89b7d2de 100644
--- a/modules/rtm/man/params.prospect5b.Rd
+++ b/modules/rtm/man/params.prospect5b.Rd
@@ -8,4 +8,7 @@
 \usage{
 params.prospect5b
 }
+\description{
+PROSPECT 5B parameters
+}
 \keyword{datasets}
diff --git a/modules/rtm/man/params2edr.Rd b/modules/rtm/man/params2edr.Rd
new file mode 100644
index 00000000000..69ce0a4ae26
--- /dev/null
+++ b/modules/rtm/man/params2edr.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/params2edr.R
+\name{params2edr}
+\alias{params2edr}
+\title{Convert named parameter vector to EDR-compatible inputs}
+\usage{
+params2edr(params, sep = ".", prospect = TRUE, version = 5)
+}
+\arguments{
+\item{params}{Named parameter vector}
+
+\item{sep}{Separator between PFT name and trait name. Must be a single
+character (default = ".").}
+
+\item{prospect}{Logical. If \code{TRUE} (default), scan for PROSPECT traits and
+pass them to PROSPECT.}
+
+\item{version}{PROSPECT version}
+}
+\value{
+List containing \code{spectra_list} and \code{trait.values}, both objects needed by \link{EDR}.
+}
+\description{
+Creates a nested list whose components are suitable for passing to EDR.
+}
+\details{
+If \code{prospect = TRUE}, parameters prefixed with \code{prospect_} are passed to
+\link{prospect} with the specified \code{version}, and other parameters are passed to
+\code{trait.values}.
+
+The regular expression defining the separation is greedy, i.e.
+\code{temperate.Early_Hardwood.SLA} will separate into \code{temperate.Early_Hardwood}
+and \code{SLA} (assuming the default \code{sep = "."}). Therefore, it is crucial that
+trait names not contain any \code{sep} characters (neither ED nor PROSPECT
+parameters should anyway). If this is a problem, use an alternate separator
+(e.g. \code{|}).
+
+Note that using \code{sep = "."} allows this function to directly invert the
+default behavior of \code{unlist}. That is, calling
+\code{unlist(params2edr(params, prospect = FALSE)$trait.values)} will return the input vector of
+trait values. This makes \code{unlist} a convenient way to go from a
+\code{trait.values} list to a properly formatted \code{params} vector.
+
+Because unused ED parameters in the \code{config.xml} are ignored, the PROSPECT
+parameters are saved in the \code{trait.values} object as well, which may be
+useful for debugging.
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/rtm/man/rtm_loglike.Rd b/modules/rtm/man/rtm_loglike.Rd
index 1096808b354..ef823b53020 100644
--- a/modules/rtm/man/rtm_loglike.Rd
+++ b/modules/rtm/man/rtm_loglike.Rd
@@ -4,7 +4,8 @@
 \alias{rtm_loglike}
 \title{Generic log-likelihood generator for RTMs}
 \usage{
-rtm_loglike(nparams, model, observed, lag.max = NULL, verbose = TRUE, ...)
+rtm_loglike(nparams, model, observed, lag.max = NULL, verbose = TRUE,
+  ...)
 }
 \description{
 Generic log-likelihood generator for RTMs
diff --git a/modules/rtm/man/setup_edr.Rd b/modules/rtm/man/setup_edr.Rd
new file mode 100644
index 00000000000..e9311393a53
--- /dev/null
+++ b/modules/rtm/man/setup_edr.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/setup_edr.R
+\name{setup_edr}
+\alias{setup_edr}
+\title{Setup EDR run}
+\usage{
+setup_edr(ed2in, output_dir, datetime = ISOdatetime(ed2in[["IYEARA"]],
+  ed2in[["IMONTHA"]], ed2in[["IDATEA"]], 12, 0, 0, tz = "UTC"), ...)
+}
+\arguments{
+\item{ed2in}{ED2IN list object (see \link[PEcAn.ED2:read_ed2in]{PEcAn.ED2::read_ed2in}).}
+
+\item{output_dir}{Directory in which run files will be stored}
+
+\item{datetime}{Date time object (or compliant string) at which to run EDR.
+Defaults to 12 noon on start date in ED2IN.}
+}
+\value{
+Path to EDR-configured ED2IN file.
+}
+\description{
+Using an existing ED2IN file as a template, create a new ED2IN and history
+file configured for running EDR.
+}
+\author{
+Alexey Shiklomanov
+}
diff --git a/modules/rtm/tests/testthat/test.foursail.R b/modules/rtm/tests/testthat/test.foursail.R
new file mode 100644
index 00000000000..3d8ae53b353
--- /dev/null
+++ b/modules/rtm/tests/testthat/test.foursail.R
@@ -0,0 +1,45 @@
+context("Testing standalone SAIL RTM")
+
+# get soil reflectance spectra
+rsoil <- system.file("extdata", "soil_reflect_par.dat", package="PEcAnRTM")
+rsoil <- read.table(rsoil,header = F)
+rsoil <- as.vector(unlist(rsoil[1,]))
+rsoil <- c(rsoil,rsoil[2100]) # make soil reflectance the correct length
+if (interactive()) {
+  plot(seq(400,2500,1), rsoil, type = "l")
+}
+
+# define sail parameters
+LIDFa <- -0.35 
+LIDFb <- -0.15
+TypeLIDF <- 1
+LAI <- 4
+q <- 0.1
+tts <- 48
+tto <- 0 
+psi <- 234
+params <- c(LIDFa,LIDFb,TypeLIDF,LAI,q,tts,tto,psi)
+param <- params
+
+# get leaf reflectance and transmittance
+LRT <- PEcAnRTM::prospect(c(2,55,10,3,0.1,0.007,0.007), 'D')
+if (interactive()) {
+  plot(LRT[,1])
+}
+refl <- LRT[,1]
+length(refl)
+tran <- LRT[,2]
+
+# generate 4SAIL canopy spectra
+sail_spec <- foursail(refl, tran, rsoil, params)
+
+expect_true(is_spectra(sail_spec))
+expect_true(nrow(sail_spec) == 2101)
+expect_true(ncol(sail_spec) == 4)
+expect_true(all(is.finite(sail_spec)))
+expect_true(all(sail_spec > 0))
+
+# plot results
+if (interactive()) {
+  matplot(sail_spec)
+}
diff --git a/modules/uncertainty/DESCRIPTION b/modules/uncertainty/DESCRIPTION
index cd9a75b8867..50833dfc80e 100644
--- a/modules/uncertainty/DESCRIPTION
+++ b/modules/uncertainty/DESCRIPTION
@@ -2,8 +2,8 @@ Package: PEcAn.uncertainty
 Type: Package
 Title: PEcAn functions used for ecological forecasts and
     reanalysis
-Version: 1.5.3
-Date: 2018-04-26
+Version: 1.6.0
+Date: 2018-08-20
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
     Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <dlebauer@illinois.edu>
@@ -15,7 +15,6 @@ Description: The Predictive Ecosystem Carbon Analyzer
     models, and to improve the efficacy of scientific
     investigation.
 Depends:
-    PEcAn.logger,
     PEcAn.utils,
     PEcAn.priors,
     ggplot2,
@@ -23,11 +22,19 @@ Depends:
     gridExtra
 Imports:
     coda (>= 0.18),
-    plyr (>= 1.8.4)
+    dplyr,
+    PEcAn.DB,
+    PEcAn.emulator,
+    PEcAn.logger,
+    plyr (>= 1.8.4),
+    purrr,
+    randtoolbox,
+    udunits2
 Suggests:
     testthat (>= 1.0.2),
 License: FreeBSD + file LICENSE
 Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 6.1.0
diff --git a/modules/uncertainty/NAMESPACE b/modules/uncertainty/NAMESPACE
index c269b1b8203..db2cf7d815e 100644
--- a/modules/uncertainty/NAMESPACE
+++ b/modules/uncertainty/NAMESPACE
@@ -5,12 +5,17 @@ export(flux.uncertainty)
 export(get.change)
 export(get.coef.var)
 export(get.elasticity)
+export(get.ensemble.samples)
+export(get.parameter.samples)
 export(get.sensitivity)
+export(input.ens.gen)
 export(plot_flux_uncertainty)
 export(plot_sensitivities)
 export(plot_sensitivity)
 export(plot_variance_decomposition)
+export(prep.data.assim)
 export(read.ameriflux.L2)
+export(read.ensemble.output)
 export(read.ensemble.ts)
 export(run.ensemble.analysis)
 export(run.sensitivity.analysis)
@@ -20,3 +25,5 @@ export(sa.splinefun)
 export(sd.var)
 export(sensitivity.analysis)
 export(spline.truncate)
+export(write.ensemble.configs)
+importFrom(dplyr,"%>%")
diff --git a/modules/uncertainty/R/ensemble.R b/modules/uncertainty/R/ensemble.R
new file mode 100644
index 00000000000..d649c5f967e
--- /dev/null
+++ b/modules/uncertainty/R/ensemble.R
@@ -0,0 +1,442 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+
+##' Reads output from model ensemble
+##'
+##' Reads output for an ensemble of length specified by \code{ensemble.size} and bounded by \code{start.year} 
+##' and \code{end.year}
+##' @title Read ensemble output
+##' @return a list of ensemble model output 
+##' @param ensemble.size the number of ensemble members run
+##' @param pecandir specifies where pecan writes its configuration files
+##' @param outdir directory with model output to use in ensemble analysis
+##' @param start.year first year to include in ensemble analysis
+##' @param end.year last year to include in ensemble analysis
+##' @param variable target variables for ensemble analysis
+##' @param ens.run.ids dataframe. Must contain a column named "id" giving the run IDs to be read.
+##'   If NULL, will attempt to read IDs from a file named "samples.Rdata" in \code{pecandir}
+##' @export
+##' @author Ryan Kelly, David LeBauer, Rob Kooper
+#--------------------------------------------------------------------------------------------------#
+read.ensemble.output <- function(ensemble.size, pecandir, outdir, start.year, end.year, 
+                                 variable, ens.run.ids = NULL) {
+  if (is.null(ens.run.ids)) {
+    samples.file <- file.path(pecandir, "samples.Rdata")
+    if (file.exists(samples.file)) {
+      load(samples.file)
+      ens.run.ids <- runs.samples$ensemble
+    } else {
+      stop(samples.file, "not found required by read.ensemble.output")
+    }
+  }
+  
+  expr <- variable$expression
+  variables <- variable$variables
+  
+  ensemble.output <- list()
+  for (row in rownames(ens.run.ids)) {
+    run.id <- ens.run.ids[row, "id"]
+    PEcAn.logger::logger.info("reading ensemble output from run id: ", run.id)
+    
+    for(var in seq_along(variables)){
+      out.tmp <- PEcAn.utils::read.output(run.id, file.path(outdir, run.id), start.year, end.year, variables[var])
+      assign(variables[var], out.tmp[[variables[var]]])
+    }
+    
+    # derivation
+    out <- eval(parse(text = expr))
+    
+    ensemble.output[[row]] <- mean(out, na.rm= TRUE) 
+    
+  }
+  return(ensemble.output)
+} # read.ensemble.output
+
+
+##' Get parameter values used in ensemble
+##'
+##' Returns a matrix of randomly or quasi-randomly sampled trait values 
+##' to be assigned to traits over several model runs.
+##' given the number of model runs and a list of sample distributions for traits
+##' The model run is indexed first by model run, then by trait
+##' 
+##' @title Get Ensemble Samples
+##' @name get.ensemble.samples
+##' @param ensemble.size number of runs in model ensemble
+##' @param pft.samples random samples from parameter distribution, e.g. from a MCMC chain  
+##' @param env.samples env samples
+##' @param method the method used to generate the ensemble samples. Random generators: uniform, uniform with latin hypercube permutation. Quasi-random generators: halton, sobol, torus. Random generation draws random variates whereas quasi-random generation is deterministic but well equidistributed. Default is uniform. For small ensemble size with relatively large parameter number (e.g ensemble size < 5 and # of traits > 5) use methods other than halton. 
+##' @param param.names a list of parameter names that were fitted either by MA or PDA, important argument, if NULL parameters will be resampled independently
+##' @param ... Other arguments passed on to the sampling method
+##' 
+##' @return matrix of (quasi-)random samples from trait distributions
+##' @export
+##' @author David LeBauer, Istem Fer
+get.ensemble.samples <- function(ensemble.size, pft.samples, env.samples, 
+                                 method = "uniform", param.names = NULL, ...) {
+  
+  if (is.null(method)) {
+    PEcAn.logger::logger.info("No sampling method supplied, defaulting to uniform random sampling")
+    method <- "uniform"
+  }
+  
+  ## force as numeric for compatibility with Fortran code in halton()
+  ensemble.size <- as.numeric(ensemble.size)
+  if (ensemble.size <= 0) {
+    ans <- NULL
+  } else if (ensemble.size == 1) {
+    ans <- PEcAn.utils::get.sa.sample.list(pft.samples, env.samples, 0.5)
+  } else {
+    pft.samples[[length(pft.samples) + 1]] <- env.samples
+    names(pft.samples)[length(pft.samples)] <- "env"
+    pft2col <- NULL
+    for (i in seq_along(pft.samples)) {
+      pft2col <- c(pft2col, rep(i, length(pft.samples[[i]])))
+    }
+    
+    total.sample.num <- sum(sapply(pft.samples, length))
+    random.samples <- NULL
+    
+    
+    if (method == "halton") {
+      PEcAn.logger::logger.info("Using ", method, "method for sampling")
+      random.samples <- randtoolbox::halton(n = ensemble.size, dim = total.sample.num, ...)
+      ## force as a matrix in case length(samples)=1
+      random.samples <- as.matrix(random.samples)
+    } else if (method == "sobol") {
+      PEcAn.logger::logger.info("Using ", method, "method for sampling")
+      random.samples <- randtoolbox::sobol(n = ensemble.size, dim = total.sample.num, ...)
+      ## force as a matrix in case length(samples)=1
+      random.samples <- as.matrix(random.samples)
+    } else if (method == "torus") {
+      PEcAn.logger::logger.info("Using ", method, "method for sampling")
+      random.samples <- randtoolbox::torus(n = ensemble.size, dim = total.sample.num, ...)
+      ## force as a matrix in case length(samples)=1
+      random.samples <- as.matrix(random.samples)
+    } else if (method == "lhc") {
+      PEcAn.logger::logger.info("Using ", method, "method for sampling")
+      random.samples <- PEcAn.emulator::lhc(t(matrix(0:1, ncol = total.sample.num, nrow = 2)), ensemble.size)
+    } else if (method == "uniform") {
+      PEcAn.logger::logger.info("Using ", method, "random sampling")
+      # uniform random
+      random.samples <- matrix(stats::runif(ensemble.size * total.sample.num),
+                               ensemble.size, 
+                               total.sample.num)
+    } else {
+      PEcAn.logger::logger.info("Method ", method, " has not been implemented yet, using uniform random sampling")
+      # uniform random
+      random.samples <- matrix(stats::runif(ensemble.size * total.sample.num),
+                               ensemble.size, 
+                               total.sample.num)
+    }
+    
+    
+    ensemble.samples <- list()
+    
+    
+    col.i <- 0
+    for (pft.i in seq(pft.samples)) {
+      ensemble.samples[[pft.i]] <- matrix(nrow = ensemble.size, ncol = length(pft.samples[[pft.i]]))
+      
+      # meaning we want to keep MCMC samples together
+      if(length(pft.samples[[pft.i]])>0 & !is.null(param.names)){ 
+        # TODO: for now we are sampling row numbers uniformly
+        # stop if other methods were requested 
+        if(method != "uniform"){
+          PEcAn.logger::logger.severe("Only uniform sampling is available for joint sampling at the moment. Other approaches are not implemented yet.")
+        }
+        same.i <- sample.int(length(pft.samples[[pft.i]][[1]]), ensemble.size)
+      }
+      
+      for (trait.i in seq(pft.samples[[pft.i]])) {
+        col.i <- col.i + 1
+        if(names(pft.samples[[pft.i]])[trait.i] %in% param.names[[pft.i]]){ # keeping samples
+          ensemble.samples[[pft.i]][, trait.i] <- pft.samples[[pft.i]][[trait.i]][same.i]
+        }else{
+          ensemble.samples[[pft.i]][, trait.i] <- stats::quantile(pft.samples[[pft.i]][[trait.i]],
+                                                                  random.samples[, col.i])
+        }
+      }  # end trait
+      ensemble.samples[[pft.i]] <- as.data.frame(ensemble.samples[[pft.i]])
+      colnames(ensemble.samples[[pft.i]]) <- names(pft.samples[[pft.i]])
+    }  #end pft
+    names(ensemble.samples) <- names(pft.samples)
+    ans <- ensemble.samples
+  }
+  return(ans)
+} # get.ensemble.samples
+
+
+##' Write ensemble config files
+##'
+##' Writes config files for use in meta-analysis and returns a list of run ids.
+##' Given a pft.xml object, a list of lists as supplied by get.sa.samples, 
+##' a name to distinguish the output files, and the directory to place the files.
+##'
+##' @param defaults pft
+##' @param ensemble.samples list of lists supplied by \link{get.ensemble.samples}
+##' @param settings list of PEcAn settings
+##' @param model name of model to be run, e.g. "ED2" or "SIPNET"
+##' @param clean remove old output first?
+##' @param write.to.db logical: Record this run in BETY?
+##' @param restart In case this is a continuation of an old simulation. restart needs to be a list with name tags of runid, inputs, new.params (parameters), new.state (initial condition), ensemble.id (ensemble id), start.time and stop.time.See Details.
+##'
+##' @return list, containing $runs = data frame of runids, $ensemble.id = the ensemble ID for these runs and $samples with ids and samples used for each tag.  Also writes sensitivity analysis configuration files as a side effect
+##' @details The restart functionality is developed using model specific functions by calling write_restart.modelname function. First, you need to make sure that this function is already exist for your desired model.See here \url{https://pecanproject.github.io/pecan-documentation/master/pecan-models.html}
+##' new state is a dataframe with a different column for each state variable. The number of the rows in this dataframe needs to be the same as the ensemble size.
+##' State variables that you can use for setting up the intial conditions differs for different models. You may check the documentation of the write_restart.modelname your model.
+##' The units for the state variables need to be in the PEcAn standard units which can be found in \link{standard_vars}.
+##' new.params also has similar structure to ensemble.samples which is sent as an argument.
+##'
+##' @importFrom dplyr %>%
+##' @export
+##' @author David LeBauer, Carl Davidson, Hamze Dokoohaki
+write.ensemble.configs <- function(defaults, ensemble.samples, settings, model, 
+                                   clean = FALSE, write.to.db = TRUE,restart=NULL) {
+  
+  my.write.config <- paste("write.config.", model, sep = "")
+  my.write_restart <- paste0("write_restart.", model)
+  
+  if (is.null(ensemble.samples)) {
+    return(list(runs = NULL, ensemble.id = NULL))
+  }
+  
+  # Open connection to database so we can store all run/ensemble information
+  if (write.to.db) {
+    con <- try(PEcAn.DB::db.open(settings$database$bety), silent = TRUE)
+    if (inherits(con, "try-error")) {
+      con <- NULL
+    } else {
+      on.exit(PEcAn.DB::db.close(con))
+    }
+  } else {
+    con <- NULL
+  }
+  
+  # Get the workflow id
+  if ("workflow" %in% names(settings)) {
+    workflow.id <- settings$workflow$id
+  } else {
+    workflow.id <- -1
+  }
+  #------------------------------------------------- if this is a new fresh run------------------  
+  if (is.null(restart)){
+    # create an ensemble id
+    if (!is.null(con)) {
+      # write ensemble first
+      ensemble.id <- PEcAn.DB::db.query(paste0(
+        "INSERT INTO ensembles (runtype, workflow_id) ",
+        "VALUES ('ensemble', ", format(workflow.id, scientific = FALSE), ")",
+        "RETURNING id"), con = con)[['id']]
+      
+      for (pft in defaults) {
+        PEcAn.DB::db.query(paste0(
+          "INSERT INTO posteriors_ensembles (posterior_id, ensemble_id) ",
+          "values (", pft$posteriorid, ", ", ensemble.id, ")"), con = con)
+      }
+    } else {
+      ensemble.id <- NA
+    }
+    #-------------------------generating met/param/soil/veg/... for all ensumbles----
+    if (!is.null(con)){
+      #-- lets first find out what tags are required for this model
+      required_tags <- dplyr::tbl(con, 'models') %>%
+        dplyr::filter(id == as.numeric(settings$model$id)) %>%
+        dplyr::inner_join(dplyr::tbl(con, "modeltypes_formats"), by = c('modeltype_id')) %>%
+        dplyr::collect() %>%
+        dplyr::filter(required == TRUE) %>%
+        dplyr::pull(tag)
+    }else{
+      required_tags<-c("met","parameters")
+    }
+
+    #now looking into the xml
+    samp <- settings$ensemble$samplingspace
+    #finding who has a parent
+    parents <- lapply(samp,'[[', 'parent')
+    #order parents based on the need of who has to be first
+    order <- names(samp)[lapply(parents, function(tr) which(names(samp) %in% tr)) %>% unlist()] 
+    #new ordered sampling space
+    samp.ordered <- samp[c(order, names(samp)[!(names(samp) %in% order)])]
+    #performing the sampling
+    samples<-list()
+    # For the tags specified in the xml I do the sampling
+    for(i in seq_along(samp.ordered)){
+      myparent<-samp.ordered[[i]]$parent # do I have a parent ?
+      #call the function responsible for generating the ensemble
+      samples[[names(samp.ordered[i])]] <- input.ens.gen(settings=settings,
+                                                         input=names(samp.ordered)[i],
+                                                         method=samp.ordered[[i]]$method,
+                                                         parent_ids=if( !is.null(myparent)) samples[[myparent]] # if I have parent then give me their ids - this is where the ordering matters making sure the parent is done before it's asked
+                                                         )
+    }
+
+    # if there is a tag required by the model but it is not specified in the xml then I replicate n times the first element 
+    required_tags%>%
+      purrr::walk(function(r_tag){
+        if (is.null(samples[[r_tag]]) & r_tag!="parameters") samples[[r_tag]]$samples <<- rep(settings$run$inputs[[tolower(r_tag)]]$path[1], settings$ensemble$size)
+      })
+    # if no ensemble piece was in the xml I replicate n times the first element in params
+    if ( is.null(samp$parameters) )            samples$parameters$samples <- ensemble.samples %>% purrr::map(~.x[rep(1, settings$ensemble$size) , ])
+    # This where we handle the parameters - ensemble.samples is already generated in run.write.config and it's sent to this function as arg - 
+    if ( is.null(samples$parameters$samples) ) samples$parameters$samples <- ensemble.samples
+    #------------------------End of generating ensembles-----------------------------------
+    # find all inputs that have an id
+    inputs <- names(settings$run$inputs)
+    inputs <- inputs[grepl(".id$", inputs)]
+
+    # write configuration for each run of the ensemble
+    runs <- data.frame()
+    for (i in seq_len(settings$ensemble$size)) {
+      if (!is.null(con)) {
+        paramlist <- paste("ensemble=", i, sep = "")
+        # inserting this into the table and getting an id back
+        run.id <- PEcAn.DB::db.query(paste0(
+          "INSERT INTO runs (model_id, site_id, start_time, finish_time, outdir, ensemble_id, parameter_list) ",
+          "values ('", 
+          settings$model$id, "', '", 
+          settings$run$site$id, "', '", 
+          settings$run$start.date, "', '", 
+          settings$run$end.date, "', '", 
+          settings$run$outdir, "', ", 
+          ensemble.id, ", '", 
+          paramlist, "') ",
+          "RETURNING id"), con = con)[['id']]
+        # associate inputs with runs
+        if (!is.null(inputs)) {
+          for (x in inputs) {
+            PEcAn.DB::db.query(paste0("INSERT INTO inputs_runs (input_id, run_id) ",
+                                      "values (", settings$run$inputs[[x]], ", ", run.id, ")"), 
+                               con = con)
+          }
+        }
+        
+      } else {
+        run.id <- PEcAn.utils::get.run.id("ENS", PEcAn.utils::left.pad.zeros(i, 5))
+      }
+      runs[i, "id"] <- run.id
+      
+      # create folders (cleaning up old ones if needed)
+      if (clean) {
+        unlink(file.path(settings$rundir, run.id))
+        unlink(file.path(settings$modeloutdir, run.id))
+      }
+      dir.create(file.path(settings$rundir, run.id), recursive = TRUE)
+      dir.create(file.path(settings$modeloutdir, run.id), recursive = TRUE)
+      # write run information to disk
+      cat("runtype     : ensemble\n",
+          "workflow id : ", workflow.id, "\n",
+          "ensemble id : ", ensemble.id, "\n",
+          "run         : ", i, "/", settings$ensemble$size, "\n",
+          "run id      : ", run.id, "\n",
+          "pft names   : ", as.character(lapply(settings$pfts, function(x) x[['name']])), "\n",
+          "model       : ", model, "\n",
+          "model id    : ", settings$model$id, "\n",
+          "site        : ", settings$run$site$name, "\n",
+          "site  id    : ", settings$run$site$id, "\n",
+          "met data    : ", samples$met$samples[[i]], "\n",
+          "start date  : ", settings$run$start.date, "\n",
+          "end date    : ", settings$run$end.date, "\n",
+          "hostname    : ", settings$host$name, "\n",
+          "rundir      : ", file.path(settings$host$rundir, run.id), "\n",
+          "outdir      : ", file.path(settings$host$outdir, run.id), "\n",
+          file = file.path(settings$rundir, run.id, "README.txt"))
+      
+      #changing the structure of input met to what the models are expecting
+      settings$run$inputs$met$path <- samples$met$samples[[i]]
+      
+      do.call(my.write.config, args = list( defaults = defaults, 
+                                            trait.values = lapply(samples$parameters$samples, function(x, n) { x[n, , drop=FALSE] }, n=i), # this is the params
+                                            settings = settings, 
+                                            run.id = run.id
+                                             )
+      )
+      cat(run.id, file = file.path(settings$rundir, "runs.txt"), sep = "\n", append = TRUE)
+     
+    }
+    return(invisible(list(runs = runs, ensemble.id = ensemble.id, samples=samples)))
+    #------------------------------------------------- if we already have everything ------------------        
+  }else{
+    #reading retstart inputs
+    inputs<-restart$inputs
+    run.id<-restart$runid
+    new.params<-restart$new.params
+    new.state<-restart$new.state
+    ensemble.id<-restart$ensemble.id
+    # stop and start time are required by bc we are wrtting them down into job.sh
+    for (i in seq_len(settings$ensemble$size)) {
+      do.call(my.write_restart, 
+              args =  list(outdir = settings$host$outdir, 
+                           runid = run.id[[i]], 
+                           start.time = restart$start.time,
+                           stop.time =restart$stop.time, 
+                           settings = settings,
+                           new.state = new.state[i, ], 
+                           new.params = new.params[[i]], 
+                           inputs =list(met=list(path=inputs$samples[[i]])), 
+                           RENAME = TRUE)
+      )
+    }
+    params<-new.params
+    return(invisible(list(runs = data.frame(id=run.id), ensemble.id = ensemble.id, samples=list(met=inputs)
+                          )
+                     ))
+  }
+  
+  
+  
+} # write.ensemble.configs
+
+
+
+#' Function for generating samples based on sampling method, parent or etc
+#'
+#' @param settings list of PEcAn settings
+#' @param method Method for sampling - For now looping or sampling with replacement is implemented
+#' @param parent_ids This is basically the order of the paths that the parent is sampled.See Details.
+#'
+#' @return For a given input/tag in the pecan xml and a method, this function returns a list with $id showing the order of sampling and $samples with samples of that input.
+#' @details If for example met was a parent and it's sampling method resulted in choosing the first, third and fourth samples, these are the ids that need to be sent as
+#' parent_ids to this function.
+#' @export
+#'
+#' @examples
+#' \dontrun{input.ens.gen(settings,"met","sampling")}
+#'  
+input.ens.gen<-function(settings,input,method="sampling",parent_ids=NULL){
+  
+  #-- reading the dots and exposing them to the inside of the function
+  samples<-list()
+  samples$ids<-c()
+  #
+  if (is.null(method)) return(NULL)
+  # parameter is exceptional it needs to be handled spearatly
+  if (input=="parameters") return(NULL)
+  #-- assing the sample ids based on different scenarios
+  if(!is.null(parent_ids)) {
+    samples$ids<-parent_ids$ids  
+    out.of.sample.size <- sample$ids[samples$ids > settings$run$inputs[[tolower(input)]]$path %>% length]
+    #sample for those that our outside the param size - forexample, parent id may send id number 200 but we have only100 sample for param
+    samples$ids[samples$ids%in%out.of.sample.size] <- samples(settings$run$inputs[[tolower(input)]]$path %>% seq_along(),
+                                                              out.of.sample.size,
+                                                              replace = T)
+  }else if( tolower(method)=="sampling") {
+    samples$ids <- sample(settings$run$inputs[[tolower(input)]]$path %>% seq_along(),
+                          settings$ensemble$size,
+                          replace = T)  
+  }else if( tolower(method)=="looping"){
+    samples$ids <- rep_len(settings$run$inputs[[tolower(input)]]$path %>% seq_along(), length.out=settings$ensemble$size)
+  }
+  #using the sample ids
+  samples$samples<-settings$run$inputs[[tolower(input)]]$path[samples$ids]
+  
+  
+  
+  return(samples)
+}
diff --git a/modules/uncertainty/R/flux_uncertainty.R b/modules/uncertainty/R/flux_uncertainty.R
index 627c89db168..353a545117c 100644
--- a/modules/uncertainty/R/flux_uncertainty.R
+++ b/modules/uncertainty/R/flux_uncertainty.R
@@ -53,7 +53,7 @@ get.change <- function(measurement) {
 ##' @param bin.num = number of bins (default = 10)
 ##' @param transform = transformation of magnitude (default = identity)
 ##' @param minBin = minimum number of points allowed in a bin
-##' @return List of parameters from the fitted uncertainty model
+##' @return return.list List of parameters from the fitted uncertainty model
 ##' @export
 ##' @author Mike Dietze, Carl Davidson
 flux.uncertainty <- function(measurement, QC = 0, flags = TRUE, bin.num = 10, 
@@ -115,19 +115,27 @@ flux.uncertainty <- function(measurement, QC = 0, flags = TRUE, bin.num = 10,
   ## would be better to fit a two line model with a common intercept, but this
   ## is quicker to implement for the time being
   E2 <- errBin - errBin[zero]
-  mp <- lm(E2[pos] ~ magBin[pos] - 1)
-  mn <- lm(E2[neg] ~ magBin[neg] - 1)
+  E2 <- errBin - errBin[zero]
   intercept <- errBin[zero]
-  slopeP <- mp$coefficients[1]
-  slopeN <- mn$coefficients[1]
   
-  return(list(mag = magBin, 
-              err = errBin, 
-              bias = biasBin, 
-              n = nBin, 
-              intercept = intercept, 
-              slopeP = slopeP,
-              slopeN = slopeN))
+  return.list <- list(mag = magBin, 
+                      err = errBin, 
+                      bias = biasBin, 
+                      n = nBin,
+                      intercept = intercept)
+  
+  if(!all(is.na(E2[pos]))){
+    mp <- lm(E2[pos] ~ magBin[pos] - 1)
+    return.list$slopeP <- mp$coefficients[1]
+  } 
+  if(!all(is.na(E2[neg]))){
+    mn <- lm(E2[neg] ~ magBin[neg] - 1)
+    return.list$slopeN <- mn$coefficients[1]
+  }else{
+    return.list$slopeN <- mp$coefficients[1]
+  }
+  
+  return(return.list)
 } # flux.uncertainty
 
 
diff --git a/base/utils/R/get.parameter.samples.R b/modules/uncertainty/R/get.parameter.samples.R
similarity index 67%
rename from base/utils/R/get.parameter.samples.R
rename to modules/uncertainty/R/get.parameter.samples.R
index 7011a9824fa..29f57a8ea36 100644
--- a/base/utils/R/get.parameter.samples.R
+++ b/modules/uncertainty/R/get.parameter.samples.R
@@ -6,7 +6,7 @@
 ##' @param pfts the pfts node of the list of pecan settings
 ##' @export
 ##'
-##' @author David LeBauer, Shawn Serbin
+##' @author David LeBauer, Shawn Serbin, Istem Fer
 ### Identify PFTs in the input settings.xml file
 get.parameter.samples <- function(settings, 
                                   posterior.files = rep(NA, length(settings$pfts)), 
@@ -16,6 +16,10 @@ get.parameter.samples <- function(settings,
   pft.names <- list()
   outdirs   <- list()
   
+  ## Open database connection
+  con <- PEcAn.DB::db.open(settings$database$bety)
+  on.exit(PEcAn.DB::db.close(con))
+  
   for (i.pft in seq_along(pfts)) {
     pft.names[i.pft] <- settings$pfts[[i.pft]]$name
     
@@ -36,7 +40,10 @@ get.parameter.samples <- function(settings,
   PEcAn.logger::logger.info("Selected PFT(s): ", pft.names)
   
   ## Generate empty list arrays for output.
-  trait.samples <- sa.samples <- ensemble.samples <- env.samples <- runs.samples <- list()
+  trait.samples <- sa.samples <- ensemble.samples <- env.samples <- runs.samples <- param.names <- list()
+  
+  # flag determining whether samples are independent (e.g. when params fitted individually)
+  independent <- TRUE
   
   ## Load PFT priors and posteriors
   for (i in seq_along(pft.names)) {
@@ -59,8 +66,28 @@ get.parameter.samples <- function(settings,
       }
     }
     
-    ### Load trait mcmc data (if exists)
-    if ("trait.mcmc.Rdata" %in% dir(unlist(outdirs[i]))) {
+    ### Load trait mcmc data (if exists, either from MA or PDA)
+    if (!is.null(settings$pfts[[i]]$posteriorid)) { # first check if there are any files associated with posterior ids
+      files <- PEcAn.DB::dbfile.check("Posterior",
+                                      settings$pfts[[i]]$posteriorid, 
+                                      con, settings$host$name, return.all = TRUE)
+      tid <- grep("trait.mcmc.*Rdata", files$file_name)
+      if (length(tid) > 0) {
+        trait.mcmc.file <- file.path(files$file_path[tid], files$file_name[tid])
+        ma.results <- TRUE
+        load(trait.mcmc.file)
+        
+        # PDA samples are fitted together, to preserve correlations downstream let workflow know they should go together
+        if(grepl("mcmc.pda", trait.mcmc.file)) independent <- FALSE 
+        # NOTE: Global MA samples will also be together, right?
+        
+        
+      }else{
+        PEcAn.logger::logger.info("No trait.mcmc file is associated with this posterior ID.")
+        ma.results <- FALSE
+      }
+    }else if ("trait.mcmc.Rdata" %in% dir(unlist(outdirs[i]))) {
+      PEcAn.logger::logger.info("Defaulting to trait.mcmc file in the pft directory.")
       ma.results <- TRUE
       load(file.path(outdirs[i], "trait.mcmc.Rdata"))
     } else {
@@ -74,21 +101,22 @@ get.parameter.samples <- function(settings,
     priors <- rownames(prior.distns)
     
     if (exists("trait.mcmc")) {
-      ma.traits <- names(trait.mcmc)
+      param.names[[i]] <- names(trait.mcmc)
+      names(param.names)[i] <- pft.name
       
       samples.num <- min(sapply(trait.mcmc, function(x) nrow(as.matrix(x))))
       
       ## report which traits use MA results, which use priors
-      if (length(ma.traits) > 0) {
+      if (length(param.names[[i]]) > 0) {
         PEcAn.logger::logger.info("PFT", pft.names[i], "has MCMC samples for:\n",
-                                  paste0(ma.traits, collapse = "\n "))
+                                  paste0(param.names[[i]], collapse = "\n "))
       }
-      if (!all(priors %in% ma.traits)) {
+      if (!all(priors %in% param.names[[i]])) {
         PEcAn.logger::logger.info("PFT", pft.names[i], "will use prior distributions for:\n", 
-                                  paste0(priors[!priors %in% ma.traits], collapse = "\n "))
+                                  paste0(priors[!priors %in% param.names[[i]]], collapse = "\n "))
       }
     } else {
-      ma.traits <- NULL
+      param.names[[i]] <- list()
       samples.num <- 20000
       PEcAn.logger::logger.info("No MCMC results for PFT", pft.names[i])
       PEcAn.logger::logger.info("PFT", pft.names[i], "will use prior distributions for", 
@@ -97,7 +125,7 @@ get.parameter.samples <- function(settings,
     
     PEcAn.logger::logger.info("using ", samples.num, "samples per trait")
     for (prior in priors) {
-      if (prior %in% ma.traits) {
+      if (prior %in% param.names[[i]]) {
         samples <- as.matrix(trait.mcmc[[prior]][, "beta.o"])
       } else {
         samples <- PEcAn.priors::get.sample(prior.distns[prior, ], samples.num)
@@ -106,6 +134,12 @@ get.parameter.samples <- function(settings,
     }
   }  ### End for loop
   
+  # if samples are independent, set param.names to NULL
+  # this is important for downstream, when param.names is not NULL MCMC will be sampled accordingly
+  if(independent){
+    param.names <- NULL
+  }
+  
   if ("sensitivity.analysis" %in% names(settings)) {
     
     ### Get info on the quantiles to be run in the sensitivity analysis (if requested)
@@ -125,11 +159,13 @@ get.parameter.samples <- function(settings,
       ## run at median if only one run in ensemble
       ensemble.samples <- get.sa.sample.list(pft = trait.samples, env = env.samples, 
                                              quantiles = 0.5)
+      #if it's not there it's one probably
+      if (is.null(settings$ensemble$size)) settings$ensemble$size<-1
     } else if (settings$ensemble$size > 1) {
       
       ## subset the trait.samples to ensemble size using Halton sequence
       ensemble.samples <- get.ensemble.samples(settings$ensemble$size, trait.samples, 
-                                               env.samples, ens.sample.method)
+                                               env.samples, ens.sample.method, param.names)
     }
   }
   
diff --git a/modules/uncertainty/R/prep.data.assim.R b/modules/uncertainty/R/prep.data.assim.R
new file mode 100644
index 00000000000..d1b360019c9
--- /dev/null
+++ b/modules/uncertainty/R/prep.data.assim.R
@@ -0,0 +1,81 @@
+##'@title prep.data.assim
+##'@section purpose:
+##'This function sets up a call to PEcAn.assim.sequential::sda.enkf()
+##'
+##'@param settings the PEcAn settings object (a collection of nested lists)
+##'@param numvals number of simulated data points for each time point
+##'@return None
+##'@export
+##'@author Luke Dramko
+prep.data.assim <- function(settings, numvals) {
+  # Obtain real data from the site
+  timestep <- 0.5 # Every half hour = 0.5
+  
+  field_data <- PEcAn.data.atmosphere::download.US_WCr(settings$run$start.date, settings$run$end.date, timestep = timestep)
+  
+  uncertainty_vals <- list()
+  
+  # Creates a proxy row for rbinding
+  sums <- NULL
+  
+  # One vector holds the mean for each variable.
+  obs.mean <- NULL
+  
+  for (i in 1:length(field_data)) {
+    AMF.params <- PEcAn.uncertainty::flux.uncertainty(field_data[[i]], QC = rep(0, length(field_data[[i]])))
+    
+    # Create proxy row for rbinding
+    random_mat = NULL
+    new_col = rep(0, length(field_data[[i]]))
+    
+    # Create a new column
+    # i: the particular variable being worked with
+    # j: the column number
+    # k: the row number
+    for (j in 1:numvals) { # number of random numbers
+      obs <- field_data[[i]][!is.na(field_data[[i]])]
+      pos <- obs >= 0
+      
+      res <- obs
+      res[pos]  <- rexp(length(obs[pos]),
+                        1 / (AMF.params$intercept[[1]] + (AMF.params$slopeP[[1]] * obs[pos])))
+      res[!pos]  <- rexp(length(obs[!pos]),
+                         1 / (AMF.params$intercept[[1]] + (AMF.params$slopeN[[1]] * obs[!pos])))
+      
+      random_multiplier <- sample(c(-1,1), length(res), replace = TRUE)
+      simulated <- obs+(random_multiplier*res)
+      
+      sim_idx = 1; # Because NA's are excluded, real time points don't match up exactly.
+      for (k in 1:length(field_data[[i]])) { # k for each real time point
+        if (!is.na(field_data[[i]][k])) {
+          new_col[k] <- simulated[sim_idx]
+          sim_idx = sim_idx + 1
+        }
+      } # end k
+      
+      random_mat = cbind(random_mat, new_col)
+    } # end j
+    
+    obs.mean <- c(obs.mean, mean(field_data[[i]], na.rm = TRUE))
+    
+    applied <- apply(random_mat, 1, mean, na.rm=TRUE)
+    sums = cbind(sums, applied)
+  } # end i
+  
+  # Remove NA's
+  sums = sums[complete.cases(sums), ]
+  
+  obs.cov <- list(cov(sums))
+  names(obs.cov) <- settings$run$end_date
+  
+  names(obs.mean) <- names(field_data)
+  obs.mean <- list(obs.mean)
+  names(obs.mean) <- settings$run$end_date
+  
+  PEcAn.logger::logger.info("Calcualted obs.mean")
+  print(obs.mean)
+  PEcAn.logger::logger.info("Calcualted obs.cov")
+  print(obs.cov)
+  
+  PEcAn.assim.sequential::sda.enkf(settings, obs.cov = obs.cov, obs.mean = obs.mean)
+} # prep.data.assim
diff --git a/modules/uncertainty/R/run.ensemble.analysis.R b/modules/uncertainty/R/run.ensemble.analysis.R
index 9ff736de9ce..2e42d9ec2bf 100644
--- a/modules/uncertainty/R/run.ensemble.analysis.R
+++ b/modules/uncertainty/R/run.ensemble.analysis.R
@@ -206,7 +206,7 @@ read.ensemble.ts <- function(settings, ensemble.id = NULL, variable = NULL,
                        variable, ")"))
   }
   
-  variables <- convert.expr(variable)
+  variables <- PEcAn.utils::convert.expr(variable)
   variable.ens <- variables$variable.eqn
   variable.fn <- variables$variable.drv
 
@@ -218,12 +218,12 @@ read.ensemble.ts <- function(settings, ensemble.id = NULL, variable = NULL,
   ### compatibility still contains the sample info for (the most recent) sensitivity
   ### and ensemble analysis combined.
   if (!is.null(ensemble.id)) {
-    fname <- ensemble.filename(settings, "ensemble.samples", "Rdata", 
+    fname <- PEcAn.utils::ensemble.filename(settings, "ensemble.samples", "Rdata",
                                ensemble.id = ensemble.id, 
                                all.var.yr = TRUE)
   } else if (!is.null(settings$ensemble$ensemble.id)) {
     ensemble.id <- settings$ensemble$ensemble.id
-    fname <- ensemble.filename(settings, "ensemble.samples", "Rdata",
+    fname <- PEcAn.utils::ensemble.filename(settings, "ensemble.samples", "Rdata",
                                ensemble.id = ensemble.id, 
                                all.var.yr = TRUE)
   } else {
@@ -252,7 +252,12 @@ read.ensemble.ts <- function(settings, ensemble.id = NULL, variable = NULL,
     print(run.id)
     
     for(var in seq_along(variables)){
-      out.tmp <- read.output(run.id, file.path(settings$outdir, "out", run.id), start.year, end.year, variables[var])
+      out.tmp <- PEcAn.utils::read.output(
+        run.id,
+        file.path(settings$outdir, "out", run.id),
+        start.year,
+        end.year,
+        variables[var])
       assign(variables[var], out.tmp[[variables[var]]])
     }
     
@@ -278,7 +283,7 @@ read.ensemble.ts <- function(settings, ensemble.id = NULL, variable = NULL,
 
   names(ensemble.ts) <- variable.fn
   # BMR 10/16/13 Save this variable now to operate later on
-  fname <- ensemble.filename(settings, "ensemble.ts", "Rdata", 
+  fname <- PEcAn.utils::ensemble.filename(settings, "ensemble.ts", "Rdata",
                              all.var.yr = FALSE, 
                              ensemble.id = ensemble.id, 
                              variable = variable, 
diff --git a/modules/uncertainty/inst/abbreviated_workflow_SIPNET.R b/modules/uncertainty/inst/abbreviated_workflow_SIPNET.R
new file mode 100755
index 00000000000..1aadd6bb67b
--- /dev/null
+++ b/modules/uncertainty/inst/abbreviated_workflow_SIPNET.R
@@ -0,0 +1,27 @@
+
+#AbbreviatedWorkflow_Sipnet
+#Variables :
+library(PEcAn.all)
+library(PEcAn.utils)
+library(RCurl)
+variable_S <- c("GPP ", "NPP", "TotalResp","AutoResp", "HeteroResp", "SoilResp", "NEE", "QLE", "leaf_carbon_content", "GWBI", "TotSoilCarb", "course_root_carbon_content", "fine_root_carbon_content", "litter_carbon_content", "Transp", "TotLivBiom", "LAI", "AGB", "SoilMoist", "SoilMoistFracSWE", "AbvGrndWood")
+
+settings <- PEcAn.settings::read.settings("pecan.CHECKED.xml")
+
+for (i in 1:seq_along(variable_S)) {
+ 
+  settings$sensitivity.analysis$variable_S <- variable_S
+  print(settings$sensitivity.analysis$variable)
+  
+  # Get results of model runs
+  
+    runModule.get.results(settings)
+    
+  # Run sensitivity analysis and variance decomposition on model output
+
+    runModule.run.sensitivity.analysis(settings)
+
+
+  
+}
+
diff --git a/modules/uncertainty/man/flux.uncertainty.Rd b/modules/uncertainty/man/flux.uncertainty.Rd
index 95452ea4f7e..4fcb037c1fc 100644
--- a/modules/uncertainty/man/flux.uncertainty.Rd
+++ b/modules/uncertainty/man/flux.uncertainty.Rd
@@ -22,7 +22,7 @@ time series, TRUE = use).}
 \item{minBin}{= minimum number of points allowed in a bin}
 }
 \value{
-List of parameters from the fitted uncertainty model
+return.list List of parameters from the fitted uncertainty model
 }
 \description{
 Calculate parameters for heteroskedastic flux uncertainty
diff --git a/modules/uncertainty/man/get.ensemble.samples.Rd b/modules/uncertainty/man/get.ensemble.samples.Rd
new file mode 100644
index 00000000000..6e00ecc5276
--- /dev/null
+++ b/modules/uncertainty/man/get.ensemble.samples.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ensemble.R
+\name{get.ensemble.samples}
+\alias{get.ensemble.samples}
+\title{Get Ensemble Samples}
+\usage{
+get.ensemble.samples(ensemble.size, pft.samples, env.samples,
+  method = "uniform", param.names = NULL, ...)
+}
+\arguments{
+\item{ensemble.size}{number of runs in model ensemble}
+
+\item{pft.samples}{random samples from parameter distribution, e.g. from a MCMC chain}
+
+\item{env.samples}{env samples}
+
+\item{method}{the method used to generate the ensemble samples. Random generators: uniform, uniform with latin hypercube permutation. Quasi-random generators: halton, sobol, torus. Random generation draws random variates whereas quasi-random generation is deterministic but well equidistributed. Default is uniform. For small ensemble size with relatively large parameter number (e.g ensemble size < 5 and # of traits > 5) use methods other than halton.}
+
+\item{param.names}{a list of parameter names that were fitted either by MA or PDA, important argument, if NULL parameters will be resampled independently}
+
+\item{...}{Other arguments passed on to the sampling method}
+}
+\value{
+matrix of (quasi-)random samples from trait distributions
+}
+\description{
+Get parameter values used in ensemble
+}
+\details{
+Returns a matrix of randomly or quasi-randomly sampled trait values 
+to be assigned to traits over several model runs.
+given the number of model runs and a list of sample distributions for traits
+The model run is indexed first by model run, then by trait
+}
+\author{
+David LeBauer, Istem Fer
+}
diff --git a/base/utils/man/get.parameter.samples.Rd b/modules/uncertainty/man/get.parameter.samples.Rd
similarity index 92%
rename from base/utils/man/get.parameter.samples.Rd
rename to modules/uncertainty/man/get.parameter.samples.Rd
index 9a81551e9a1..d2e069327b6 100644
--- a/base/utils/man/get.parameter.samples.Rd
+++ b/modules/uncertainty/man/get.parameter.samples.Rd
@@ -14,5 +14,5 @@ get.parameter.samples(settings, posterior.files = rep(NA,
 Convert priors / MCMC samples to chains that can be sampled for model parameters
 }
 \author{
-David LeBauer, Shawn Serbin
+David LeBauer, Shawn Serbin, Istem Fer
 }
diff --git a/modules/uncertainty/man/input.ens.gen.Rd b/modules/uncertainty/man/input.ens.gen.Rd
new file mode 100644
index 00000000000..9cd4c71a21c
--- /dev/null
+++ b/modules/uncertainty/man/input.ens.gen.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ensemble.R
+\name{input.ens.gen}
+\alias{input.ens.gen}
+\title{Function for generating samples based on sampling method, parent or etc}
+\usage{
+input.ens.gen(settings, input, method = "sampling", parent_ids = NULL)
+}
+\arguments{
+\item{settings}{list of PEcAn settings}
+
+\item{method}{Method for sampling - For now looping or sampling with replacement is implemented}
+
+\item{parent_ids}{This is basically the order of the paths that the parent is sampled.See Details.}
+}
+\value{
+For a given input/tag in the pecan xml and a method, this function returns a list with $id showing the order of sampling and $samples with samples of that input.
+}
+\description{
+Function for generating samples based on sampling method, parent or etc
+}
+\details{
+If for example met was a parent and it's sampling method resulted in choosing the first, third and fourth samples, these are the ids that need to be sent as
+parent_ids to this function.
+}
+\examples{
+\dontrun{input.ens.gen(settings,"met","sampling")}
+ 
+}
diff --git a/modules/uncertainty/man/plot_variance_decomposition.Rd b/modules/uncertainty/man/plot_variance_decomposition.Rd
index bd19095559d..e8a12b9b493 100644
--- a/modules/uncertainty/man/plot_variance_decomposition.Rd
+++ b/modules/uncertainty/man/plot_variance_decomposition.Rd
@@ -4,8 +4,8 @@
 \alias{plot_variance_decomposition}
 \title{Variance Decomposition Plots}
 \usage{
-plot_variance_decomposition(plot.inputs, fontsize = list(title = 18, axis =
-  14))
+plot_variance_decomposition(plot.inputs, fontsize = list(title = 18, axis
+  = 14))
 }
 \arguments{
 \item{fontsize}{list specifying the font size of the titles and axes of the graph}
diff --git a/modules/uncertainty/man/prep.data.assim.Rd b/modules/uncertainty/man/prep.data.assim.Rd
new file mode 100644
index 00000000000..53c8b0ed296
--- /dev/null
+++ b/modules/uncertainty/man/prep.data.assim.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prep.data.assim.R
+\name{prep.data.assim}
+\alias{prep.data.assim}
+\title{prep.data.assim}
+\usage{
+prep.data.assim(settings, numvals)
+}
+\arguments{
+\item{settings}{the PEcAn settings object (a collection of nested lists)}
+
+\item{numvals}{number of simulated data points for each time point}
+}
+\value{
+None
+}
+\description{
+prep.data.assim
+}
+\section{purpose}{
+
+This function sets up a call to PEcAn.assim.sequential::sda.enkf()
+}
+
+\author{
+Luke Dramko
+}
diff --git a/modules/uncertainty/man/read.ensemble.output.Rd b/modules/uncertainty/man/read.ensemble.output.Rd
new file mode 100644
index 00000000000..91745f27c51
--- /dev/null
+++ b/modules/uncertainty/man/read.ensemble.output.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ensemble.R
+\name{read.ensemble.output}
+\alias{read.ensemble.output}
+\title{Read ensemble output}
+\usage{
+read.ensemble.output(ensemble.size, pecandir, outdir, start.year, end.year,
+  variable, ens.run.ids = NULL)
+}
+\arguments{
+\item{ensemble.size}{the number of ensemble members run}
+
+\item{pecandir}{specifies where pecan writes its configuration files}
+
+\item{outdir}{directory with model output to use in ensemble analysis}
+
+\item{start.year}{first year to include in ensemble analysis}
+
+\item{end.year}{last year to include in ensemble analysis}
+
+\item{variable}{target variables for ensemble analysis}
+
+\item{ens.run.ids}{dataframe. Must contain a column named "id" giving the run IDs to be read.
+If NULL, will attempt to read IDs from a file named "samples.Rdata" in \code{pecandir}}
+}
+\value{
+a list of ensemble model output
+}
+\description{
+Reads output from model ensemble
+}
+\details{
+Reads output for an ensemble of length specified by \code{ensemble.size} and bounded by \code{start.year} 
+and \code{end.year}
+}
+\author{
+Ryan Kelly, David LeBauer, Rob Kooper
+}
diff --git a/modules/uncertainty/man/run.ensemble.analysis.Rd b/modules/uncertainty/man/run.ensemble.analysis.Rd
index c216dde3d82..8e840dbea0d 100644
--- a/modules/uncertainty/man/run.ensemble.analysis.Rd
+++ b/modules/uncertainty/man/run.ensemble.analysis.Rd
@@ -4,8 +4,9 @@
 \alias{run.ensemble.analysis}
 \title{run ensemble.analysis}
 \usage{
-run.ensemble.analysis(settings, plot.timeseries = NA, ensemble.id = NULL,
-  variable = NULL, start.year = NULL, end.year = NULL, ...)
+run.ensemble.analysis(settings, plot.timeseries = NA,
+  ensemble.id = NULL, variable = NULL, start.year = NULL,
+  end.year = NULL, ...)
 }
 \arguments{
 \item{plot.timeseries}{if TRUE plots a modeled timeseries of target variable(s) with CIs}
diff --git a/modules/uncertainty/man/write.ensemble.configs.Rd b/modules/uncertainty/man/write.ensemble.configs.Rd
new file mode 100644
index 00000000000..05ffa4e39c6
--- /dev/null
+++ b/modules/uncertainty/man/write.ensemble.configs.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ensemble.R
+\name{write.ensemble.configs}
+\alias{write.ensemble.configs}
+\title{Write ensemble config files}
+\usage{
+write.ensemble.configs(defaults, ensemble.samples, settings, model,
+  clean = FALSE, write.to.db = TRUE, restart = NULL)
+}
+\arguments{
+\item{defaults}{pft}
+
+\item{ensemble.samples}{list of lists supplied by \link{get.ensemble.samples}}
+
+\item{settings}{list of PEcAn settings}
+
+\item{model}{name of model to be run, e.g. "ED2" or "SIPNET"}
+
+\item{clean}{remove old output first?}
+
+\item{write.to.db}{logical: Record this run in BETY?}
+
+\item{restart}{In case this is a continuation of an old simulation. restart needs to be a list with name tags of runid, inputs, new.params (parameters), new.state (initial condition), ensemble.id (ensemble id), start.time and stop.time.See Details.}
+}
+\value{
+list, containing $runs = data frame of runids, $ensemble.id = the ensemble ID for these runs and $samples with ids and samples used for each tag.  Also writes sensitivity analysis configuration files as a side effect
+}
+\description{
+Writes config files for use in meta-analysis and returns a list of run ids.
+Given a pft.xml object, a list of lists as supplied by get.sa.samples, 
+a name to distinguish the output files, and the directory to place the files.
+}
+\details{
+The restart functionality is developed using model specific functions by calling write_restart.modelname function. First, you need to make sure that this function is already exist for your desired model.See here \url{https://pecanproject.github.io/pecan-documentation/master/pecan-models.html}
+new state is a dataframe with a different column for each state variable. The number of the rows in this dataframe needs to be the same as the ensemble size.
+State variables that you can use for setting up the intial conditions differs for different models. You may check the documentation of the write_restart.modelname your model.
+The units for the state variables need to be in the PEcAn standard units which can be found in \link{standard_vars}.
+new.params also has similar structure to ensemble.samples which is sent as an argument.
+}
+\author{
+David LeBauer, Carl Davidson, Hamze Dokoohaki
+}
diff --git a/release.sh b/release.sh
new file mode 100755
index 00000000000..52cd59f66b2
--- /dev/null
+++ b/release.sh
@@ -0,0 +1,53 @@
+#!/bin/bash
+
+set -e
+
+DEBUG=${DEBUG:-""}
+SERVER=${SERVER:-""}
+DEPEND=${DEPEND:-""}
+
+# get version number
+VERSION=${VERSION:-"$(awk '/Version:/ { print $2 }' base/all/DESCRIPTION)"}
+
+# build images first
+VERSION=${VERSION} DEBUG=${DEBUG} DEPEND=${DEPEND} ./docker.sh
+
+# check branch and set version
+if [ "${PECAN_GIT_BRANCH}" = "master" ]; then
+    TAGS="${VERSION} latest"
+elif [ "${PECAN_GIT_BRANCH}" = "develop" ]; then
+    TAGS="develop"
+fi
+if [ "${TAGS}" == "" ]; then
+    echo "No tags specified, not pushing to server."
+    exit 1
+fi
+
+# push pecan images
+for i in depends base executor web data; do
+    for v in ${TAGS}; do
+        if [ "$v" != "latest" -o "$SERVER" != "" ]; then
+            ${DEBUG} docker tag pecan/${i}:latest ${SERVER}pecan/${i}:${v}
+        fi
+        ${DEBUG} docker push ${SERVER}pecan/${i}:${v}
+    done
+done
+
+# push model images
+for i in ls; do
+    for v in ${TAGS}; do
+        if [ "$v" != "latest" -o "$SERVER" != "" ]; then
+            ${DEBUG} docker tag pecan/${i}:latest ${SERVER}pecan/${i}:${v}
+        fi
+        ${DEBUG} docker push ${SERVER}pecan/${i}:${v}
+    done
+done
+
+for i in model-sipnet-136 model-ed2-git; do
+    for v in ${TAGS}; do
+        if [ "$v" != "latest" -o "$SERVER" != "" ]; then
+            ${DEBUG} docker tag pecan/${i}:latest ${SERVER}pecan/${i}:${v}
+        fi
+        ${DEBUG} docker push ${SERVER}pecan/${i}:${v}
+    done
+done
diff --git a/scripts/install.dependencies.R b/scripts/install.dependencies.R
index 0232d50cb03..e65fa72fd6c 100755
--- a/scripts/install.dependencies.R
+++ b/scripts/install.dependencies.R
@@ -38,11 +38,6 @@ if (length(new.packages)) {
   warning("If Maeswrap Package download fails, please refer to PEcAn documentation for download instructions")
 }
 
-# install packages from forge
-if (!("REddyProc" %in% installed.packages()[, "Package"])) {
-  install.packages("REddyProc", repos = "http://R-Forge.R-project.org", type = "source")
-}
-
 # install packages from github
 if (!("BioCro" %in% installed.packages()[, "Package"])) {
   devtools::install_github("ebimodeling/biocro")
diff --git a/scripts/install_pecan.sh b/scripts/install_pecan.sh
index 0a943788c3d..50b9e7f12ab 100644
--- a/scripts/install_pecan.sh
+++ b/scripts/install_pecan.sh
@@ -18,8 +18,10 @@ SETUP_VM=""
 SETUP_PALEON=""
 REBUILD=""
 
-RSTUDIO_SERVER="1.1.442"
-SHINY_SERVER="1.5.6.875"
+PECAN_BRANCH=""
+
+RSTUDIO_SERVER="1.1.456"
+SHINY_SERVER="1.5.7.907"
 
 if [ -e $(dirname $0)/install_pecan.config ]; then
   . $(dirname $0)/install_pecan.config
@@ -84,14 +86,14 @@ case "$OS_VERSION" in
     setsebool -P httpd_can_network_connect 1
     ;;
   Ubuntu)
-    if [ ! -e /etc/apt/sources.list.d/R.list ]; then
-      sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -s -c`/" > /etc/apt/sources.list.d/R.list'
-      sudo apt-key adv --keyserver keyserver.ubuntu.com --recv E084DAB9
-    fi
-    if [ ! -e /etc/apt/sources.list.d/ruby.list ]; then
-      sudo sh -c 'echo "deb http://ppa.launchpad.net/brightbox/ruby-ng/ubuntu trusty main" > /etc/apt/sources.list.d/ruby.list'
-      sudo apt-key adv --keyserver keyserver.ubuntu.com --recv C3173AA6
-    fi
+    # if [ ! -e /etc/apt/sources.list.d/R.list ]; then
+    #   sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -s -c`/" > /etc/apt/sources.list.d/R.list'
+    #   sudo apt-key adv --keyserver keyserver.ubuntu.com --recv E084DAB9
+    # fi
+    #if [ ! -e /etc/apt/sources.list.d/ruby.list ]; then
+    #  sudo sh -c 'echo "deb http://ppa.launchpad.net/brightbox/ruby-ng/ubuntu trusty main" > /etc/apt/sources.list.d/ruby.list'
+    #  sudo apt-key adv --keyserver keyserver.ubuntu.com --recv C3173AA6
+    #fi
     if [ ! -e /etc/apt/sources.list.d/pgdg.list ]; then
       sudo sh -c 'echo "deb http://apt.postgresql.org/pub/repos/apt `lsb_release -s -c`-pgdg main" > /etc/apt/sources.list.d/pgdg.list'
       wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
@@ -123,15 +125,15 @@ case "$OS_VERSION" in
     sudo yum install -y httpd php php-pgsql php-xml expect expectk
     ;;
   Ubuntu)
-    sudo apt-get -y install build-essential gfortran git r-base-core jags liblapack-dev libnetcdf-dev netcdf-bin bc libcurl4-gnutls-dev curl udunits-bin libudunits2-dev libgmp-dev python-dev libgdal1-dev libproj-dev expect
+    sudo apt-get -y install build-essential gfortran git r-base-core jags liblapack-dev libnetcdf-dev netcdf-bin bc libcurl4-gnutls-dev curl udunits-bin libudunits2-dev libgmp-dev python-dev libgdal-dev libproj-dev expect librdf0-dev
     sudo apt-get -y install openmpi-bin libopenmpi-dev
     sudo apt-get -y install libgsl0-dev libssl-dev
     # for maeswrap
     sudo apt-get -y install r-cran-rgl
     # for R doc
     sudo apt-get -y install texinfo texlive-latex-base texlive-latex-extra texlive-fonts-recommended
-    # ruby
-    sudo apt-get -y install ruby2.1 ruby2.1-dev
+    # BETY
+    sudo apt-get -y install ruby ruby-dev nodejs
     # for LPJ-GUESS
     sudo apt-get -y install cmake
     # for PostgreSQL
@@ -226,12 +228,9 @@ echo "ED"
 echo "######################################################################"
 if [ ! -e ${HOME}/ED2 ]; then
   cd
-  git clone https://github.com/rykelly/ED2.git
-  cd ED2
-  git checkout modularize
-  sed -i 's/-a ${USE_GIT}/-a ${USE_GIT} == "true"/' ${HOME}/ED2/ED/build/install.sh
+  git clone https://github.com/EDmodel/ED2.git
   cd ${HOME}/ED2/ED/build
-  curl -o make/include.mk.opt.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s`
+  curl -o make/include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s`
   if [ "$OS_VERSION" == "RH_6" ]; then
     sed -i 's/ -fno-whole-file//' make/include.mk.opt.VM
   fi
@@ -355,6 +354,9 @@ if [ ! -e ${HOME}/pecan ]; then
 fi
 cd ${HOME}/pecan
 git pull
+if [ "${PECAN_BRANCH}" != "" ]; then
+  git checkout ${PECAN_BRANCH}
+fi
 make
 
 sudo curl -o /var/www/html/pecan.pdf https://www.gitbook.com/download/pdf/book/pecan/pecan-documentation
@@ -391,7 +393,7 @@ if [ ! -e ${HOME}/bety ]; then
 fi
 cd ${HOME}/bety
 git pull
-sudo gem2.1 install bundler
+sudo gem install bundler
 bundle install --without development:test:javascript_testing:debug --path vendor/bundle
 
 if [ ! -e paperclip/files ]; then
@@ -409,7 +411,7 @@ if [ ! -e log ]; then
   chmod 0666 log/production.log
 fi
 
-chmod go+w public/javascripts/cache/
+# chmod go+w public/javascripts/cache/
 
 if [ ! -e config/database.yml ]; then
   cat > config/database.yml << EOF
@@ -428,7 +430,8 @@ if [ ! -e ${HTTP_CONF}/bety.conf ]; then
   cat > /tmp/bety.conf << EOF
 RailsEnv production
 RailsBaseURI /bety
-PassengerRuby /usr/bin/ruby2.1
+PassengerRuby /usr/bin/ruby
+SetEnv SECRET_KEY_BASE $(bundle exec rake secret)
 <Directory /var/www/html/bety>
   Options +FollowSymLinks
   Require all granted
@@ -438,10 +441,12 @@ EOF
   rm /tmp/bety.conf
   sudo ln -s $HOME/bety/public /var/www/html/bety
 
-  sudo sh -c "echo '\n## BETY secret key\nexport SECRET_KEY_BASE=$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 120 | head -n 1)' >> /etc/apache2/envvars"
-  cp $HOME/bety/public/javascripts/cache/all.js-sample $HOME/bety/public/javascripts/cache/all.js
+  # sudo sh -c "echo '\n## BETY secret key\nexport SECRET_KEY_BASE=$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 120 | head -n 1)' >> /etc/apache2/envvars"
+  # cp $HOME/bety/public/javascripts/cache/all.js-sample $HOME/bety/public/javascripts/cache/all.js
 fi
 
+bundle exec rake assets:precompile RAILS_ENV=production RAILS_RELATIVE_URL_ROOT=/bety
+
 echo "######################################################################"
 echo "DATA"
 echo "######################################################################"
@@ -521,7 +526,7 @@ fi
 sudo rm -rf ${HOME}/output
 mkdir ${HOME}/output
 chmod 2777 ${HOME}/output
-sudo -u postgres ${HOME}/pecan/scripts/load.bety.sh -g -m 99 -r 0 -c -u -w https://ebi-forecast.igb.illinois.edu/pecan/dumpall/bety.tar.gz
+sudo -u postgres ${HOME}/pecan/scripts/load.bety.sh -g -m 99 -r 0 -c -u -w https://ebi-forecast.igb.illinois.edu/pecan/dump/all//bety.tar.gz
 ${HOME}/pecan/scripts/add.models.sh
 ${HOME}/pecan/scripts/add.data.sh
 
@@ -567,6 +572,11 @@ echo "######################################################################"
 if [ "${SHINY_SERVER}" != "" -a $( uname -m ) == "x86_64" ]; then
   sudo su - -c "R -e \"install.packages(c('rmarkdown', 'shiny'), repos='https://cran.rstudio.com/')\""
 
+  R -e "install.packages(c('https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.26.0.tar.gz', 'http://www.bioconductor.org/packages/release/bioc/src/contrib/graph_1.58.0.tar.gz'), repos=NULL)"
+  R -e "devtools::install_github('duncantl/CodeDepends')"
+  R -e "devtools::install_github('OakleyJ/SHELF')"
+  R -e "install.packages(c('shinythemes', 'shinytoastr', 'SHELF', 'shiny'), repos='https://cran.rstudio.com/')"
+
   case "$OS_VERSION" in
     RH_*)
       curl -s -o shiny.rpm https://download3.rstudio.org/centos5.9/x86_64/shiny-server-${SHINY_SERVER}-rh5-x86_64.rpm
@@ -575,12 +585,9 @@ if [ "${SHINY_SERVER}" != "" -a $( uname -m ) == "x86_64" ]; then
       ;;
     Ubuntu)
       sudo apt-get -y install gdebi-core
-      curl -s -o shiny.deb https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-${SHINY_SERVER}-amd64.deb
-      if [ $( uname -m ) == "x86_64" ]; then
-        curl -s -o shiny.deb https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-${SHINY_SERVER}-amd64.deb
-        sudo gdebi -q -n shiny.deb
-        rm shiny.deb
-      fi
+      curl -s -o shiny.deb https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-${SHINY_SERVER}-amd64.deb
+      sudo gdebi -q -n shiny.deb
+      rm shiny.deb
       ;;
   esac
 
diff --git a/scripts/load.bety.sh b/scripts/load.bety.sh
index 7aa1daea3d9..1cd10c1055f 100755
--- a/scripts/load.bety.sh
+++ b/scripts/load.bety.sh
@@ -244,7 +244,7 @@ fi
 ID_RANGE=1000000000
 
 # before anything is done, check to make sure database exists
-if ! psql ${PG_OPT} ${PG_USER} -lqt | cut -d \| -f 1 | grep -w "${DATABASE}" > /dev/null ; then
+if ! psql ${PG_OPT} ${PG_USER} -lqt | cut -d \| -f 1 | grep -w "^ *${DATABASE} *$" > /dev/null ; then
   echo "Database ${DATABASE} does not exist, please create it:"
   echo "(see https://pecan.gitbooks.io/betydb-documentation/content/installing_betydb.html)"
   echo "  psql ${PG_OPT} ${PG_USER} -c \"CREATE ROLE ${OWNER} WITH LOGIN CREATEDB NOSUPERUSER NOCREATEROLE PASSWORD 'password'\""
@@ -393,9 +393,9 @@ for T in ${EMPTY_TABLES} ${CLEAN_TABLES} ${CHECK_TABLES} ${MANY_TABLES}; do
     if [ "${QUIET}" != "YES" ]; then
       if [ "$DEL" != "0" -o "$ADD" != "0" ]; then
         if [ "$DIFF" != "0" ]; then
-          printf "Updated  %-25s : %6d (%+d)\n" "${T}" ${ADD} ${DIFF}
+          printf "Updated  %-25s : %11d (%+d)\n" "${T}" ${ADD} ${DIFF}
         else
-          printf "Updated  %-25s : %6d\n" "${T}" ${ADD}
+          printf "Updated  %-25s : %11d\n" "${T}" ${ADD}
         fi
       fi
     fi
diff --git a/scripts/syncgit.sh b/scripts/syncgit.sh
new file mode 100755
index 00000000000..ec9ca59611a
--- /dev/null
+++ b/scripts/syncgit.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+# save old state
+BRANCH=$(git branch | awk '/^\*/ { print $2}')
+git stash -u
+
+# update all remotes
+git fetch --all
+
+# update master
+git checkout master
+git merge upstream/master
+git push
+
+# update develop
+git checkout develop
+git merge upstream/develop
+git push
+
+# restore
+git checkout ${BRANCH}
+git stash pop
diff --git a/scripts/workflow.wcr.assim.R b/scripts/workflow.wcr.assim.R
new file mode 100644
index 00000000000..2ec0ea7d996
--- /dev/null
+++ b/scripts/workflow.wcr.assim.R
@@ -0,0 +1,160 @@
+#!/usr/bin/env Rscript
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+# ----------------------------------------------------------------------
+# Load required libraries
+# ----------------------------------------------------------------------
+library(PEcAn.all)
+library(PEcAn.utils)
+library(RCurl)
+# make sure always to call status.end
+options(warn=1)
+options(error=quote({
+  PEcAn.utils::status.end("ERROR")
+  PEcAn.remote::kill.tunnel(settings)
+  if (!interactive()) {
+    q()
+  }
+}))
+#options(warning.expression=status.end("ERROR"))
+# ----------------------------------------------------------------------
+# PEcAn Workflow
+# ----------------------------------------------------------------------
+# Open and read in settings file for PEcAn run.
+args <- commandArgs(trailingOnly = TRUE)
+if (is.na(args[1])){
+  settings <- PEcAn.settings::read.settings("pecan.xml") 
+} else {
+  settings.file = args[1]
+  settings <- PEcAn.settings::read.settings(settings.file)
+}
+# Check for additional modules that will require adding settings
+if("benchmarking" %in% names(settings)){
+  library(PEcAn.benchmark)
+  settings <- papply(settings, read_settings_BRR)
+}
+if("sitegroup" %in% names(settings)){
+  if(is.null(settings$sitegroup$nSite)){
+    settings <- PEcAn.settings::createSitegroupMultiSettings(settings, sitegroupId = settings$sitegroup$id)
+  } else {
+    settings <- PEcAn.settings::createSitegroupMultiSettings(settings, sitegroupId = settings$sitegroup$id,nSite = settings$sitegroup$nSite)
+  }
+  settings$sitegroup <- NULL ## zero out so don't expand a second time if re-reading
+}
+# Update/fix/check settings. Will only run the first time it's called, unless force=TRUE
+settings <- PEcAn.settings::prepare.settings(settings, force=FALSE)
+# Write pecan.CHECKED.xml
+PEcAn.settings::write.settings(settings, outputfile = "pecan.CHECKED.xml")
+# start from scratch if no continue is passed in
+statusFile <- file.path(settings$outdir, "STATUS")
+if (length(which(commandArgs() == "--continue")) == 0 && file.exists(statusFile)) {
+  file.remove(statusFile)
+}
+# Do conversions
+settings <- PEcAn.utils::do_conversions(settings)
+# Query the trait database for data and priors
+if (PEcAn.utils::status.check("TRAIT") == 0){
+  PEcAn.utils::status.start("TRAIT")
+  settings <- PEcAn.workflow::runModule.get.trait.data(settings)
+  PEcAn.settings::write.settings(settings, outputfile='pecan.TRAIT.xml')
+  PEcAn.utils::status.end()
+} else if (file.exists(file.path(settings$outdir, 'pecan.TRAIT.xml'))) {
+  settings <- PEcAn.settings::read.settings(file.path(settings$outdir, 'pecan.TRAIT.xml'))
+}
+# Run the PEcAn meta.analysis
+if(!is.null(settings$meta.analysis)) {
+  if (PEcAn.utils::status.check("META") == 0){
+    PEcAn.utils::status.start("META")
+    PEcAn.MA::runModule.run.meta.analysis(settings)
+    PEcAn.utils::status.end()
+  }
+}
+# Write model specific configs
+if (PEcAn.utils::status.check("CONFIG") == 0){
+  PEcAn.utils::status.start("CONFIG")
+  settings <- PEcAn.workflow::runModule.run.write.configs(settings)
+  PEcAn.settings::write.settings(settings, outputfile='pecan.CONFIGS.xml')
+  PEcAn.utils::status.end()
+} else if (file.exists(file.path(settings$outdir, 'pecan.CONFIGS.xml'))) {
+  settings <- PEcAn.settings::read.settings(file.path(settings$outdir, 'pecan.CONFIGS.xml'))
+}
+if ((length(which(commandArgs() == "--advanced")) != 0) && (PEcAn.utils::status.check("ADVANCED") == 0)) {
+  PEcAn.utils::status.start("ADVANCED")
+  q();
+}
+# Start ecosystem model runs
+if (PEcAn.utils::status.check("MODEL") == 0) {
+  PEcAn.utils::status.start("MODEL")
+  PEcAn.remote::runModule.start.model.runs(settings,stop.on.error=FALSE)
+  PEcAn.utils::status.end()
+}
+# Get results of model runs
+if (PEcAn.utils::status.check("OUTPUT") == 0) {
+  PEcAn.utils::status.start("OUTPUT")
+  runModule.get.results(settings)
+  PEcAn.utils::status.end()
+}
+print("Done reading stuff")
+# Run ensemble analysis on model output. 
+if (FALSE && 'ensemble' %in% names(settings) & PEcAn.utils::status.check("ENSEMBLE") == 0) {
+  PEcAn.utils::status.start("ENSEMBLE")
+  runModule.run.ensemble.analysis(settings, TRUE)    
+  PEcAn.utils::status.end()
+}
+print("Past ensemble section")
+# Run sensitivity analysis and variance decomposition on model output
+if (FALSE && 'sensitivity.analysis' %in% names(settings) & PEcAn.utils::status.check("SENSITIVITY") == 0) {
+  PEcAn.utils::status.start("SENSITIVITY")
+  runModule.run.sensitivity.analysis(settings)
+  PEcAn.utils::status.end()
+}
+PEcAn.settings::write.settings(settings, outputfile = "sa.xml", outputdir = "~/")
+print("past SA section")
+# Run parameter data assimilation
+if (FALSE && 'assim.batch' %in% names(settings)) {
+  if (PEcAn.utils::status.check("PDA") == 0) {
+    PEcAn.utils::status.start("PDA")
+    settings <- PEcAn.assim.batch::runModule.assim.batch(settings)
+    PEcAn.utils::status.end()
+  }
+}
+print("past pda section")
+# Run state data assimilation
+if ('state.data.assimilation' %in% names(settings)) {
+  print("Entering SDA section")
+  if (PEcAn.utils::status.check("SDA") == 0) {
+    PEcAn.utils::status.start("SDA")
+    settings <- PEcAn.uncertainty::prep.data.assim(settings, 5000) # Not sure where the numvals argument is going to be coming from
+    PEcAn.utils::status.end()
+  }
+}
+print("past sda section")
+# Run benchmarking
+if("benchmarking" %in% names(settings) & "benchmark" %in% names(settings$benchmarking)){
+  PEcAn.utils::status.start("BENCHMARKING")
+  results <- papply(settings, function(x) calc_benchmark(x, bety))
+  PEcAn.utils::status.end()
+}
+print("past benchmarking")
+# Pecan workflow complete
+if (PEcAn.utils::status.check("FINISHED") == 0) {
+  PEcAn.utils::status.start("FINISHED")
+  PEcAn.remote::kill.tunnel(settings)
+  db.query(paste("UPDATE workflows SET finished_at=NOW() WHERE id=", settings$workflow$id, "AND finished_at IS NULL"), params=settings$database$bety)
+  
+  # Send email if configured
+  if (!is.null(settings$email) && !is.null(settings$email$to) && (settings$email$to != "")) {
+    sendmail(settings$email$from, settings$email$to,
+             paste0("Workflow has finished executing at ", base::date()),
+             paste0("You can find the results on ", settings$email$url))
+  }
+  PEcAn.utils::status.end()
+}
+db.print.connections()
+print("---------- PEcAn Workflow Complete ----------")
diff --git a/shiny/BrownDog/DESCRIPTION b/shiny/BrownDog/DESCRIPTION
index 4e4b7984eea..d08f67ee393 100644
--- a/shiny/BrownDog/DESCRIPTION
+++ b/shiny/BrownDog/DESCRIPTION
@@ -5,3 +5,4 @@ Author: Yan Zhao <yanzhao3@illinois.edu>
 AuthorUrl: https://github.com/yan130
 Tags: PEcAn
 DisplayMode: Normal
+RoxygenNote: 6.1.0
diff --git a/shiny/BrownDog/server.R b/shiny/BrownDog/server.R
index 651864baf50..5225484911e 100644
--- a/shiny/BrownDog/server.R
+++ b/shiny/BrownDog/server.R
@@ -1,8 +1,22 @@
-library(shiny)
-library(leaflet)
-library(RPostgreSQL)
-library(PEcAn.DB)
-library(PEcAn.visualization)
+## Check and load Packages
+lapply(c( "shiny",
+          "leaflet",
+          "RPostgreSQL"
+        ),function(pkg){
+          if (!(pkg %in% installed.packages()[,1])){
+                install.packages(pkg)
+                }
+                library(pkg,character.only = TRUE,quietly = TRUE)
+          }
+      )
+
+lapply(c( "PEcAn.DB",
+          "PEcAn.visualization"
+      ),function(pkg){
+        library(pkg,character.only = TRUE,quietly = TRUE)
+        }
+      )
+
 
 
 # Define server logic
diff --git a/shiny/BrownDog/ui.R b/shiny/BrownDog/ui.R
index 8c55a73bc98..97a39d64303 100644
--- a/shiny/BrownDog/ui.R
+++ b/shiny/BrownDog/ui.R
@@ -1,3 +1,4 @@
+## load packages
 library(shiny)
 library(leaflet)
 
diff --git a/shiny/Data-Ingest/DESCRIPTION b/shiny/Data-Ingest/DESCRIPTION
new file mode 100644
index 00000000000..48cc825c0d3
--- /dev/null
+++ b/shiny/Data-Ingest/DESCRIPTION
@@ -0,0 +1,8 @@
+Type: Shiny
+Title: Data-Ingest
+License: FreeBSD + file LICENSE
+Date: 2018-08-20
+Author: Liam Burke liam.burke24@gmail.com
+Tags: PEcAn
+DisplayMode: showcase 
+RoxygenNote: 6.1.0
diff --git a/shiny/Data-Ingest/Data_Ingest_Functions.R b/shiny/Data-Ingest/Data_Ingest_Functions.R
new file mode 100644
index 00000000000..e45a944a05b
--- /dev/null
+++ b/shiny/Data-Ingest/Data_Ingest_Functions.R
@@ -0,0 +1,5 @@
+# resolve.id <- function(attributeTable, attribute, input, output) dplyr::filter(attributeTable, attribute == input) %>% pull(output)
+# 
+# resolve.id(attributeTable = sites_sub, attribute = sitename, input = sitename_test, output = id)
+# 
+# dplyr::filter(sites_sub, sitename == sitename_test) %>% pull(id)
diff --git a/shiny/Data-Ingest/LICENSE b/shiny/Data-Ingest/LICENSE
new file mode 100644
index 00000000000..5a9e44128f1
--- /dev/null
+++ b/shiny/Data-Ingest/LICENSE
@@ -0,0 +1,34 @@
+## This is the master copy of the PEcAn License
+
+University of Illinois/NCSA Open Source License
+
+Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
+
+PEcAn project
+www.pecanproject.org
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the 
+"Software"), to deal with the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+- Redistributions of source code must retain the above copyright
+  notice, this list of conditions and the following disclaimers.
+- Redistributions in binary form must reproduce the above copyright
+  notice, this list of conditions and the following disclaimers in the
+  documentation and/or other materials provided with the distribution.
+- Neither the names of University of Illinois, NCSA, nor the names
+  of its contributors may be used to endorse or promote products
+  derived from this Software without specific prior written permission.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR
+ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF 
+CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
+
diff --git a/shiny/Data-Ingest/app.R b/shiny/Data-Ingest/app.R
index dfe39b2c21e..2b5420660e5 100644
--- a/shiny/Data-Ingest/app.R
+++ b/shiny/Data-Ingest/app.R
@@ -1,97 +1,120 @@
-library(shiny)
-library(PEcAn.data.land)
-library(PEcAn.utils)
-library(shinydashboard)
-library(dataone)
+lapply(c( "shiny",
+          "shinydashboard",
+          "dataone",
+          "stringr",
+          "DT",
+          "shiny",
+          "shinytoastr",
+          "shinyWidgets",
+          "shinyjs",
+          "shinyTime",
+          "dplyr"),function(pkg){
+            if (!(pkg %in% installed.packages()[,1])){
+                  install.packages(pkg)
+              }
+                  library(pkg,character.only = TRUE,quietly = TRUE)
+            }
+      )
 
+lapply(c( "PEcAn.data.land",
+          "PEcAn.visualization",
+          "PEcAn.utils",
+          "PEcAn.DB"),function(pkg){
+            library(pkg,character.only = TRUE,quietly = TRUE)
+          }
+       )
 
-# Define UI for application
 
-ui <- dashboardPage(
+ 
+ source("ui_utils.R", local = TRUE)
+ source("helper.R", local = TRUE)
+ 
+ 
+ ##### Bety Calls ######
+ bety <- betyConnect()
+ 
+ sites <- dplyr::tbl(bety, "sites") %>% dplyr::select(sitename, id) %>% dplyr::arrange(sitename)
+ sitenames <- sites %>% pull(sitename)
+ 
+ inputs <- dplyr::tbl(bety, "inputs") %>% dplyr::select(name, id) %>% dplyr::arrange(name)
+ input_names <- inputs %>% pull(name)
+ 
+ formats <- dplyr::tbl(bety, "formats") %>% distinct(name) %>% dplyr::arrange(name) %>% pull(name)
+ formats_sub <- dplyr::tbl(bety, "formats") %>% dplyr::select(name, id) %>% dplyr::arrange(name)
+ 
+ variables_ids <- dplyr::tbl(bety, "variables") %>% dplyr::select(id, name) %>% dplyr::arrange(name)
+ variables <- variables_ids %>% pull(name)
   
-  dashboardHeader(title = "Data Ingest"),
-  dashboardSidebar(
-    sidebarMenu(
-      menuItem("Import Data", tabName = "importData", icon = icon("file")),
-      menuItem("Step 2 -- dbfiles record", tabName = "step2", icon = icon("cog")),
-      menuItem("Step 3 -- format record", tabName = "step3", icon = icon("cog")),
-      menuItem("Step 4 -- etc.", tabName = "step4", icon = icon("cog"))
-    )
+ # machines <- dplyr::tbl(bety, "machines") %>% distinct(hostname) %>% dplyr::arrange(hostname)%>% pull(hostname)
+ # machines_sub <- dplyr::tbl(bety, "machines") %>% dplyr::select(hostname, id) %>% dplyr::arrange(hostname)
+ 
+ mimetypes <- dplyr::tbl(bety, "mimetypes") %>% distinct(type_string) %>% dplyr::arrange(type_string) %>% pull(type_string)
+ mimetype_sub <- dplyr::tbl(bety, "mimetypes") %>% dplyr::select(type_string, id) %>% dplyr::arrange(type_string)
+
+
+#############################################################################
+################################## UI #######################################
+#############################################################################
+
+ui <- dashboardPage(
+  dashboardHeader(title = "Data Ingest Workflow"), 
+  dashboardSidebar(collapsed = TRUE,
+    source_ui("sidebar_ui.R")
   ),
   dashboardBody(
+    useToastr(), # Call error handling package
+    useShinyjs(), #Include shinyjs
     tabItems(
-      tabItem(tabName = "importData",
-              fluidRow( 
-                box(
-                  textInput("id", label = h3("Import From DataONE"), placeholder = "Enter doi or id here"),
-                  actionButton(inputId = "D1Button", label = "Upload"),
-                  hr(),
-                  fluidRow(column(12, verbatimTextOutput("identifier"))) 
-                ),
-                
-                box(
-                  # https://github.com/rstudio/shiny-examples/blob/master/009-upload/app.R
-                  fileInput(inputId = "file", label = h3("Upload Local Files"), accept = NULL, multiple = TRUE, placeholder = "Drag and drop files here"),
-                  p("This is a placeholder and is not yet functional"),
-                  tableOutput("contents")
-                )
-              )
-      ),
-      
-      tabItem(tabName = "step2",
-              h2("under construction")
+    ## Tab 1 -- Ingest Workflow
+    tabItem(tabName = "ingestWorkflow",
+              source_ui("ingest_workflow_ui.R")
       ),
-      
-      tabItem(tabName = "step3",
-              h2("under construction")
-      ),
-      
-      tabItem(tabName = "step4",
-              h2("under construction")
-      )
-      
-      
-    )
-  )
+    ## Tab 2 -- About
+    tabItem(tabName = "About",
+            source_ui("homepage_ui.R")
+            )
+ 
+  )),
+  title = "PEcAn Data Ingest",
+  skin =  "green"
 )
+####################################################################################
+################################ SERVER ############################################
+####################################################################################
 
-server <- function(input, output) {
-  options(shiny.maxRequestSize=30*1024^2) #maximum file input size
+server <- function(input, output, session) {
+  options(shiny.maxRequestSize = 100 * 1024 ^ 2) #maximum file input size
   
-   path <- PEcAn.utils::read_web_config("../../web/config.php")
-    
-   d1d <- eventReactive(input$D1Button, { PEcAn.data.land::dataone_download(input$id, filepath = path) }) #run dataone_download with input from id on click
+  ## Setup ##
+  Shared.data <- reactiveValues(downloaded = NULL, selected_row = NULL, 
+                                local_files = NULL, selected_row_local = NULL, 
+                                new_format = NULL, input_record_df = NULL, 
+                                format_vars_df = NULL, input_method = NULL)
   
-  output$identifier <- renderText({
-    d1d()
-  })
+  Shared.data$variables_rd <- variables
   
+  temp <- tempdir() 
+  PEcAn_path <- PEcAn.utils::read_web_config("../../web/config.php")$dbfiles_folder
   
-###### FileInput <-- Will add this functionality shortly
-#  output$contents <- renderTable({
-    # input$file1 will be NULL initially. After the user selects
-    # and uploads a file, it will be a data frame with 'name',
-    # 'size', 'type', and 'datapath' columns. The 'datapath'
-    # column will contain the local filenames where the data can
-    # be found.
-#    inFile <- input$file
-    
-#    if (is.null(inFile))
-#      return(NULL)
-#    read.csv(inFile$datapath, header = TRUE)
-    
-#  })
-
-
-
-    #file.copy(inFile$datapath, header = input$header)
-
-
+  ## Create two sub-directories in the tempfile ##
+  d1_tempdir <<- file.path(temp, "d1_tempdir")
+  dir.create(d1_tempdir, showWarnings = F)
+  local_tempdir <<- file.path(temp, "local_tempdir")
+  dir.create(local_tempdir, showWarnings = F)
   
+  ##################### DataONE Download #####################
+  source("server_files/d1_download_svr.R", local = TRUE)
 
+  ######### FileInput ########################################
+  source("server_files/local_upload_svr.R", local = TRUE)
+  
+  ######### Ingest Workflow ##############################
+  source("server_files/ingest_workflow_svr.R", local = TRUE)
+  
+  
 }
 
-# Run the application 
+# Run the application... = 
 shinyApp(ui = ui, server = server)
 
-# example data: doi:10.6073/pasta/63ad7159306bc031520f09b2faefcf87
\ No newline at end of file
+# example data: doi:10.6073/pasta/63ad7159306bc031520f09b2faefcf87, doi:10.6073-pasta-f31b28b912e6051bf1d383ff1ef18987
diff --git a/shiny/Data-Ingest/helper.R b/shiny/Data-Ingest/helper.R
new file mode 100644
index 00000000000..b19abbed8c3
--- /dev/null
+++ b/shiny/Data-Ingest/helper.R
@@ -0,0 +1,26 @@
+# This helper file stores all the relevant functions to be called in the shiny app
+#' Auto-create directory name for local file upload
+#'
+#' @param format_name Format name in type: character string
+#' @param site_id Integer, scientific notation, or character string that will be converted to an integer and will be the trailing identifier for the firectory name
+#'
+#' @return Self-generated directory name to store files uploaded via local upload. 
+#' @export
+#' @author Liam Burke (liam.burke24@gmail.com)
+#'
+#' @examples
+#' auto.name.directory(format_name = "LTER-hf-103", site_id = 1000004955)
+auto.name.directory <- function(format_name, site_id){
+  
+  # replace all non-alphanumeric characters with "_"
+  basename <- base::gsub("[^a-zA-Z0-9 :]", "_", format_name)
+  
+  ## Convert site_id into shorter format
+  long_id <- as.numeric(site_id) # convert scientific notation to numeric
+  new_id <- paste0(long_id %/% 1e+09, "-", long_id %% 1e+09) 
+  
+  # Combine
+  autoDirName <- paste(basename, "site", new_id, sep = "_")
+  return(autoDirName)
+}
+
diff --git a/shiny/Data-Ingest/modules/d1_download_module.R b/shiny/Data-Ingest/modules/d1_download_module.R
new file mode 100644
index 00000000000..f5366ba5e74
--- /dev/null
+++ b/shiny/Data-Ingest/modules/d1_download_module.R
@@ -0,0 +1,78 @@
+d1DownloadUI <- function(id){
+  ns <- NS(id)
+  
+  box(width = 4, title = h2("Import From DataONE"), solidHeader = TRUE, status = "success",
+      textInput(
+        ns("id"),
+        label = "Import from dataONE",
+        placeholder = "Enter doi or id here"
+      ),
+      p("Copy and Paste the following example data sets:"),
+      p("doi:10.6073/pasta/63ad7159306bc031520f09b2faefcf87"),
+      p("doi:10.6073-pasta-f31b28b912e6051bf1d383ff1ef18987"),
+      actionButton(ns("D1Button"), label = "Download"),
+      #  actionButton(inputId = "CancelD1Download", label = "Cancel Download"), This is WAY tricky. Not sure if I can add this functionality... 
+      hr(),
+      conditionalPanel(condition="$('html').hasClass('shiny-busy')",
+                       tags$div(id="loadmessage",
+                                HTML(paste0("<div> <h3>Download in Progress.</h3> <p>This download may take a couple of minutes.</p> <img src=\'http://www.lettersmarket.com/uploads/lettersmarket/blog/loaders/common_green/ajax_loader_green_64.gif' height=\"64\" width=\"64\"> </div>"))
+                       )), 
+      DT::DTOutput(ns("identifier")),
+      p("Selected Row (For Testing Purposes)"),
+      verbatimTextOutput(ns("rowSelection")), ## For testing only
+      actionButton(ns("D1FinishButton"), label = "Finish Download"),
+      hr(),
+      p("Location of Downloaded files:"),
+      verbatimTextOutput(ns("D1dbfilesPath"))
+  )
+  
+}
+
+d1Download <- function(input, output, session){
+  
+  ## Create two sub-directories in the tempfile ##
+  d1_tempdir <- file.path(temp, "d1_tempdir")
+  dir.create(d1_tempdir, showWarnings = F)
+  local_tempdir <- file.path(temp, "local_tempdir")
+  dir.create(local_tempdir, showWarnings = F)
+  
+  observeEvent(input$D1Button, {
+    # run dataone_download with input from id on click
+    #  PEcAn.data.land::dataone_download(trimws(input$id), filepath = d1_tempdir) # store files in tempfile
+    list_of_d1_files <<- c("f1", "f2", "f3", "f4", "f5")# list.files(newdir_D1)
+    D1_file_df <- as.data.frame(list_of_d1_files)
+    
+    names(D1_file_df) <- "Available Files"
+    
+    Shared.data$d1fileList <- list_of_d1_files
+    
+    # Grab the name of the D1_file from newdir_D1
+    #  d1_dirname <<- base::sub("/tmp/Rtmp[[:alnum:]]{6}/d1_tempdir/", "", newdir_D1) # let users create their own filenames eventually
+    
+    Shared.data$downloaded <- D1_file_df # Reactive Variable 
+  })
+  
+  # Display downloaded files in data.frame
+  output$identifier <-  DT::renderDT({Shared.data$downloaded}, selection = 'single', options = list(ordering = F, dom = 'tp'))
+  
+  observe({
+    Shared.data$selected_row <- as.character(Shared.data$downloaded[input$identifier_rows_selected,])
+  })
+  
+  output$rowSelection <- renderPrint({Shared.data$selected_row})
+  
+  # Move files to correct dbfiles location (make a custom function for this?)
+  observeEvent(input$D1FinishButton, {
+    # create the new directory in /dbfiles
+    dir.create(paste0(PEcAn_path, d1_dirname))
+    
+    n <- length(list_of_d1_files) 
+    for (i in 1:n){
+      base::file.copy(file.path(newdir_D1, list_of_d1_files[i]), file.path(PEcAn_path, d1_dirname, list_of_d1_files[i]))
+    }
+    output$D1dbfilesPath <- renderText({paste0(PEcAn_path, d1_dirname)}) # Print path to data
+  })
+  
+  
+  
+}
\ No newline at end of file
diff --git a/shiny/Data-Ingest/modules/dbFiles_module.R b/shiny/Data-Ingest/modules/dbFiles_module.R
new file mode 100644
index 00000000000..359e18667a8
--- /dev/null
+++ b/shiny/Data-Ingest/modules/dbFiles_module.R
@@ -0,0 +1,54 @@
+### UI ###
+dbfilesUI <- function(id) {
+  ns <- NS(id)
+  
+  box(
+    title = h2("2. DbFiles Record"), width = 3, collapsible = TRUE, collapsed = TRUE, 
+    hr(),
+    selectizeInput(ns("InputMachineName"), label = "Machine *", choices = NULL,  #remember to set default to local
+                   options = list(
+                     placeholder = 'Please search machine by name',
+                     onInitialize = I('function() { this.setValue(""); }')
+                   )),
+    hr(),
+    textInput(
+      ns("InputFilePath"),
+      label = "File Path *",
+      placeholder = "This file path will be autogenerated by the download process. The user can edit the filepath here?"),
+    hr(),
+    textInput(
+      ns("InputFileName"),
+      label = "File Name *",
+      placeholder = "This file name will be displayed from the download process. The user can edit the file name here"),
+    actionButton(ns("createDBFilesRecord"), label = "Create dbFiles Record"),
+    p("* Denotes a Required Field"),
+    hr(),
+    verbatimTextOutput(ns("dbFilesRecordOut"))
+  )
+}
+
+### Server ###
+dbfiles <- function(input, output, session){
+  
+  ##Output list 
+  dbFilesRecordList <- list()
+  
+  ## Machine Name ##
+  updateSelectizeInput(session, "InputMachineName", choices = machines, server = TRUE)
+  
+  observeEvent(input$createDBFilesRecord, {
+    ## MachineID 
+    dbFilesRecordList$machine <- input$InputMachineName
+    dbFilesRecordList$machineID <- machines_sub %>% dplyr::filter(hostname %in% dbFilesRecordList$machine) %>% pull(id)
+    
+    dbFilesRecordList$filePath <- input$InputFilePath
+    dbFilesRecordList$fileName <- input$InputFileName
+    
+    output$dbFilesRecordOut <- renderPrint({print(dbFilesRecordList)})
+    
+  })
+  
+  
+  
+  
+}
\ No newline at end of file
diff --git a/shiny/Data-Ingest/modules/formats_module.R b/shiny/Data-Ingest/modules/formats_module.R
new file mode 100644
index 00000000000..3183f238f6b
--- /dev/null
+++ b/shiny/Data-Ingest/modules/formats_module.R
@@ -0,0 +1,73 @@
+#### UI #####
+formatsRecordUI <- function(id){
+  ns <- NS(id)
+  
+  shinyjs::hidden(
+    div(id = "formatbox",
+      box(title = h2("3. Create New Format"),
+          width = 4, collapsible = TRUE, collapsed = FALSE, solidHeader = TRUE, status = "warning",
+          selectizeInput(ns("MimetypeName"), label = "Mimetype *", choices = NULL,
+                         options = list(
+                           placeholder = 'Please search inputs by name or site',
+                           onInitialize = I('function() { this.setValue(""); }')
+                         )),
+          p("or"),
+          # uiOutput(ns("tab")), ## Link to BETYdb
+          a(id = ns("betyURL"), "Create New Mimetype", href = "https://www.betydb.org/formats/new", target = "_blank"),
+          hr(),
+          textInput(
+            ns("NewFormatName"),
+            label = "New Format Name *",
+            placeholder = "Create a New Format Name"),
+          hr(),
+          radioButtons(
+            ns("HeaderBoolean"),
+            label = "Is There a Header ?", 
+            choices =  c("Yes", "No")
+          ),
+          hr(),
+          textInput( # I should Render UI only if Header = TRUE
+            ns("SkipLines"),
+            label = "Skip",
+            placeholder = "Enter number of header lines to skip."),
+          hr(),
+          textAreaInput(
+            ns("FormatNotes"),
+            label = "Notes",
+            height = '150px'
+          ),
+          actionButton(ns("createFormatRecord"), label = "Create Format Record"),
+          p("* Denotes a Required Field"),
+          hr(),
+          verbatimTextOutput(ns("FormatRecordOut"))
+      )
+    )
+  )
+}
+
+#### Server #####
+formatsRecord <- function(input, output, session){
+  
+  ## Output List ##
+  FormatRecordList <- list()
+  
+  ######### Mimetype Name ##################
+  updateSelectizeInput(session, "MimetypeName", choices = mimetypes, server = TRUE)
+  
+  observeEvent(input$createFormatRecord, {
+    ## MimetypeID
+    FormatRecordList$mimetypeName <- input$MimetypeName
+    FormatRecordList$mimetypeID <- mimetype_sub %>% dplyr::filter(type_string %in% FormatRecordList$mimetypeName) %>% pull(id)
+    
+    ## Everything else
+    FormatRecordList$NewFormatName <- input$NewFormatName
+    FormatRecordList$HeaderBoolean <- input$HeaderBoolean
+    FormatRecordList$SkipLines <- input$SkipLines #This should appear only if header = TRUE
+    FormatRecordList$FormatNotes <- input$FormatNotes
+    
+    output$FormatRecordOut <- renderPrint({print(FormatRecordList)})
+    
+  })
+  
+
+}
\ No newline at end of file
diff --git a/shiny/Data-Ingest/modules/inputs_module.R b/shiny/Data-Ingest/modules/inputs_module.R
new file mode 100644
index 00000000000..ea4667318ae
--- /dev/null
+++ b/shiny/Data-Ingest/modules/inputs_module.R
@@ -0,0 +1,111 @@
+## UI #####
+inputsRecordUI <- function(id){
+  ns <- NS(id)
+  
+  box(
+    title = h2("2. Input Record"), width = 4, collapsible = TRUE, solidHeader = TRUE, status = "success",
+    selectizeInput(ns("InputSiteName"), label = "Site *", choices = NULL,
+                   options = list(
+                     placeholder = 'Please search or select a site below',
+                     onInitialize = I('function() { this.setValue(""); }')
+                   )
+    ),
+    hr(),
+    selectizeInput(ns("InputParentName"), label = "Parent *", choices = NULL,
+                   options = list(
+                     placeholder = 'Please search inputs by name or site',
+                     onInitialize = I('function() { this.setValue(""); }')
+                   )
+    ),
+    hr(),
+    textInput(ns("InputName"),
+              label = "Name *",
+              placeholder = ""),
+    verbatimTextOutput(ns("autoname")),
+    hr(),
+    selectizeInput(ns("InputFormatName"), label = "Choose Format *", choices = NULL,
+                   options = list(
+                     placeholder = 'Please search Formats by name',
+                     onInitialize = I('function() { this.setValue(""); }')
+                   )
+    ),
+    p("or"),
+  #  actionButton("NewFormat", label = "Create New Format"),
+    hr(),
+    dateInput(
+      ns("InputStartDate"),
+      label = "Start Date",
+      format = "yyyy-mm-dd",
+      startview = "decade"
+    ),
+    shinyTime::timeInput(ns("StartTimeInput"),
+                         label = "Start Time (Hours - Minutes)",
+                         seconds = FALSE),
+    dateInput(
+      ns('InputEndDate'),
+      label = 'End Date',
+      format = 'yyyy-mm-dd',
+      startview = 'decade'
+    ),
+    shinyTime::timeInput(ns("EndTimeInput"),
+                         label = "End Time (Hours-Minutes)",
+                         seconds = FALSE),
+    textInput(ns("Timezone"),
+              label = "Timezone (UTC)",
+              placeholder = "UTC +/-"),
+    hr(),
+    textAreaInput(ns("InputNotes"),
+                  label = "Notes",
+                  height = '150px'),
+    actionButton(ns("createInput"), label = "Create Input"),
+    p("* Denotes a Required Field"),
+    hr(),
+    verbatimTextOutput(ns("summInputs"))
+  )
+}
+
+### Server #####
+
+inputsRecord <- function(input, output, session){
+  ## List of outputs
+  inputsList <- list()
+  
+  
+  ######### Select Site ###############
+  updateSelectizeInput(session, "InputSiteName",  choices = sitenames, server = TRUE)
+  
+  ######### Select Parent ID #################
+  updateSelectizeInput(session, "InputParentName",  choices = input_names, server = TRUE)
+  
+  ####### Select Format ##############
+  updateSelectizeInput(session, "InputFormatName", choices = formats, server = TRUE)
+  
+  ####### Print all selections for Testing ##########
+  
+  observeEvent(input$createInput, {
+    ## siteID
+    inputsList$siteName <- input$InputSiteName
+    inputsList$siteID <- sites %>% dplyr::filter(sitename %in% inputsList$siteName) %>% pull(id)
+    
+    ## ParentID
+    inputsList$parentName <- input$InputParentName
+    inputsList$parentID <- inputs %>% dplyr::filter(name %in% inputsList$parentName) %>% pull(id)
+    
+    ## FormatID
+    inputsList$formatName <- input$InputFormatName
+    inputsList$formatID <- formats_sub %>% dplyr::filter(name %in% inputsList$formatName) %>% pull(id)
+    
+    ## Other Info
+    inputsList$Name <- input$InputName
+    inputsList$StartDate <- input$InputStartDate
+    inputsList$StartTime <- input$StartTimeInput
+    inputsList$EndDate <- input$InputEndDate
+    inputsList$EndTime <- input$EndTimeInput
+    inputsList$Timezone <- input$Timezone
+    inputsList$Notes <- input$InputNotes
+    
+    output$summInputs <- renderPrint({print(inputsList)})
+  })
+#output$autoname <- renderPrint({Shared.data$selected_row_local})
+
+}
diff --git a/shiny/Data-Ingest/modules/local_upload_module.R b/shiny/Data-Ingest/modules/local_upload_module.R
new file mode 100644
index 00000000000..ea06421aadd
--- /dev/null
+++ b/shiny/Data-Ingest/modules/local_upload_module.R
@@ -0,0 +1,85 @@
+localUploadUI <- function(id){
+  ns <- NS(id)
+  
+  box(width = 4, title = h2("Upload Local Files"), solidHeader = T, status = "success",
+      # https://github.com/rstudio/shiny-examples/blob/master/009-upload/app.R
+      fileInput(
+        inputId = ns("file"),
+        label = "Upload Local Files", 
+        accept = NULL,
+        multiple = TRUE,
+        placeholder = "Drag and drop files here"
+      ),
+      DT::DTOutput(ns("dtfiles")),
+      verbatimTextOutput(ns("test")),
+      hr(),
+      textInput(
+        ns("new_local_filename"),
+        label = "Set Destination Directory (for testing only)",
+        placeholder = "Enter New Directory Name Here"
+      ),
+      actionButton(ns("LocalFinishButton"), label = "Finish Download"),
+      hr(),
+      p("Location of Downloaded Files: (Testing Only)"),
+      verbatimTextOutput(ns("LocaldbfilesPath"))
+  )
+  
+}
+
+localUpload <- function(input, output, session){
+  
+  observe({
+    inFile <- input$file
+    n <- length(inFile$name)
+    names <- inFile$name
+    
+    if (is.null(inFile))  
+      return(NULL)
+    
+    splits <- list()
+    
+    for (i in 1:n) {
+      splits <- base::sub("/tmp/Rtmp[[:alnum:]]{6}/", "", inFile[i, "datapath"])  # Consider making this more program agnostic?
+      print(splits)
+      
+      filenames <- list.files(temp)
+      oldpath <- file.path(temp, splits[i])
+      print(oldpath[i])
+      print(list.files(temp)[i])
+      print(file.path(temp, inFile[i, "name"]))
+      base::file.rename(oldpath[i], file.path(temp, "local_tempdir", inFile[i, "name"])) # rename the file to include the original filename
+      base::unlink(dirname(oldpath[i]), recursive = TRUE) # remove the file with the userhostile name
+    }
+    uploaded_local <- as.data.frame(list.files(file.path(temp, "local_tempdir")))
+    names(uploaded_local) <- "Available Files"
+    Shared.data$local_files <- uploaded_local 
+    
+  })
+  
+  output$dtfiles <- DT::renderDT({Shared.data$local_files}, selection = 'single', options = list(ordering = F, dom = 'tp'))
+  
+  observe({
+    Shared.data$selected_row_local <- as.character(Shared.data$local_files[input$dtfiles_rows_selected,])
+  })
+  
+  output$test <- renderPrint({Shared.data$selected_row_local})
+  
+  # Move files to correct dbfiles location (make a custom function for this?)
+  observeEvent(input$LocalFinishButton, {
+    # create the new directory in /dbfiles
+    local_dirname <- gsub(" ", "_", input$new_local_filename) # Are there any other types of breaking chatacters that I should avoid with directory naming? 
+    dir.create(file.path(PEcAn_path, local_dirname))
+    
+    path_to_local_tempdir <- file.path(local_tempdir)
+    list_of_local_files <- list.files(path_to_local_tempdir) 
+    
+    n <- length(list_of_d1_files)
+    for (i in 1:n){
+      base::file.copy(file.path(path_to_local_tempdir, list_of_local_files[i]), file.path(PEcAn_path, local_dirname, list_of_local_files[i]))
+    }
+    output$LocaldbfilesPath <- renderText({paste0(PEcAn_path, local_dirname)}) # Print path to dbfiles
+  })
+  
+  
+    
+}
\ No newline at end of file
diff --git a/shiny/Data-Ingest/server_files/create_input_record_svr.R b/shiny/Data-Ingest/server_files/create_input_record_svr.R
new file mode 100644
index 00000000000..0b64bf1a5af
--- /dev/null
+++ b/shiny/Data-Ingest/server_files/create_input_record_svr.R
@@ -0,0 +1,35 @@
+######### Select Site ###############
+updateSelectizeInput(session, "InputSiteName",  choices = sitenames, server = TRUE)
+
+######### Select Parent ID #################
+updateSelectizeInput(session, "InputParentName",  choices = input_names, server = TRUE)
+
+####### Select Format ##############
+updateSelectizeInput(session, "InputFormatName", choices = formats, server = TRUE)
+
+####### Print all selections for Testing ##########
+
+observeEvent(input$createInput, {
+  ## siteID
+  inputsList$siteName <- input$InputSiteName
+  inputsList$siteID <- sites %>% dplyr::filter(sitename %in% inputsList$siteName) %>% pull(id)
+  
+  ## ParentID
+  inputsList$parentName <- input$InputParentName
+  inputsList$parentID <- inputs %>% dplyr::filter(name %in% inputsList$parentName) %>% pull(id)
+  
+  ## FormatID
+  inputsList$formatName <- input$InputFormatName
+  inputsList$formatID <- formats_sub %>% dplyr::filter(name %in% inputsList$formatName) %>% pull(id)
+  
+  ## Other Info
+  inputsList$Name <- input$InputName
+  inputsList$StartDate <- input$InputStartDate
+  inputsList$StartTime <- input$StartTimeInput
+  inputsList$EndDate <- input$InputEndDate
+  inputsList$EndTime <- input$EndTimeInput
+  inputsList$Timezone <- input$Timezone
+  inputsList$Notes <- input$InputNotes
+  
+  output$summInputs <- renderPrint({print(inputsList)})
+})
diff --git a/shiny/Data-Ingest/server_files/d1_download_svr.R b/shiny/Data-Ingest/server_files/d1_download_svr.R
new file mode 100644
index 00000000000..9f2441a54ae
--- /dev/null
+++ b/shiny/Data-Ingest/server_files/d1_download_svr.R
@@ -0,0 +1,76 @@
+## Hide Download button until doi is entered ##
+observe({
+  if (is.null(input$id) || input$id == "") {
+    shinyjs::disable("D1Button")
+  } else {
+    shinyjs::enable("D1Button")
+  }
+})
+
+observeEvent(input$D1Button, {
+  tryCatch({
+  # run dataone_download with input from id on click
+  PEcAn.data.land::dataone_download(trimws(input$id), filepath = d1_tempdir) #store files in tempfile
+    toastr_success("Files Successfully Downloadded")
+  },
+  error = function(e){
+    toastr_error(title = "Error in Select DataONE Files", conditionMessage(e))
+  },
+  warning = function(e){
+    toastr_warning(title = "Warning in Select DataONE Files", conditionMessage(e))
+  }
+  )
+  list_of_d1_files <<- list.files(newdir_D1) 
+  
+  # ## df to store href buttons for file preview ## Uncomment when preview is functional. 
+  # d1_paths_df <- data.frame(href = NA)
+  # for(i in 1:length(list_of_d1_files)){
+  #   d1_paths_df[i,1] <- as.character(a("Preview", href = file.path(newdir_D1, list_of_d1_files[i]), target = "_blank"))
+  # }
+  
+  D1_file_df <- as.data.frame(list_of_d1_files) #cbind(list_of_d1_files, d1_paths_df)
+  
+  names(D1_file_df) <- c("Available Files") # c("Available Files", "")
+  
+  Shared.data$d1fileList <- list_of_d1_files
+  
+  # Grab the name of the D1_file from newdir_D1
+  d1_dirname <<- base::sub("/tmp/Rtmp[[:alnum:]]{6}/d1_tempdir/", "", newdir_D1) 
+  
+  Shared.data$downloaded <- D1_file_df # Reactive Variable 
+})
+
+# Display downloaded files in data.frame
+output$identifier <-  DT::renderDT(datatable({Shared.data$downloaded}, escape = FALSE, selection = 'single', options = list(ordering = F, dom = 'tp')))
+
+observe({
+  Shared.data$selected_row <- as.character(Shared.data$downloaded[input$identifier_rows_selected, 1])
+})
+
+# Move files to correct dbfiles location (make a custom function for this?)
+observeEvent(input$complete_ingest_d1, {
+  tryCatch({
+  # create the new directory in /dbfiles
+  dir.create(paste0(PEcAn_path, d1_dirname))
+  
+  n <- length(list_of_d1_files) 
+  for (i in 1:n){
+    base::file.copy(file.path(newdir_D1, list_of_d1_files[i]), file.path(PEcAn_path, d1_dirname, list_of_d1_files[i]))
+  }
+  show("d1_new_dir_output") # print message when rendering path to dbfiles
+  output$D1dbfilesPath <- renderText({paste0(PEcAn_path, d1_dirname)}) # Print path to data
+  },
+  error = function(e){
+    toastr_error(title = "Error in Select DataONE Files", conditionMessage(e))
+  },
+  warning = function(e){
+    toastr_warning(title = "Warning in Select DataONE Files", conditionMessage(e))
+  }
+  )
+})
+
+observeEvent(input$nextFromD1, {
+  show("input_record_box")
+  hide("nextFromD1_div")
+})
+
diff --git a/shiny/Data-Ingest/server_files/dbfiles_record_svr.R b/shiny/Data-Ingest/server_files/dbfiles_record_svr.R
new file mode 100644
index 00000000000..8f632156c3b
--- /dev/null
+++ b/shiny/Data-Ingest/server_files/dbfiles_record_svr.R
@@ -0,0 +1,18 @@
+###################################################
+####### Db Files Record ###########################
+###################################################
+
+################ MachineID ########################
+updateSelectizeInput(session, "InputMachineName", choices = machines, server = TRUE)
+
+observeEvent(input$createDBFilesRecord, {
+  ## MachineID 
+  dbFilesRecordList$machine <- input$InputMachineName
+  dbFilesRecordList$machineID <- machines_sub %>% dplyr::filter(hostname %in% dbFilesRecordList$machine) %>% pull(id)
+  
+  dbFilesRecordList$filePath <- input$InputFilePath
+  dbFilesRecordList$fileName <- input$InputFileName
+  
+  output$dbFilesRecordOut <- renderPrint({print(dbFilesRecordList)})
+  
+})
\ No newline at end of file
diff --git a/shiny/Data-Ingest/server_files/formats_record_svr.R b/shiny/Data-Ingest/server_files/formats_record_svr.R
new file mode 100644
index 00000000000..73dda05f984
--- /dev/null
+++ b/shiny/Data-Ingest/server_files/formats_record_svr.R
@@ -0,0 +1,22 @@
+###################################################
+############# Format ID ###########################
+###################################################
+
+######### Mimetype ID ##################
+updateSelectizeInput(session, "MimetypeName", choices = mimetypes, server = TRUE)
+
+observeEvent(input$createFormatRecord, {
+  ## MimetypeID
+  FormatRecordList$mimetypeName <- input$MimetypeName
+  FormatRecordList$mimetypeID <- mimetype_sub %>% dplyr::filter(type_string %in% FormatRecordList$mimetypeName) %>% pull(id)
+  
+  ## Everything else
+  FormatRecordList$NewMimeType <- input$NewMimeType
+  FormatRecordList$NewFormatName <- input$NewFormatName
+  FormatRecordList$HeaderBoolean <- input$HeaderBoolean
+  FormatRecordList$SkipLines <- input$SkipLines #This should appear only if header = TRUE
+  FormatRecordList$FormatNotes <- input$FormatNotes
+  
+  output$FormatRecordOut <- renderPrint({print(FormatRecordList)})
+  
+})
\ No newline at end of file
diff --git a/shiny/Data-Ingest/server_files/ingest_workflow_svr.R b/shiny/Data-Ingest/server_files/ingest_workflow_svr.R
new file mode 100644
index 00000000000..05777319b06
--- /dev/null
+++ b/shiny/Data-Ingest/server_files/ingest_workflow_svr.R
@@ -0,0 +1,282 @@
+#### Conditional Pannel to Switch between d1 and local upload ####
+observeEvent(input$inputMethod,{
+  if(input$inputMethod == "DataONE"){
+    show("d1_ui")
+    hide("lcl_ui")
+  }else{
+    show("lcl_ui")
+    hide("d1_ui")
+  }
+})
+
+observeEvent(input$lclUpload, {
+  show("lcl_ui")
+  hide("d1_ui")
+})
+
+########### Inputs svr ############# 
+
+## List of outputs##
+inputsList <- list()
+
+######### Select Site ###############
+updateSelectizeInput(session, "InputSiteName",  choices = sitenames, server = TRUE)
+
+######### Select Parent ID #################
+updateSelectizeInput(session, "InputParentName",  choices = input_names, server = TRUE)
+
+####### Select Format ##############
+updateSelectizeInput(session, "InputFormatName", choices = formats, server = TRUE)
+
+observeEvent(input$createFormatRecord, {
+  new_format <- input$NewFormatName
+  updateSelectizeInput(session, "InputFormatName", choices = new_format, selected = tail(new_format,1), server = TRUE)
+  
+})
+
+###### Select Mimetype #########
+updateSelectizeInput(session, "MimetypeNameCurrent", choices = mimetypes, server = TRUE)
+
+observeEvent(input$createFormatRecord, {
+  updateSelectizeInput(session, "MimetypeNameCurrent", choices = input$MimetypeName, selected = input$MimetypeName, server = TRUE)
+  
+})
+
+####### Update Text Input for fileName ######
+observe({
+updateTextInput(session, "InputName", value = Shared.data$selected_row)
+})
+
+####### Update Selections of Format and Corresponding Mimetype ############
+observeEvent(input$FormatRecordDone,{
+  updateSelectizeInput(session, "InputFormatName", choices = c(input$NewFormatName), selected = c(input$NewFormatName), server = TRUE)
+  updateSelectizeInput(session, "MimetypeNameCurrent", choices = c(input$MimetypeName), selected = c(input$MimetypeName), server = TRUE)
+})
+
+
+# ####### Update Selectize Input for Timezone ########### Not sure if Timezone is a necessary input
+# updateSelectizeInput(session, "Timezone", choices = timezones, server = TRUE)
+
+####### Make Inputs List ##########
+
+observeEvent(input$nextFromInput, {
+  ## siteID
+  if(input$InputSiteName == ""){
+    inputsList$siteName <<- ""
+    inputsList$siteID <<- ""
+  }else{
+    inputsList$siteName <<- input$InputSiteName
+    inputsList$siteID <<- sites %>% dplyr::filter(sitename %in% input$InputSiteName) %>% pull(id)
+  }
+    
+  ## ParentID
+  if(input$InputParentName == ""){
+    inputsList$parentName <<- ""
+    inputsList$parentID <<- NA
+  }else{
+    inputsList$parentName <<- input$InputParentName
+    inputsList$parentID <<- inputs %>% dplyr::filter(name %in% input$InputParentName) %>% pull(id)
+  }
+
+  ## FormatID
+  if(input$InputFormatName == ""){
+    inputsList$formatName <<- ""
+  }else{
+    inputsList$formatName <<- input$InputFormatName
+  }
+
+  ## Mimetype (should I find the ID as well?)##
+  inputsList$Mimetype <<- input$MimetypeNameCurrent
+  
+  inputsList$StartTime_sub <<- trimws(base::sub("[0-9]{4}[.-][0-9]{2}[.-][0-9]{2}[ \t]", "", input$StartTimeInput))
+  inputsList$EndTime_sub <<- trimws(base::sub("[0-9]{4}[.-][0-9]{2}[.-][0-9]{2}[ \t]", "", input$EndTimeInput))
+  
+  inputsList$StartDateTime <<- trimws(paste(input$InputStartDate, inputsList$StartTime_sub, " "))
+  inputsList$EndDateTime <<- trimws(paste(input$InputEndDate, inputsList$EndTime_sub, " "))
+  
+  
+
+  ## Other Info
+  inputsList$Method <<- input$inputMethod
+  inputsList$Name <<- input$InputName
+  inputsList$Path <<- ifelse(inputsList$Method == "DataONE", file.path(newdir_D1, input$InputName), file.path(local_tempdir, input$InputName))
+  inputsList$StartDate <<- input$InputStartDate
+  inputsList$StartTime <<- input$StartTimeInput
+  inputsList$EndDate <<- input$InputEndDate
+  inputsList$EndTime <<- input$EndTimeInput
+  inputsList$Timezone <<- input$Timezone
+  inputsList$Notes <<- input$InputNotes
+  
+  ## Print List
+  #output$summInputs <- renderPrint({inputsList})
+})
+
+output$input_record_df <- renderPrint({Shared.data$input_record_df})
+
+######### Formats Svr #############
+output$autoname <- renderPrint({Shared.data$selected_row}) #_local
+
+######### Mimetype Name ##################
+updateSelectizeInput(session, "MimetypeName", choices = mimetypes, server = TRUE)
+
+observeEvent(input$FormatRecordDone, {
+  ## Output List ##
+  FormatRecordList <<- list()
+  
+  ## MimetypeID
+  FormatRecordList$MimetypeName <- input$MimetypeName
+  FormatRecordList$NewmimetypeID <- ifelse((input$MimetypeName == ""), "", mimetype_sub %>% dplyr::filter(type_string %in% input$MimetypeName) %>% pull(id))
+  
+  ## Everything else
+  FormatRecordList$NewFormatName <- input$NewFormatName
+  FormatRecordList$HeaderBoolean <- ifelse((input$HeaderBoolean == "Yes"), "TRUE", "FALSE")
+  FormatRecordList$SkipLines <- input$SkipLines #This should appear only if header = TRUE
+  FormatRecordList$FormatNotes <- input$FormatNotes
+  
+  ## Make 'data.frame' for format record query 
+  FormatsRecord_df <- data.frame(
+    header = FormatRecordList$HeaderBoolean,
+    skip = FormatRecordList$SkipLines,
+    mimetype_id = FormatRecordList$NewmimetypeID,
+    notes = FormatRecordList$FormatNotes,
+    name = FormatRecordList$NewFormatName
+  )
+  ## Print format record for testing
+#  output$FormatRecordOut <- renderPrint({print(FormatRecordList)})
+
+})
+
+# ## Insert Format Record
+# PEcAn.DB::insert.format.vars(con = bety$con, formats_df = FormatsRecord_df, formats_variables_df = NULL)
+
+###### Formats Vars Server ##############
+##Output list 
+FormatVars <- list()
+
+## Variable Name ##
+updateSelectizeInput(session = getDefaultReactiveDomain(), "pecan_var", choices = variables, server = TRUE)
+
+#### Show inputs on click only ####
+observeEvent(input$nextFromInput,{
+    show("formats.vars_box")
+    if(input$inputMethod == "DataONE"){
+      show("finishButton_d1")
+      }else{
+        show("finishButton_lcl")
+      }
+})
+
+### Create empty matrix with headers to store infinite entries ###
+Shared.data$format_vars_df <- matrix(data = NA, nrow = 0, ncol = 6, dimnames = list(c(), c("BETY_variable_name", "variable_id", "name", "unit", "storage_type", "column_number")))
+
+### Store inputs in a data.frame ###
+observeEvent(input$register_variable, {
+format_vars_entry <- tibble::tibble(
+                                var_name = input$pecan_var, 
+                                variable_id = variables_ids %>% dplyr::filter(name %in% input$pecan_var) %>% pull(id),
+                                name = input$var_name, 
+                                unit = input$var_unit, 
+                                storage_type = input$storage_type,
+                                column_number = as.numeric(input$col_num)
+                              )
+
+Shared.data$format_vars_df <- rbind(format_vars_entry, Shared.data$format_vars_df)
+output$format_vars_df <- DT::renderDT(datatable({Shared.data$format_vars_df}, escape = FALSE, selection = 'single', options = list(ordering = F, dom = 'tp')))
+})
+
+
+observeEvent(input$complete_ingest_d1, {
+  # Drop var_name column from format_vars_df
+  Shared.data$format_vars_df <- Shared.data$format_vars_df %>% select(-one_of("var_name"))
+  
+  # 1. Create Format and the format variable records
+  tryCatch({
+  PEcAn.DB::insert.format.vars(con = bety$con, 
+                               format_name = input$NewFormatName, 
+                               mimetype_id = ifelse((input$MimetypeName == ""), "", mimetype_sub %>% dplyr::filter(type_string %in% input$MimetypeName) %>% pull(id)),
+                               header = ifelse((input$HeaderBoolean == "Yes"), TRUE, FALSE),
+                               skip = input$SkipLines,
+                               notes = input$FormatNotes,
+                               formats_variables = Shared.data$format_vars_df
+                               )
+    toastr_success("Successfully Created Format Record")
+  },
+  error = function(e){
+    toastr_error(title = "Error in Creating Format & Format Variable Record", conditionMessage(e))
+  },
+  warning = function(e){
+    toastr_warning(title = "Format & Format-Variable Warning", conditionMessage(e))
+  }
+  )
+  tryCatch({
+    #2. Create the Inputs Record and dbfiles record
+    Shared.data$input_record_df <- PEcAn.DB::dbfile.input.insert(in.path = inputsList$Path,
+                                                                 in.prefix = inputsList$Name,
+                                                                 siteid =   inputsList$siteID,
+                                                                 startdate = inputsList$StartDateTime,
+                                                                 enddate =   inputsList$EndDateTime,
+                                                                 mimetype = inputsList$Mimetype,
+                                                                 formatname = inputsList$formatName,
+                                                                 parentid = inputsList$parentID,
+                                                                 con = bety$con
+                                                                 #hostname = localhost #?, #default to localhost for now
+                                                                 #allow.conflicting.dates#? #default to FALSE for now
+    )
+    toastr_success("Successfully Created Input Record")
+  },
+  error = function(e){
+    toastr_error(title = "Error in Completing Input Record", conditionMessage(e))
+  },
+  warning = function(e){
+    toastr_warning(title = "Input Record Warning", conditionMessage(e))
+  }
+)
+
+})
+
+observeEvent(input$complete_ingest_lcl, {
+  # Drop var_name column from format_vars_df
+  Shared.data$format_vars_df <- Shared.data$format_vars_df %>% select(-one_of("var_name"))
+  # 1. Create Format and the format variable records
+  tryCatch({
+    PEcAn.DB::insert.format.vars(con = bety$con,
+                                 format_name = input$NewFormatName,
+                                 mimetype_id = ifelse((input$MimetypeName == ""), "", mimetype_sub %>% dplyr::filter(type_string %in% input$MimetypeName) %>% pull(id)),
+                                 header = ifelse((input$HeaderBoolean == "Yes"), TRUE, FALSE),
+                                 skip = input$SkipLines,
+                                 notes = input$FormatNotes,
+                                 formats_variables = Shared.data$format_vars_df
+    )
+    toastr_success("Successfully Created Format Record")
+  },
+  error = function(e){
+    toastr_error(title = "Error in Creating Format & Format-Variable Record", conditionMessage(e))
+  },
+  warning = function(e){
+    toastr_warning(title = "Format & Format-Variable Record Warning", conditionMessage(e))
+  }
+  )
+  tryCatch({
+    #2. Create the Inputs Record and dbfiles record
+    Shared.data$input_record_df <- PEcAn.DB::dbfile.input.insert(in.path = inputsList$Path,
+                                                                 in.prefix = inputsList$Name,
+                                                                 siteid =   inputsList$siteID,
+                                                                 startdate = inputsList$StartDateTime,
+                                                                 enddate =   inputsList$EndDateTime,
+                                                                 mimetype = inputsList$Mimetype,
+                                                                 formatname = inputsList$formatName,
+                                                                 parentid = inputsList$parentID,
+                                                                 con = bety$con
+                                                                 #hostname = localhost #?, #default to localhost for now
+                                                                 #allow.conflicting.dates#? #default to FALSE for now
+    )
+    toastr_success("Successfully Created Input Record")
+  },
+  error = function(e){
+    toastr_error(title = "Error in Creating Input Record", conditionMessage(e))
+  },
+  warning = function(e){
+    toastr_warning(title = "Input Record Warning", conditionMessage(e))
+  }
+  )
+})
diff --git a/shiny/Data-Ingest/server_files/input_record_svr.R b/shiny/Data-Ingest/server_files/input_record_svr.R
new file mode 100644
index 00000000000..072c98dc368
--- /dev/null
+++ b/shiny/Data-Ingest/server_files/input_record_svr.R
@@ -0,0 +1,81 @@
+inputsList <- list()
+dbFilesRecordList <- list()
+FormatRecordList <- list()
+######### Select Site ###############
+updateSelectizeInput(session, "InputSiteName",  choices = sitenames, server = TRUE)
+
+######### Select Parent ID #################
+updateSelectizeInput(session, "InputParentName",  choices = input_names, server = TRUE)
+
+####### Select Format ##############
+updateSelectizeInput(session, "InputFormatName", choices = formats, server = TRUE)
+
+####### Print all selections for Testing ##########
+
+observeEvent(input$createInput, {
+  ## siteID
+  inputsList$siteName <- input$InputSiteName
+  inputsList$siteID <- sites %>% dplyr::filter(sitename %in% inputsList$siteName) %>% pull(id)
+  
+  ## ParentID
+  inputsList$parentName <- input$InputParentName
+  inputsList$parentID <- inputs %>% dplyr::filter(name %in% inputsList$parentName) %>% pull(id)
+  
+  ## FormatID
+  inputsList$formatName <- input$InputFormatName
+  inputsList$formatID <- formats_sub %>% dplyr::filter(name %in% inputsList$formatName) %>% pull(id)
+
+  ## Other Info
+  inputsList$Name <- input$InputName
+  inputsList$StartDate <- input$InputStartDate
+  inputsList$StartTime <- input$StartTimeInput
+  inputsList$EndDate <- input$InputEndDate
+  inputsList$EndTime <- input$EndTimeInput
+  inputsList$Timezone <- input$Timezone
+  inputsList$Notes <- input$InputNotes
+
+ output$summInputs <- renderPrint({print(inputsList)})
+})
+
+###################################################
+####### Db Files Record ###########################
+###################################################
+
+################ MachineID ########################
+updateSelectizeInput(session, "InputMachineName", choices = machines, server = TRUE)
+
+observeEvent(input$createDBFilesRecord, {
+  ## MachineID 
+  dbFilesRecordList$machine <- input$InputMachineName
+  dbFilesRecordList$machineID <- machines_sub %>% dplyr::filter(hostname %in% dbFilesRecordList$machine) %>% pull(id)
+  
+  dbFilesRecordList$filePath <- input$InputFilePath
+  dbFilesRecordList$fileName <- input$InputFileName
+  
+  output$dbFilesRecordOut <- renderPrint({print(dbFilesRecordList)})
+  
+})
+
+###################################################
+############# Format ID ###########################
+###################################################
+
+######### Mimetype ID ##################
+updateSelectizeInput(session, "MimetypeName", choices = mimetypes, server = TRUE)
+
+observeEvent(input$createFormatRecord, {
+  ## MimetypeID
+  FormatRecordList$mimetypeName <- input$MimetypeName
+  FormatRecordList$mimetypeID <- mimetype_sub %>% dplyr::filter(type_string %in% FormatRecordList$mimetypeName) %>% pull(id)
+  
+  ## Everything else
+  FormatRecordList$NewMimeType <- input$NewMimeType
+  FormatRecordList$NewFormatName <- input$NewFormatName
+  FormatRecordList$HeaderBoolean <- input$HeaderBoolean
+  FormatRecordList$SkipLines <- input$SkipLines #This should appear only if header = TRUE
+  FormatRecordList$FormatNotes <- input$FormatNotes
+  
+  output$FormatRecordOut <- renderPrint({print(FormatRecordList)})
+  
+})
+
diff --git a/shiny/Data-Ingest/server_files/local_upload_svr.R b/shiny/Data-Ingest/server_files/local_upload_svr.R
new file mode 100644
index 00000000000..a55ebd1945c
--- /dev/null
+++ b/shiny/Data-Ingest/server_files/local_upload_svr.R
@@ -0,0 +1,58 @@
+observe({
+  inFile <- input$file
+  n <- length(inFile$name)
+  names <- inFile$name
+  
+  if (is.null(inFile))  
+    return(NULL)
+  
+  splits <- list()
+  
+  for (i in 1:n) {
+    splits <- base::sub("/tmp/Rtmp[[:alnum:]]{6}/", "", inFile[i, "datapath"])  # Consider making this more program agnostic?
+    filenames <- list.files(temp)
+    oldpath <- file.path(temp, splits[i])
+    base::file.rename(oldpath[i], file.path(temp, "local_tempdir", inFile[i, "name"])) # rename the file to include the original filename
+    base::unlink(dirname(oldpath[i]), recursive = TRUE) # remove the file with the userhostile name
+  }
+  uploaded_local <- as.data.frame(list.files(file.path(temp, "local_tempdir")))
+  names(uploaded_local) <- "Available Files"
+  Shared.data$local_files <- uploaded_local 
+ 
+})
+
+output$dtfiles <- DT::renderDT({Shared.data$local_files}, selection = 'single', options = list(ordering = F, dom = 'tp'))
+
+observe({
+  Shared.data$selected_row <- as.character(Shared.data$local_files[input$dtfiles_rows_selected,]) #_local
+})
+
+observeEvent(input$complete_ingest_lcl, {
+  tryCatch({
+  # create the new directory in /dbfiles
+  local_dirname <- auto.name.directory(format_name = input$InputFormatName, site_id = inputsList$siteID) # Create name from format and site_id 
+  dir.create(file.path(PEcAn_path, local_dirname))
+  
+  path_to_local_tempdir <- file.path(local_tempdir)
+  list_of_local_files <- list.files(path_to_local_tempdir) 
+  
+  n <- length(list_of_local_files)
+  for (i in 1:n){
+    base::file.copy(file.path(path_to_local_tempdir, list_of_local_files[i]), file.path(PEcAn_path, local_dirname, list_of_local_files[i]))
+  }
+  show("local_path_out") # Message to render path to dbfiles
+  output$LocaldbfilesPath <- renderText({paste0(PEcAn_path, local_dirname)}) # Print path to dbfiles
+  },
+  error = function(e){
+    toastr_error(title = "Error in Select Local Files", conditionMessage(e))
+  },
+  warning = function(e){
+    toastr_warning(title = "Warning in Select Local Files", conditionMessage(e))
+  }
+  )
+})
+
+observeEvent(input$nextFromLocal, {
+  show("input_record_box")
+  hide("nextFromLocal_div")
+})
diff --git a/shiny/Data-Ingest/ui_files/create_input_record_ui.R b/shiny/Data-Ingest/ui_files/create_input_record_ui.R
new file mode 100644
index 00000000000..966d146f4f4
--- /dev/null
+++ b/shiny/Data-Ingest/ui_files/create_input_record_ui.R
@@ -0,0 +1,59 @@
+box(
+  title = h2("1. Input Record"), width = 3, collapsible = TRUE, 
+  hr(),
+  selectizeInput("InputSiteName", label = "Site *", choices = NULL,
+    options = list(
+      placeholder = 'Please search or select a site below',
+      onInitialize = I('function() { this.setValue(""); }')
+    )
+  ),
+  hr(),
+  selectizeInput("InputParentName", label = "Parent", choices = NULL,
+    options = list(
+      placeholder = 'Please search inputs by name or site',
+      onInitialize = I('function() { this.setValue(""); }')
+    )
+  ),
+  hr(),
+  textInput("InputName",
+            label = "Name *",
+            placeholder = ""),
+  hr(),
+  selectizeInput("InputFormatName", label = "Format *", choices = NULL,
+    options = list(
+      placeholder = 'Please search Formats by name',
+      onInitialize = I('function() { this.setValue(""); }')
+    )
+  ),
+  hr(),
+  dateInput(
+    "InputStartDate",
+    label = "Start Date",
+    format = "yyyy-mm-dd",
+    startview = "decade"
+  ),
+  shinyTime::timeInput("StartTimeInput",
+                       label = "Start Time (Hours - Minutes) *",
+                       seconds = FALSE),
+  dateInput(
+    'InputEndDate',
+    label = 'End Date',
+    format = 'yyyy-mm-dd',
+    startview = 'decade'
+  ),
+  shinyTime::timeInput("EndTimeInput",
+                       label = "End Time (Hours-Minutes) *",
+                       seconds = FALSE),
+  textInput("Timezone",
+            label = "Timezone (UTC) *",
+            placeholder = "UTC +/-"),
+  hr(),
+  textAreaInput("InputNotes",
+                label = "Notes",
+                height = '150px'),
+  actionButton("createInput", label = "Create Input"),
+  # Not sure if I want this here or only available when all forms are filled in.
+  p("* Denotes a Required Field"),
+  hr(),
+  verbatimTextOutput("summInputs")
+  )
\ No newline at end of file
diff --git a/shiny/Data-Ingest/ui_files/d1_download_ui.R b/shiny/Data-Ingest/ui_files/d1_download_ui.R
new file mode 100644
index 00000000000..db5fe041930
--- /dev/null
+++ b/shiny/Data-Ingest/ui_files/d1_download_ui.R
@@ -0,0 +1,31 @@
+div(id = "d1_ui",
+tagList(
+    textInput(
+      "id",
+      label = "Import from dataONE",
+      placeholder = "Enter doi or id here"
+    ),
+    actionBttn(inputId = "D1Button", label = "Download", size = "sm", color = "success"),
+    hr(),
+    conditionalPanel(condition="$('html').hasClass('shiny-busy')",
+                     tags$div(id="loadmessage",
+                              HTML(paste0("<div> <h3>Download in Progress.</h3> <p>This download may take a couple of minutes.</p> <img src=\'http://www.lettersmarket.com/uploads/lettersmarket/blog/loaders/common_green/ajax_loader_green_64.gif' height=\"64\" width=\"64\"> </div>"))
+                     )), 
+    DT::DTOutput("identifier"),
+    div(id = "nextFromD1_div",
+    fluidRow(
+      column(8),
+      column(4,
+        actionBttn(inputId = "nextFromD1", label = "Next Step", size = "sm", color = "success")
+        )
+      )
+    ),
+    shinyjs::hidden(
+      div(id = "d1_new_dir_output",
+          hr(),
+    p("Location of Downloaded files:"),
+    verbatimTextOutput("D1dbfilesPath")
+      )
+    )
+)
+)
\ No newline at end of file
diff --git a/shiny/Data-Ingest/ui_files/dbfiles_record_ui.R b/shiny/Data-Ingest/ui_files/dbfiles_record_ui.R
new file mode 100644
index 00000000000..31ecd927cdb
--- /dev/null
+++ b/shiny/Data-Ingest/ui_files/dbfiles_record_ui.R
@@ -0,0 +1,23 @@
+box(
+  title = h2("2. DbFiles Record"), width = 3, collapsible = TRUE, collapsed = TRUE, 
+    hr(),
+    selectizeInput("InputMachineName", label = "Machine *", choices = NULL,  #remember to set default to local
+                   options = list(
+                     placeholder = 'Please search machine by name',
+                     onInitialize = I('function() { this.setValue(""); }')
+                   )),
+    hr(),
+    textInput(
+      "InputFilePath",
+      label = "File Path *",
+      placeholder = "This file path will be autogenerated by the download process. The user can edit the filepath here?"),
+    hr(),
+    textInput(
+      "InputFileName",
+      label = "File Name *",
+      placeholder = "This file name will be displayed from the download process. The user can edit the file name here"),
+    actionButton("createDBFilesRecord", label = "Create dbFiles Record"),
+    p("* Denotes a Required Field"),
+    hr(),
+    verbatimTextOutput("dbFilesRecordOut")
+)
diff --git a/shiny/Data-Ingest/ui_files/formats_record_ui.R b/shiny/Data-Ingest/ui_files/formats_record_ui.R
new file mode 100644
index 00000000000..dedbb121a5c
--- /dev/null
+++ b/shiny/Data-Ingest/ui_files/formats_record_ui.R
@@ -0,0 +1,41 @@
+box(title = h2("3. Format Record"), width = 3, collapsible = TRUE, collapsed = TRUE,
+    hr(),
+    selectizeInput("MimetypeName", label = "Mimetype *", choices = NULL,
+                   options = list(
+                     placeholder = 'Please search inputs by name or site',
+                     onInitialize = I('function() { this.setValue(""); }')
+                   )),
+    hr(),
+    textInput(
+      "NewMimeType",
+      label = "New Mime Type *",
+      placeholder = "Create a New Mimetype"),
+    hr(),
+    textInput(
+      "NewFormatName",
+      label = "New Format Name *",
+      placeholder = "Create a New Format Name"),
+    hr(),
+    radioButtons(
+      "HeaderBoolean",
+      label = "Is There a Header ?", 
+      choices =  c("Yes", "No")
+    ),
+    hr(),
+    textInput( # I should Render UI only if Header = TRUE
+      "SkipLines",
+      label = "Skip",
+      placeholder = "Enter number of header lines to skip."),
+    hr(),
+    textAreaInput(
+      "FormatNotes",
+      label = "Notes",
+      height = '150px'
+    ),
+    actionButton("createFormatRecord", label = "Create Format Record"),
+    p("* Denotes a Required Field"),
+    hr(),
+    verbatimTextOutput("FormatRecordOut")
+)
+
+
diff --git a/shiny/Data-Ingest/ui_files/homepage_ui.R b/shiny/Data-Ingest/ui_files/homepage_ui.R
new file mode 100644
index 00000000000..98e921b30f3
--- /dev/null
+++ b/shiny/Data-Ingest/ui_files/homepage_ui.R
@@ -0,0 +1,7 @@
+box(width = 12,
+  title = h2("Welcome to the PEcAn Data Ingest Workflow."),
+  hr(),
+  h3("This application is designed to make it easier for researchers to import data from local and remote sources into PEcAn.
+    To do so, this application combines two methods of ingesting data with an improved ingest workflow that registers new data with
+    the BETY database. To begin, please select one method of importing data from in the sidebar on the left.")
+)
\ No newline at end of file
diff --git a/shiny/Data-Ingest/ui_files/ingest_workflow_ui.R b/shiny/Data-Ingest/ui_files/ingest_workflow_ui.R
new file mode 100644
index 00000000000..aa0e52ebbbd
--- /dev/null
+++ b/shiny/Data-Ingest/ui_files/ingest_workflow_ui.R
@@ -0,0 +1,195 @@
+fluidPage(
+fluidRow(
+## 1. D1 Download or Local Upload
+box(
+  title = h2("1. Select Files"), width = 4, solidHeader = TRUE, status = "success", collapsible = TRUE,
+  shinyWidgets::radioGroupButtons("inputMethod", label = "Select Input Method", 
+                                 choices = c("DataONE", "Local Files"), status = "success", selected = NULL),
+  shinyjs::hidden(source_ui("d1_download_ui.R")),
+  shinyjs::hidden(source_ui("local_file_upload_ui.R"))
+),
+
+### 2. Inputs
+shinyjs::hidden(
+  div(id = "input_record_box",
+  box(
+  title = h2("2. Input Record"), width = 8, collapsible = TRUE, solidHeader = TRUE, status = "success",
+  fluidRow(column(6,
+  selectizeInput("InputSiteName", label = "Site *", choices = NULL,
+                 options = list(
+                   placeholder = 'Please search or select a site below',
+                   onInitialize = I('function() { this.setValue(""); }')
+                 )
+  )
+  ),
+  column(6,
+  selectizeInput("InputParentName", label = "Parent *", choices = NULL,
+                 options = list(
+                   placeholder = 'Please search inputs by name or site',
+                   onInitialize = I('function() { this.setValue(""); }')
+                 )
+  )
+  )),
+  textInput("InputName",
+            label = "Name *",
+            placeholder = ""),
+  hr(),
+  fluidRow(column(6,
+  selectizeInput("InputFormatName", label = "Format *", choices = NULL,
+                 options = list(
+                   placeholder = 'Please search Formats by name',
+                   onInitialize = I('function() { this.setValue(""); }')
+                 )
+  )
+  ),
+  column(6,
+  selectizeInput("MimetypeNameCurrent", label = "Corresponding Mimetype *", choices = NULL,
+               options = list(
+                 placeholder = 'Please search mimetypes by name',
+                 onInitialize = I('function() { this.setValue(""); }')
+               )
+  )
+  )
+  ),
+  p("or"),
+  shinyWidgets::dropdownButton(circle = FALSE, label = "Create New Format", width = '350px',
+      box(width = '350px', solidHeader = TRUE, status = "warning",
+        selectizeInput("MimetypeName", label = "Mimetype *", choices = NULL,
+                     options = list(
+                       placeholder = 'Please search formats by name or site',
+                       onInitialize = I('function() { this.setValue(""); }')
+                     )),
+      p("or"),
+      a(id = "betyURL", "Create New Mimetype", href = "https://www.betydb.org/formats/new", target = "_blank"),
+      hr(),
+      textInput(
+        "NewFormatName",
+        label = "New Format Name *",
+        placeholder = "Create a New Format Name"),
+      radioButtons(
+        "HeaderBoolean",
+        label = "Is There a Header ?",
+        choices =  c("Yes", "No")
+      ),
+      textInput( # I should Render UI only if Header = TRUE
+        "SkipLines",
+        label = "Skip",
+        placeholder = "Enter number of header lines to skip."),
+      textAreaInput(
+        "FormatNotes",
+        label = "Notes",
+        height = '75px'
+      ),
+      actionBttn("FormatRecordDone", label = "Done", color = "warning", size = "sm"),
+      p("* Denotes a Required Field")
+    )
+    ),
+  hr(),
+fluidRow(column(6,
+  dateInput(
+    "InputStartDate",
+    label = "Start Date",
+    format = "yyyy-mm-dd",
+    startview = "decade"
+  )
+  ),
+  column(3,
+  shinyTime::timeInput("StartTimeInput",
+                       label = "Start Time (HH-MM)",
+                       seconds = FALSE)
+  ),
+  column(3 ## Now I'm not sure if we need timezone since sites are known
+   # selectizeInput("Timezone", label = "Timezone *", choices = NULL,
+   #                options = list(
+   #                  placeholder = 'Please search inputs by name or site',
+   #                  onInitialize = I('function() { this.setValue(""); }')
+   #                ))
+  )
+  ),
+fluidRow(column(6,
+  dateInput(
+    'InputEndDate',
+    label = 'End Date',
+    format = 'yyyy-mm-dd',
+    startview = 'decade'
+  )
+  ),
+  column(3,
+  shinyTime::timeInput("EndTimeInput",
+                       label = "End Time (HH-MM)",
+                       seconds = FALSE)
+  ),
+column(3)), # Empty Space
+  hr(),
+  textAreaInput("InputNotes",
+                label = "Notes",
+                height = '50px'),
+fluidRow(
+  column(10),
+  column(2,
+         actionBttn("nextFromInput", 
+                    label = "Next Step", 
+                    color = "success", 
+                    size = "sm")
+  )
+),
+  p("* Denotes a Required Field")
+  )
+)
+)
+),#End Fluid Row
+fluidRow(
+  ## 4. Formats-Variables
+shinyjs::hidden(  
+div(id = "formats.vars_box",  
+  box(title = h2("3. Formats-Variables"), width = 12, solidHeader = TRUE, status = "success", collapsible = TRUE, collapsed = FALSE,
+      fluidRow(column(3,
+                      selectizeInput("pecan_var", choices = NULL, label = "Variable",
+                                     options = list(
+                                       placeholder = 'Please search for a variable in PEcAn',
+                                       onInitialize = I('function() { this.setValue(""); }')
+                                     )
+                      )
+      ),
+      column(3,
+             textInput("var_name", label = "Name")
+      ),
+      column(2,
+             textInput("var_unit", label = "Unit")
+      ),
+      column(2,
+             textInput("storage_type", label = "Storage Type", placeholder = "e.g. POSIX code")
+      ),
+      column(2,
+             textInput("col_num", label = "Column Number")
+      )
+      ),
+      actionButton("register_variable", label = "Add Variable"),
+      DT::DTOutput("format_vars_df")
+  )
+),
+div(id = "finishButton_d1",
+  fluidRow(
+    column(10),
+    column(2,
+           actionBttn("complete_ingest_d1", 
+                      label = "Complete Ingest of DataONE Files", 
+                      color = "success", 
+                      size = "md")
+    )
+  )
+),
+div(id = "finishButton_lcl",
+    fluidRow(
+      column(10),
+      column(2,
+             actionBttn("complete_ingest_lcl", 
+                        label = "Complete Ingest of Local Files", 
+                        color = "success", 
+                        size = "md")
+      )
+    )
+)
+)
+)
+)# End Fluid Page
\ No newline at end of file
diff --git a/shiny/Data-Ingest/ui_files/input_record_ui.R b/shiny/Data-Ingest/ui_files/input_record_ui.R
new file mode 100644
index 00000000000..d7d05cf9f36
--- /dev/null
+++ b/shiny/Data-Ingest/ui_files/input_record_ui.R
@@ -0,0 +1,129 @@
+fluidRow(title = "New Input",
+   box(title = h2("New Input"), width = 4, collapsible = TRUE, 
+     hr(),
+     selectizeInput("InputSiteName", label = "Site *", choices = NULL,
+                    options = list(
+                      placeholder = 'Please search or select a site below',
+                      onInitialize = I('function() { this.setValue(""); }')
+                      )),
+     hr(),
+     selectizeInput("InputParentName", label = "Parent", choices = NULL,
+                    options = list(
+                      placeholder = 'Please search inputs by name or site',
+                      onInitialize = I('function() { this.setValue(""); }')
+                    )),
+     hr(),
+     textInput(
+       "InputName",
+       label = "Name *",
+       placeholder = ""
+     ),
+     hr(),
+     selectizeInput("InputFormatName", label = "Format*", choices = NULL,
+                    options = list(
+                      placeholder = 'Please search Formats by name',
+                      onInitialize = I('function() { this.setValue(""); }')
+     )),
+     hr(),
+     dateInput(
+       "InputStartDate",
+       label = "Start Date *",
+       format = "yyyy-mm-dd",
+       startview = "decade"
+     ),
+     shinyTime::timeInput(
+       "StartTimeInput",
+       label = "Start Time (Hours - Minutes) *",
+       seconds = FALSE
+     ),
+     dateInput(
+       'InputEndDate',
+       label = 'End Date *',
+       format = 'yyyy-mm-dd',
+       startview = 'decade'
+     ),
+     shinyTime::timeInput(
+       "EndTimeInput",
+       label = "End Time (Hours-Minutes) *",
+       seconds = FALSE
+     ),
+     textInput(
+       "Timezone",
+       label = "Timezone (UTC) *",
+       placeholder = "UTC +/-"
+     ),
+     hr(),
+     textAreaInput(
+       "InputNotes",
+       label = "Notes",
+       height = '150px'
+     ),
+     actionButton("createInput", label = "Create Input"), # Not sure if I want this here or only available when all forms are filled in.
+     p("* Denotes a Required Field"),
+     hr(),
+     verbatimTextOutput("summInputs")
+   ),
+   box(title = h2("DbFiles Record"), width = 4, collapsible = TRUE, collapsed = TRUE, 
+       hr(),
+       selectizeInput("InputMachineName", label = "Machine *", choices = NULL,  #remember to set default to local
+                      options = list(
+                        placeholder = 'Please search machine by name',
+                        onInitialize = I('function() { this.setValue(""); }')
+                        )),
+       hr(),
+       textInput(
+         "InputFilePath",
+         label = "File Path *",
+         placeholder = "This file path will be autogenerated by the download process. The user can edit the filepath here?"),
+       hr(),
+       textInput(
+         "InputFileName",
+         label = "File Name *",
+         placeholder = "This file name will be displayed from the download process. The user can edit the file name here"),
+       actionButton("createDBFilesRecord", label = "Create dbFiles Record"),
+       p("* Denotes a Required Field"),
+       hr(),
+       verbatimTextOutput("dbFilesRecordOut")
+       ),
+   box(title = h2("Format ID"), width = 4, collapsible = TRUE, collapsed = TRUE,
+       hr(),
+       selectizeInput("MimetypeName", label = "Mimetype *", choices = NULL,
+                      options = list(
+                        placeholder = 'Please search inputs by name or site',
+                        onInitialize = I('function() { this.setValue(""); }')
+                      )),
+       hr(),
+       textInput(
+         "NewMimeType",
+         label = "New Mime Type *",
+         placeholder = "Create a New Mimetype"),
+       hr(),
+       textInput(
+         "NewFormatName",
+         label = "New Format Name *",
+         placeholder = "Create a New Format Name"),
+       hr(),
+       radioButtons(
+         "HeaderBoolean",
+         label = "Is There a Header ?", 
+         choices =  c("Yes", "No")
+       ),
+       hr(),
+       textInput( # I should Render UI only if Header = TRUE
+         "SkipLines",
+         label = "Skip",
+         placeholder = "Enter number of header lines to skip."),
+       hr(),
+       textAreaInput(
+         "FormatNotes",
+         label = "Notes",
+         height = '150px'
+       ),
+       actionButton("createFormatRecord", label = "Create Format Record"),
+       p("* Denotes a Required Field"),
+       hr(),
+       verbatimTextOutput("FormatRecordOut")
+       )
+  
+ )
+
diff --git a/shiny/Data-Ingest/ui_files/local_file_upload_ui.R b/shiny/Data-Ingest/ui_files/local_file_upload_ui.R
new file mode 100644
index 00000000000..bff8c39d54c
--- /dev/null
+++ b/shiny/Data-Ingest/ui_files/local_file_upload_ui.R
@@ -0,0 +1,30 @@
+div(id = "lcl_ui",
+  tagList(
+      fileInput(
+        inputId = "file",
+        label = "Upload Local Files", 
+        accept = NULL,
+        multiple = TRUE,
+        placeholder = "Drag and drop files here"
+      ),
+      DT::DTOutput("dtfiles"),
+     fluidRow(
+       column(8),
+       column(4,
+              div(id = "nextFromLocal_div",
+                  actionBttn(inputId = "nextFromLocal", 
+                             label = "Next Step", 
+                             size = "sm", 
+                             color = "success")
+              )
+       )
+     ),
+     shinyjs::hidden(
+       div(id = "local_path_out",
+           hr(),
+      p("Location of Downloaded Files:"),
+      verbatimTextOutput("LocaldbfilesPath")
+       )
+     )
+    )
+  )
\ No newline at end of file
diff --git a/shiny/Data-Ingest/ui_files/sidebar_ui.R b/shiny/Data-Ingest/ui_files/sidebar_ui.R
new file mode 100644
index 00000000000..88b5bec519c
--- /dev/null
+++ b/shiny/Data-Ingest/ui_files/sidebar_ui.R
@@ -0,0 +1,23 @@
+sidebarMenu(
+ 
+  menuItem(
+    "Ingest Workflow",
+    tabName = "ingestWorkflow",
+    icon = icon("database", lib = "font-awesome")
+  ),
+  menuItem(
+    "About",
+    tabName = "About",
+    icon = icon("info-circle", lib = "font-awesome")
+  ),
+  shinyjs::hidden(
+    div(id = "select_in",
+      actionBttn("d1Input", label = "Import from DataONE",
+                 icon = icon("download", lib = "font-awesome"),
+                 size = "xs", color = "success"),
+      actionBttn("lclUpload", label = "Upload Local Files",
+                 icon = icon("upload", lib = "font-awesome"),
+                 size = "xs", color = "success")
+    )
+  )
+)
diff --git a/shiny/Data-Ingest/ui_utils.R b/shiny/Data-Ingest/ui_utils.R
new file mode 100644
index 00000000000..daea5e9797c
--- /dev/null
+++ b/shiny/Data-Ingest/ui_utils.R
@@ -0,0 +1,7 @@
+source_ui <- function(...) {
+  source(
+    file.path("ui_files", ...),
+    local = TRUE
+  )$value
+}
+
diff --git a/shiny/Elicitation/server.R b/shiny/Elicitation/server.R
index 1ee922a3d82..cfcc78805fd 100644
--- a/shiny/Elicitation/server.R
+++ b/shiny/Elicitation/server.R
@@ -1,7 +1,17 @@
-library(shiny)
-library(PEcAn.DB)
-library(ggplot2)
+lapply(c( "shiny",
+          "ggplot"
+          ),function(pkg){
+            if (!(pkg %in% installed.packages()[,1])){
+                install.packages(pkg)
+              }
+            library(pkg,character.only = TRUE,quietly = TRUE)
+          }
+       )
+if(!("SHELF" %in% install.packages()[,1])) devtools::install_github('OakleyJ/SHELF')
+
 library(SHELF)
+library(PEcAn.DB)
+
 
 # Define server logic
 server <- shinyServer(function(input, output, session) {
diff --git a/shiny/Pecan.depend/SERVER.R b/shiny/Pecan.depend/SERVER.R
new file mode 100644
index 00000000000..82d66f50976
--- /dev/null
+++ b/shiny/Pecan.depend/SERVER.R
@@ -0,0 +1,314 @@
+optionsDT_fixe <- list(paging = FALSE, searching = FALSE, bInfo = FALSE, search.caseInsensitive = TRUE)
+
+
+shinyServer(function(input, output, session) {
+    observe({
+        input$GOPackage
+        isolate({
+            # print(input$Pack)
+            if (length(input$packages) > 0) {
+                data <- Pck.load.to.vis(input$packages)
+                
+                func <- c(input$packages)
+                # print(func)
+                
+                
+                nb.func.slave = NULL
+                nb.func.master = NULL
+                for (i in 1:length(func)) {
+                  
+                  id.call <- as.numeric(as.character(data$Nomfun$id[which(func[i] == data$Nomfun$label)]))
+                  
+                  id.call.slave <- as.numeric(as.character(data$fromto$from[which(id.call == data$fromto$to)]))
+                  id.call.master <- as.numeric(as.character(data$fromto$from[which(id.call == data$fromto$from)]))
+                  
+                  nb.call <- length(as.character(data$Nomfun$label[id.call.slave]))
+                  nb.func.slave[i] = nb.call
+                  
+                  nb.call <- length(as.character(data$Nomfun$label[id.call.master]))
+                  nb.func.master[i] = nb.call
+                  
+                }
+                
+                optionsDT_fixe$drawCallback <- I("function( settings ) {document.getElementById('tabledep').style.width = '400px';}")
+                ## Output first graph
+                df <- data.frame(Package = func, Import = nb.func.master, `Imported by` = nb.func.slave)
+                
+                
+                
+                output$tabledep <- renderDataTable({
+                  df
+                }, options = optionsDT_fixe)
+                
+                output$main_plot <- renderVisNetwork({
+                  data$fromto%>%filter(title%>%gsub('<p>','',.)%>%gsub('</p>','',.)%in%input$variablesp)->data$fromto
+                  if (nrow(data$fromto)){
+                                      net <- plot(data, block = TRUE)
+                  
+                  # add legend
+                  data_legend <- unique(data$fromto[, c("title", "color")])
+                  data_legend$label <- gsub("<p>", "", data_legend$title, fixed = TRUE)
+                  data_legend$label <- gsub("</p>", "", data_legend$label, fixed = TRUE)
+                  data_legend$title <- NULL
+                  data_legend$arrows <- "to"
+                  
+                  net %>%
+                    visLegend(addEdges = data_legend, useGroups = FALSE, width = 0.1)
+                  }
+
+                  
+                })
+                curentd1 <<- data
+                output$titledatatabel <- renderText({
+                  "Dependencies between package(s)"
+                })
+                
+            }
+        })
+    })
+    
+    
+    observe({
+        current.package <- input$main_plot_selected
+        current.package <- as.character(curentd1$Nomfun[as.numeric(current.package), "label"])
+        updateSelectizeInput(session, "package", NULL, choices = installed.packages()[, 1]%>%grep("^PEcAn",.,value = T,ignore.case = T), selected = current.package)
+    })
+    
+    observe({
+        input$GOFunc2
+        isolate({
+            if (input$package != "" && input$GOFunc2 > 0) {
+                
+                func <- input$package
+                # print(func)
+                func
+                
+                if (!func %in% installed.packages()[, 1]) {
+                  install.packages(func)
+                }
+                library(func, character.only = TRUE)
+                dep1 <- envirDependencies(paste0("package:", func))
+                nb.fun <- length(dep1$Nomfun$label)
+                
+                
+                updateTabsetPanel(session, "Tabsetpan", selected = "Functions")
+                optionsDT_fixe$drawCallback <- I("function( settings ) {document.getElementById('datatable2').style.width = '100px';}")
+                output$datatable2 <- renderDataTable(data.frame(Number.of.functions = nb.fun), options = optionsDT_fixe)
+                
+                output$zoomin <- renderText(paste("Zoom on package ", func))
+                output$info <- renderText(paste("Information on package ", func))
+                curentd3 <<- func
+                
+                output$main_plot1 <- renderVisNetwork({
+                  plot(dep1, block = TRUE)
+                })
+                curentd2 <<- dep1
+            }
+        })
+    })
+    
+    observe({
+        input$GOFunc1
+        isolate({
+            if (!is.null(input$main_plot_selected) && input$main_plot_selected != "" && input$GOFunc1 > 0) {
+                
+                func <- as.character(curentd1$Nomfun$label[input$main_plot_selected == curentd1$Nomfun$id])
+                # print(func)
+                func
+                
+                if (!func %in% installed.packages()[, 1]) {
+                  install.packages(func)
+                }
+                library(func, character.only = TRUE)
+                dep1 <- envirDependencies(paste0("package:", func))
+                nb.fun <- length(dep1$Nomfun$label)
+                
+                
+                updateTabsetPanel(session, "Tabsetpan", selected = "Functions")
+                optionsDT_fixe$drawCallback <- I("function( settings ) {document.getElementById('datatable2').style.width = '100px';}")
+                output$datatable2 <- renderDataTable(data.frame(Number.of.functions = nb.fun), options = optionsDT_fixe)
+                
+                output$zoomin <- renderText(paste("Zoom on package : ", func))
+                output$info <- renderText(paste("Information on : ", func))
+                curentd3 <<- func
+                
+                output$main_plot1 <- renderVisNetwork({
+                  plot(dep1, block = TRUE)
+                })
+                curentd2 <<- dep1
+            }
+        })
+    })
+    
+    ### chossefunction
+    
+    observe({
+        input$chargedf
+        isolate({
+            input$packageslist
+            sapply(input$packageslist, function(x) {
+                library(x, character.only = TRUE)
+            })
+            allFun <- unique(unlist(sapply(input$packageslist, function(x) {
+                allFunctionEnv(paste0("package:", x))
+            })))
+            
+            updateSelectizeInput(session, inputId = "functionlist", choices = allFun)
+        })
+    })
+    
+    output$chossefunctionplot <- renderVisNetwork({
+        input$makegraph
+        
+        isolate({
+            if (input$makegraph >= 1) {
+                
+                dep<-my.allDepFunction(input$packageslist, unlist(strsplit(input$functionlist, split = ";")))
+                #- lets exlude the ones in the base or more widely used ones
+               # which(dep[["Nomfun"]]$label%in%c('papply','stop','warning','logger.warn','logger.error','logger.debug','logger.severe','logger.info'))->excludes
+              #  dep[["fromto"]]<-(dep[["fromto"]])%>%dplyr::filter(!(from%in%excludes))%>%dplyr::filter(!(to%in%excludes))
+                #- nolink
+               # which(!(dep[["Nomfun"]]$id%in%as.numeric(unlist(dep[["fromto"]]))))->nolinks
+              #  dep[["Nomfun"]]<-dep[["Nomfun"]]%>%dplyr::filter(!(id%in%c(excludes,nolinks)))
+                #-- plotting
+                 visNetwork(dep[[1]], dep[[2]])%>%
+                       visGroups()%>%
+                       visOptions(selectedBy = "group",
+                                  collapse = TRUE,
+                                  highlightNearest = TRUE, 
+                                  nodesIdSelection = list(enabled = TRUE))%>%
+                   visExport() %>%
+                   visPhysics(stabilization=list(iterations=100))%>%
+                   visEdges(arrows =list(from = list(enabled = TRUE)),
+                            color = list(color = "lightblue", highlight = "red")) %>%
+                   visLegend(zoom = T,width = 0.1)->netw
+                 if (input$igraphcheck)
+                   netw%>%visIgraphLayout()->netw
+                 return(netw)
+                 
+            }
+        })
+        
+    })
+    
+    observeEvent(input$showsourcebtn,{
+      if (length(isolate(input$packageslist))>0){
+        dep<-my.allDepFunction(isolate(input$packageslist), unlist(strsplit(input$functionlist, split = ";")))
+        showModal(
+          modalDialog(
+            # Output: Tabset w/ plot, summary, and table ----
+            tabsetPanel(type = "tabs",
+                        tabPanel("Source code", fluidRow( column(12,verbatimTextOutput("console")))),
+                        tabPanel("Variable definitions timelines",  plotOutput('VDT',width = "100%",height = "500px"))
+
+            ),
+            size='l',
+            easyClose = T
+          )
+        )
+        
+      }
+      
+      #----------- finding and printing the source code
+      srcode<-getAnywhere( dep[["Nomfun"]][input$chossefunctionplot_selected,2]%>%as.character())
+      #readScript(txt= paste(deparse(body()%>%as.character())))
+      
+      srcode$objs[[1]]%>%
+        body(.)%>%
+        as.list()%>%
+        #deparse(.)%>%
+        paste(.,collapse = " \n ")%>%
+        readScript(txt=.)->sc
+      
+      output$console<-renderPrint({
+        srcode
+      })
+      output$consoleH<-renderPrint({
+        help( dep[["Nomfun"]][input$chossefunctionplot_selected,2]%>%as.character())->shelp
+        utils:::print.help_files_with_topic(shelp)
+      })
+      #Variable definitions timelines
+      output$VDT<-renderPlot({
+        
+        dtm = getDetailedTimelines(sc, getInputs(sc))
+        #-plotting
+        dtm$start<-ifelse(dtm$defined,dtm$step,NA)
+        dtm$end<-ifelse(dtm$used,dtm$step,NA)
+        dtm%>%filter(!is.na(start) | !is.na(end))->dtm
+        
+        
+        dtm%>%
+          ggplot()+
+          geom_point(aes(x=start,y=var,color="Start"),shape=16,size=5)+
+          geom_point(aes(x=end,y=var,color="End"),size=5,shape=2)+
+          scale_color_manual(values=c("red","blue"),name="")+
+          theme_minimal(base_size = 16)+
+          labs(x="Steps",y="variable")+
+          theme(legend.position = "top")
+        
+      })
+    })
+    
+    observe({
+        
+        if (!is.null(input$main_plot1_selected) && input$main_plot1_selected != "") {
+            isolate({
+                pck <- curentd3
+                
+                # print(pck)
+                
+                func <- as.character(curentd2$Nomfun$label[input$main_plot1_selected == curentd2$Nomfun$id])
+                # print(func)
+                try(add.html.help(pck, func), TRUE)
+                
+                if (length(htmlTreeParse(paste0(getwd(), "/temp.html"))$children$html) > 0) {
+                  output$help <- renderUI(includeHTML(paste0(getwd(), "/temp.html")))
+                  
+                } else {
+                  output$help <- renderUI("Not available help for this function")
+                }
+            })
+        } else {
+            
+            output$help <- renderUI("Select a function")
+        }
+        
+    })
+    
+    observe({
+        
+        if (!is.null(input$main_plot_selected) && input$main_plot_selected != "") {
+            
+            func <- as.character(curentd1$Nomfun$label[input$main_plot_selected == curentd1$Nomfun$id])
+            
+            output$Groupebutton <- renderUI({
+                
+                div(hr(), actionButton("GOFunc1", paste0("Launch zoom on : ", func), icon = icon("line-chart")), align = "center")
+                
+            })
+        } else {
+            output$Groupebutton <- renderUI({
+                NULL
+            })
+        }
+        
+    })
+    
+    
+    
+    observe({
+        
+        input$GObott
+        # input$file1 will be NULL initially. After the user selects and uploads a file, it will be a data frame with 'name', 'size',
+        # 'type', and 'datapath' columns. The 'datapath' column will contain the local filenames where the data can be found.
+        
+        inFile <- input$file1
+        
+        if (!is.null(inFile)) {
+            dep <- data.graph.script(inFile$datapath)
+            output$plotscript <- renderVisNetwork({
+                plot(dep, block = TRUE)
+            })
+        }
+    })
+})
diff --git a/shiny/Pecan.depend/UI.R b/shiny/Pecan.depend/UI.R
new file mode 100644
index 00000000000..082a58d8942
--- /dev/null
+++ b/shiny/Pecan.depend/UI.R
@@ -0,0 +1,145 @@
+dashboardPage(
+  dashboardHeader(title = "PEcAn dependencies graphs"),
+  dashboardSidebar(sidebarMenu(id = "Tabsetpan",
+                               menuItem("Packages", tabName = "Packages", icon = icon("archive")),
+                               conditionalPanel(condition = "input.Tabsetpan === 'Packages'",
+                                                selectInput('packages', "Package(s) :", choices = installed.packages()[,1]%>%grep("^PEcAn",.,value = T,ignore.case = T), multiple = T, width = "100%"),
+                                                div(actionButton("GOPackage", "Go !",icon = icon("line-chart")), align = "center")
+                               ),
+                               menuItem("Functions", tabName = "Functions", icon = icon("code")),
+                               conditionalPanel(condition = "input.Tabsetpan === 'Functions'",
+                                                selectInput('package', "Package : ", choices = installed.packages()[,1]%>%grep("^PEcAn",.,value = T,ignore.case = T), multiple = FALSE, width = "100%"),
+                                                div(actionButton("GOFunc2", "Go !",icon = icon("line-chart")), align = "center")
+                               ),
+                               menuItem("Custom", tabName = "Custom", icon = icon("th"))
+                               
+  )),
+  dashboardBody(
+    # Boxes need to be put in a row (or column)
+    tags$head(tags$link(rel='stylesheet', type='text/css', href='style.css')),
+    tabItems(
+      # First tab content
+      tabItem(tabName = "Packages",
+              # fluidRow(
+              #   column(3, div(h3('Package(s) selection :'), align = "center")),
+              #   column(6, br(), selectInput('packages', NULL, choices = installed.packages()[,1], multiple = T, width = "100%")),
+              #   column(3, br(), div(actionButton("GOPackage", "Launch",icon = icon("line-chart")), align = "center"))
+              # ),
+              # hr(),
+              
+              fluidRow(
+                box(
+                  solidHeader = TRUE, collapsible = TRUE, title = "Dependencies between package(s)",
+                  status = "primary",
+                  checkboxGroupInput("variablesp", "Dependencies to show:",
+                                     c("Imports" = "Imports",
+                                       "Suggests" = "Suggests",
+                                       "Depends" = "Depends"),selected = "Depends"),
+                  visNetworkOutput("main_plot", width = "100%",height = "750px"),
+                  br()
+                  ,width = 12
+                ),
+                box(
+                  solidHeader = TRUE, collapsible = TRUE, title = "Informations",
+                  status = "primary",
+                  div(
+                    dataTableOutput("tabledep"),
+                    uiOutput("Groupebutton"),
+                    align="center"
+                  ), 
+                  width=12)
+              )
+              
+      ),
+      tabItem(tabName = "Functions",
+              fluidRow(
+                box(
+                  solidHeader = TRUE, collapsible = TRUE, title = "Dependencies between functions",
+                  status = "primary",
+                  div(h4(textOutput("zoomin")), align = "center"),
+                  visNetworkOutput("main_plot1", width = "100%",height = "750px"),
+                  br()
+                  ,width = 12
+                ),
+                box(
+                  solidHeader = TRUE, collapsible = TRUE, title = "Informations",
+                  status = "primary",
+                  div(
+                    # h4(textOutput("info")),
+                    dataTableOutput("datatable2")
+                    ,align="center"
+                  ),
+                  width=12)
+              ),
+              
+              fluidRow(
+                box(
+                  uiOutput("help"),width = 12
+                )
+              )
+      ),
+      #                 tabPanel("Script",
+      #                          
+      #                          
+      #                          fluidRow(
+      #                            box(
+      #                              fileInput('file1', 'Choose R File',
+      #                                        accept=NULL),
+      #                              visNetworkOutput("plotscript", width = "100%",height = "700px")
+      #                              ,width = 12)
+      #                          )
+      #                 ),
+      
+      tabItem(tabName = "Custom",
+              
+              
+              fluidRow(
+                box(
+                  fluidRow(
+                    column(width=4,
+                           pickerInput(inputId = "packageslist" , "Package(s) :", choices = installed.packages()[,1]%>%grep("^PEcAn",.,value = T,ignore.case = T), multiple = TRUE,
+                                       options = list(
+                                         `actions-box` = TRUE,
+                                         `live-search` = TRUE)
+                           )
+                    ),
+                    column(width=2, 
+                           br(), div(actionButton("chargedf", "Find functions", style = "padding: 8px 20px 8px 20px;"),align="center")
+                    ),
+                    column(width=4,
+                           #selectizeInput(inputId = "functionlist" , "Function(s) :", choices = NULL, multiple = TRUE),
+                           pickerInput(
+                             inputId = "functionlist",
+                             label = "Function(s) :", 
+                             choices = NULL,
+                             options = list(
+                               `actions-box` = TRUE,
+                               `live-search` = TRUE), 
+                             multiple = TRUE
+                           )
+                    ),
+                    column(width=2, 
+                           br(), div(actionButton("makegraph", "Make graph", style = "padding: 8px 20px 8px 20px;"),align = "center")
+                    )
+                  ),
+                  fluidRow(
+                    column(4,checkboxInput('igraphcheck','Igraph Layout (more stable layout)',value = F)),
+                    column(4, actionButton("showsourcebtn", "Show the source", style = "padding: 8px 20px 8px 20px;")),
+                    column(4)
+                    
+                  ),
+                 
+                  hr(),
+                  visNetworkOutput("chossefunctionplot", width = "100%",height = "750px"),
+                  br(),
+                  width = 12)
+              )
+      )
+      
+      
+    )
+  )
+)
+
+
+
diff --git a/shiny/Pecan.depend/global.R b/shiny/Pecan.depend/global.R
new file mode 100644
index 00000000000..62e498c7d04
--- /dev/null
+++ b/shiny/Pecan.depend/global.R
@@ -0,0 +1,70 @@
+#install what we need
+lapply(c('dplyr',
+         'shinyWidgets',
+         'CodeDepends',
+         'visNetwork',
+         'ggplot2',
+         'XML',
+         'shinydashboard'),function(pkg){
+    if (!(pkg %in% installed.packages()[,1])){
+          install.packages(pkg)
+          }
+           library(pkg,character.only = TRUE,quietly = TRUE)
+    }
+)
+
+if (!('DependenciesGraphs' %in% installed.packages()[,1])) devtools::install_github("datastorm-open/DependenciesGraphs")
+
+
+curentd2 <<- NULL
+curentd1 <<- NULL
+curentd3 <<- NULL
+#------------- My dependen - I added group to this
+my.allDepFunction<-function (envir, name.functions) 
+{
+  envir2 <- paste0("package:", envir)
+  toutfonc <- linksForOne(envir2, name.functions)
+  link <- toutfonc
+  functions.list <- unique(as.character(unlist(c(toutfonc))))
+  Visdata <- list()
+  Nomfun <- functions.list
+  #--- source env
+  envs.found<-lapply(functions.list,find)
+  #-taking out the my own all functions packge
+  lapply(envs.found, function(ll){
+    ll[which(!(ll%in%c("package:Pecan.functions")))][1]->tmp
+    if (length(tmp)!=0){
+      return((strsplit(tmp,":")[[1]])[2])
+    }else{
+      return("Pecan.functions")
+    }
+    
+  })%>%unlist()->envs.fi
+  Nomfun <- data.frame(cbind(id = 1:length(Nomfun), label = Nomfun,group=envs.fi))
+  
+  if (!is.null(link)) {
+    fromto <- matrix(0, ncol = dim(link)[2], nrow = dim(link)[1])
+    if (length(fromto) > 0) {
+      for (i in 1:dim(link)[1]) {
+        fromto[i, 1] <- which(as.character(link[i, 2]) == 
+                                Nomfun[, 2])
+        fromto[i, 2] <- which(as.character(link[i, 1]) == 
+                                Nomfun[, 2])
+        if (dim(link)[2] > 2) {
+          fromto[i, 3:length(link[i, ])] <- link[i, 3:length(link[i, 
+                                                                  ])]
+        }
+      }
+    }
+  }
+  else {
+    fromto <- cbind(0, 0)
+  }
+  fromto <- data.frame(fromto)
+  names(fromto) <- c("from", "to")
+  Visdata$Nomfun <- Nomfun
+  Visdata$fromto <- fromto
+  class(Visdata) <- "dependenciesGraphs"
+  return(Visdata)
+}
+
diff --git a/shiny/Pecan.depend/www/style.css b/shiny/Pecan.depend/www/style.css
new file mode 100644
index 00000000000..3fec3f65b09
--- /dev/null
+++ b/shiny/Pecan.depend/www/style.css
@@ -0,0 +1,45 @@
+button.btn.btn-default.action-button {
+display:inline-block;
+padding:0.7em 1.7em;
+margin:0 0.3em 0.3em 0;
+border-radius:0.2em;
+box-sizing: border-box;
+text-decoration:none;
+font-family:'Roboto',sans-serif;
+font-weight:400;
+color:#FFFFFF;
+background-color:#3cb0fd;
+box-shadow:inset 0 -0.6em 1em -0.35em rgba(0,0,0,0.17),inset 0 0.6em 2em -0.3em rgba(255,255,255,0.15),inset 0 0 0em 0.05em rgba(255,255,255,0.12);
+text-align:center;
+position:relative;
+}
+
+button.btn.btn-default.action-button:hover {
+  background: #3cb0fd;
+  background-image: -webkit-linear-gradient(top, #3cb0fd, #3498db);
+  background-image: -moz-linear-gradient(top, #3cb0fd, #3498db);
+  background-image: -ms-linear-gradient(top, #3cb0fd, #3498db);
+  background-image: -o-linear-gradient(top, #3cb0fd, #3498db);
+  background-image: linear-gradient(to bottom, #3cb0fd, #3498db);
+  text-decoration: none;
+}
+
+
+
+
+
+
+  table.dataTable tr.selected td, table.dataTable td.selected {
+                    background-color: #2F373E !important;
+                    color: white;
+                    border-style: solid;
+                    border-color: white;
+                    border: 2px;
+                 }
+ table.dataTable.hover tbody tr:hover, table.dataTable.display tbody tr:hover {
+                   background-color: #2F373E !important;
+                    color: white !important;
+                    border-style: solid;
+                    border-color: white;
+                    border: 2px;
+                  }
\ No newline at end of file
diff --git a/shiny/README.md b/shiny/README.md
new file mode 100644
index 00000000000..b61515aec35
--- /dev/null
+++ b/shiny/README.md
@@ -0,0 +1,46 @@
+The Following Packages are Dependencies called from PEcAn Shiny Apps:
+Data-Ingest
+    PEcAn.data.land,
+    PEcAn.utils,
+    PEcAn.visualization,
+    shinydashboard,
+    dataone,
+    stringr,
+    DT,
+    shinytoastr,
+    shinyWidgets,
+    shinyjs
+PEcAn.Depends
+    dplyr,
+    shinyWidgets,
+    CodeDepends,
+    visNetwork,
+    ggplot2,
+    XML,
+    shinydashboard,
+    DependenciesGraphs
+Elicitation
+    SHELF,
+    ggplot
+BrownDog
+    leaflet,
+    RPostgreSQL,
+    PEcAn.DB,
+    PEcAn.visualization
+WorkflowPlot
+    shiny,
+    ggplot2,
+    plotly,
+    shinyjs,
+    dplyr,
+    reshape2,
+    purrr,
+    ncdf4,
+    scales,
+    lubridate,
+    shiny.themes,
+    PEcAn.visualization,
+    PEcAn.DB,
+    PEcAn.settings,
+    PEcAn.benchmark,
+    PEcAn.utils
diff --git a/shiny/ViewMet/server.R b/shiny/ViewMet/server.R
new file mode 100644
index 00000000000..ed4cd4325af
--- /dev/null
+++ b/shiny/ViewMet/server.R
@@ -0,0 +1,202 @@
+# ViewMet Server 
+lapply(c( "shiny",
+          "ggplot2",
+          "stringr",
+          "ncdf4",
+          "ncdf4.helpers",
+          "DT",
+          "plyr",
+          "dplyr"),function(pkg){
+            if (!(pkg %in% installed.packages()[,1])){
+              install.packages(pkg)
+            }
+            library(pkg,character.only = TRUE,quietly = TRUE)
+          }
+)
+
+lapply(c( "PEcAn.benchmark",
+          "PEcAn.visualization",
+          "PEcAn.logger",
+          "PEcAn.remote"),function(pkg){
+            library(pkg,character.only = TRUE,quietly = TRUE)
+          }
+)
+
+
+
+options(shiny.maxRequestSize=30*1024^2) #maximum file input size
+
+server <- function(input, output, session) {
+  
+  bety <- betyConnect()
+  rv <- reactiveValues()
+  
+  observe({
+    # Look in the database for all inputs that are in CF format 
+    # and grab their site ids
+    inputs <- tbl(bety, "inputs") %>% filter(format_id == 33) %>% collect 
+    updateSelectizeInput(session, "site.id", choices = sort(unique(inputs$site_id)))
+    
+  })
+  
+  
+  observeEvent({input$site.id}, ignoreInit = TRUE, {
+    
+    site <- input$site.id
+    PEcAn.logger::logger.debug("Site", site, "selected")
+    
+    if(is.na(as.numeric(site))){
+      full.paths <- ""
+    }else{
+      
+      # Given site id, get info about the input 
+      inputs <- tbl(bety, "inputs") %>% filter(format_id == 33) %>% 
+        filter(site_id == site) %>% collect
+      
+      # Check the machine
+      # If the machine is one of the three pecan servers then files that have
+      # dbfile entries for any of the three servers can be loaded 
+      host <- PEcAn.remote::fqdn()
+      if(host %in% c("test-pecan.bu.edu", "pecan1.bu.edu", "pecan2.bu.edu")){
+        host <- c("test-pecan.bu.edu", "pecan1.bu.edu", "pecan2.bu.edu")
+      }
+      machine <- tbl(bety, "machines") %>% filter(hostname %in% host) %>% collect
+      
+      dbfiles <- tbl(bety, "dbfiles") %>%
+        filter(container_type == "Input") %>%
+        filter(container_id %in% inputs$id) %>%
+        filter(machine_id %in% machine$id) %>%
+        collect 
+      
+      if(all(dim(dbfiles) == 0)){
+        full.paths <- ""
+      }else{
+        dbfiles <- dbfiles %>%
+          mutate(file = gsub("//", "/",file.path(file_path, file_name)))
+        
+        types <- unique(dbfiles$file_path) %>% basename() %>%
+          gsub(pattern = "\\_site_.*",replacement = "", x = .) %>%
+          unique() %>% sort()
+        
+        updateCheckboxGroupInput(session, "met", choices = types)
+        
+        paths <- unique(dbfiles$file)
+        full.paths <- c()
+        yrs <- c()
+        for(i in seq_along(paths)){
+          new.files <- dir(dirname(paths[i]), pattern = basename(paths[i]),
+                          full.names = TRUE)
+          yrs <- c(yrs, stringr::str_extract(new.files, pattern="[0-9]{4}"))
+          full.paths <- c(full.paths,new.files)
+        }
+        updateCheckboxGroupInput(session, "years", choices = sort(unique(yrs)))
+      }
+    }
+    rv$full.paths <- full.paths
+    
+  })
+  
+  # Once met and years are selected, the paths to available files on the server 
+  # will show in a tabel
+  observeEvent({
+    input$met 
+    input$years},{
+    
+    met <- input$met
+    years <- input$years
+    
+    full.paths <- rv$full.paths
+
+    load.paths <- c()
+    for(i in seq_along(met)){
+      new.paths <- full.paths[grep(paste0(met[i],"_site_"), full.paths)]
+      year_sub <- stringr::str_extract(new.paths, pattern="[0-9]{4}") %in% years
+      new.paths <- new.paths[year_sub]
+      load.paths <- c(load.paths, new.paths)
+    }
+    rv$load.paths <- load.paths
+  })
+  
+  
+  observeEvent({rv$load.paths},{
+    output$results_table <- DT::renderDataTable(DT::datatable(as.matrix(rv$load.paths)))
+  })
+  
+  # Click the load data to read in the met data
+  load.model.data <- eventReactive(input$load_data, {
+    req(input$met)
+    req(input$years)
+    
+    PEcAn.logger::logger.debug("Loading", input$met)
+    PEcAn.logger::logger.debug("Loading", input$years)
+    
+    data <- list()
+    for(i in seq_along(rv$load.paths)){
+      
+      fpath <- dirname(rv$load.paths[i])
+      inputid <- tbl(bety, "dbfiles") %>% filter(file_path == fpath) %>% 
+        pull(container_id) %>% unique() %>% .[1]
+      formatid <- tbl(bety, "inputs") %>% filter(id == inputid) %>% pull(format_id)
+      siteid <- tbl(bety, "inputs") %>% filter(id == inputid) %>% pull(site_id)
+      
+      site = query.site(con = bety$con, siteid)
+      
+      vars_in_file <- ncdf4::nc_open(rv$load.paths[i]) %>% ncdf4.helpers::nc.get.variable.list()
+      format = query.format.vars(bety, inputid, formatid)
+      format$vars <- format$vars %>% filter(input_name %in% vars_in_file)
+      
+      
+      dat <- try(load_data(data.path = rv$load.paths[i],
+                           format = format, site = site, ))
+      
+      if(class(dat) == "data.frame"){
+        dat$met <- rv$load.paths[i] %>% dirname() %>% basename() %>%
+          gsub(pattern = "\\_site_.*",replacement = "", x = .)
+        data[[i]] <- dat
+      }
+    }
+    data.final <- do.call(plyr::rbind.fill, data)
+    return(data.final)
+  })
+  
+  observeEvent(input$load_data, {
+    data.final <- load.model.data()
+    rv$data.final <- data.final
+    updateSelectizeInput(session, "var", choices = colnames(data.final))
+  })
+  
+  observeEvent({input$var},{
+    PEcAn.logger::logger.debug(input$var)
+    var <- input$var
+    if(input$var != ""){
+      plot.data <- rv$data.final %>% dplyr::select(one_of(c("posix", var, "met")))
+      # print(head(plot.data))
+      colnames(plot.data) <- c("date", "var", "met")
+      rv$plot.data <- plot.data
+    }
+  })
+  
+  observeEvent(input$plot_data,{
+    req(rv$plot.data)
+    req(input$var)
+
+    rv$plot.data$met <- factor(rv$plot.data$met, 
+           levels = sort(unique(rv$plot.data$met), decreasing = TRUE))
+  
+    p_overlay <- ggplot(rv$plot.data) + geom_line(aes(x=date, y=var, color=met)) + 
+      ylab(input$var) + ggtitle(input$var)
+    
+    p_facet <-   ggplot(rv$plot.data) + geom_line(aes(x=date, y=var, color=met), size=1) + 
+      ylab(input$var) + ggtitle(input$var) + 
+      facet_grid(met ~ .)
+    
+    output$plot_overlay <- renderPlot(p_overlay)
+    PEcAn.logger::logger.debug("Overlay plot finished")
+    output$plot_facet <- renderPlot(p_facet)
+    PEcAn.logger::logger.debug("Facet plot finished")
+  
+  })
+
+
+
+}
\ No newline at end of file
diff --git a/shiny/ViewMet/ui.R b/shiny/ViewMet/ui.R
new file mode 100644
index 00000000000..f818ee52250
--- /dev/null
+++ b/shiny/ViewMet/ui.R
@@ -0,0 +1,29 @@
+# ViewMet UI 
+
+ui <- fluidPage(sidebarPanel(
+                  h3("Select Files"),
+                  wellPanel(
+                  selectizeInput(inputId = "site.id", "Site ID", c()),
+                    checkboxGroupInput(inputId = "met", label = "Met product", choices = c()),
+                  checkboxGroupInput(inputId = "years", label = "Years", choices = c()),
+                    actionButton(inputId ="load_data", label = "Load Met Data")
+                  ),
+                  h3("Select Plots"),
+                  wellPanel(
+                    selectizeInput(inputId = "var", "Variable", c()),
+                    actionButton(inputId ="plot_data", label = "Plot Met Data")
+                  )
+                ),
+                mainPanel(navbarPage(title = NULL,
+                                     tabPanel("Files to be loaded", 
+                                              DT::dataTableOutput("results_table")
+                                     ),
+                                     tabPanel("Combined Plot", 
+                                              plotOutput("plot_overlay")
+                                     ),
+                                     tabPanel("Facet Plot", 
+                                              plotOutput("plot_facet")
+                                     )
+                )
+                )
+)
\ No newline at end of file
diff --git a/shiny/workflowPlot/DESCRIPTION b/shiny/workflowPlot/DESCRIPTION
index c686fa5a76b..3ee851b784e 100644
--- a/shiny/workflowPlot/DESCRIPTION
+++ b/shiny/workflowPlot/DESCRIPTION
@@ -6,3 +6,4 @@ AuthorUrl: http://www.ncsa.illinois.edu/assets/php/directory/contact.php?contact
 Tags: PEcAn
 DisplayMode: showcase
 Depends: DT
+RoxygenNote: 6.1.0
diff --git a/shiny/workflowPlot/markdown/workflowPlot_doc.Rmd b/shiny/workflowPlot/markdown/workflowPlot_doc.Rmd
new file mode 100644
index 00000000000..0ee8ecbbf62
--- /dev/null
+++ b/shiny/workflowPlot/markdown/workflowPlot_doc.Rmd
@@ -0,0 +1,90 @@
+---
+title: "Documentation for the Visualization and Benchmarking Shiny App"
+output: 
+  html_document:
+    theme: united
+---
+
+## App Documentation
+
+This is the shiny app for:
+
+- Visualizing model output data alongside external data
+- Registering Reference Runs
+- Calculating Benchmarks
+
+Do you have ideas for new features? 
+
+[Add your comments here!](https://github.com/PecanProject/pecan/issues/1894)
+
+--------------------------------------------------------------------------------
+
+## Setup page
+
+For now this is just a place to see some information about the run you just loaded. 
+
+--------------------------------------------------------------------------------
+
+## Exploratory Plots
+
+All our plots are made with [plotly](https://plot.ly/).
+
+They are interactive and packed full of features. All plotly plots have a toolbar with the following features:
+
+![](plotly_bar.png)
+
+- Download plot as a png
+- Zoom
+- Pan
+- Box select
+- Lasso select
+- Zoom in
+- Zoom out
+- Autoscale
+- Reset axes
+- Toggle spike lines
+- Show closest data on hover
+- Compare data on hover
+- Collaborate
+
+--------------------------------------------------------------------------------
+
+## Benchmarking
+
+[See additional documentation on benchmarking](https://pecanproject.github.io/pecan-documentation/develop/settings-configured-analyses.html#Benchmarking)
+
+### Settings
+
+All benchmarks that are calcualted are automatcally registered in to the database.
+
+#### Setup Reference Run
+
+You need to register a run before performing benchmarks. 
+
+[See documentation on reference runs](https://pecanproject.github.io/pecan-documentation/develop/reference-runs.html)
+
+#### Setup Benchmarks
+
+**Variables**
+
+These are the variables that the model and data have in common.
+
+**Metrics**
+
+Warning: Don't use Frechet for large datasets, it is not efficient at all. I should probably remove it if data dimensions are too large.
+
+**Plots**
+
+These plots will be saved as PDFs in the model output directory. You can also load them interactively in Benchmarking > Plots. 
+
+### Scores
+
+A table of all outputs of the selected metrics. 
+- For numerical metrics, the score is printed.
+- For visual metrics, the path to the PDF is printed. Eventually it might be nice to have a download button. For now, you can navigate back to rstudio and download from there. 
+
+### Plots
+
+More interactive ploty plots!
+
+--------------------------------------------------------------------------------
diff --git a/shiny/workflowPlot/server.R b/shiny/workflowPlot/server.R
index cf4e941499f..75e4bdc002e 100644
--- a/shiny/workflowPlot/server.R
+++ b/shiny/workflowPlot/server.R
@@ -1,212 +1,72 @@
-library(PEcAn.visualization)
-library(PEcAn.DB)
-library(PEcAn.settings)
-library(PEcAn.benchmark)
-library(PEcAn.utils)
-library(shiny)
-library(ncdf4)
-library(ggplot2)
-# Helper allows to load functions and variables that could be shared both by server.R and ui.R 
-# source('helper.R')
-library(plotly)
-library(scales)
-library(lubridate)
-library(dplyr)
-library(reshape2)
-library(purrr)
-# Maximum size of file allowed to be uploaded: 100MB 
-options(shiny.maxRequestSize=100*1024^2) 
+# Load PEcAn specific packages, does this need to be so specific?
+lapply(c("PEcAn.visualization",
+         "PEcAn.DB",
+         "PEcAn.settings",
+         "PEcAn.benchmark",
+         "PEcAn.utils"),function(pkg){
+           library(pkg,character.only = TRUE,quietly = TRUE)
+         }
+      )
+
+
+# Shiny and plotting packages
+lapply(c( "shiny",
+          "ggplot2",
+          "plotly",
+          "shinyjs",
+          "dplyr",
+          "reshape2",
+          "purrr",
+          "ncdf4",
+          "scales",
+          "lubridate",
+          "shinythemes"
+          ),function(pkg){
+            if (!(pkg %in% installed.packages()[,1])){
+                  install.packages(pkg)
+               }
+                library(pkg,character.only = TRUE,quietly = TRUE)
+            }
+      )
+
+
+# Maximum size of file allowed to be uploaded: 100MB
+options(shiny.maxRequestSize=100*1024^2)
+
 # Define server logic
 server <- shinyServer(function(input, output, session) {
   bety <- betyConnect()
+
+  # Hiding the animation and showing the application content
+  hide(id = "loading-content", anim = TRUE, animType = "fade")
+  showElement("app")
+
+  # Source Extra Funtions
   source("workflowPlot_fcns.R", local = TRUE) # Load all functions that need to be defined for this script
-  
-  
-  # Update all workflow ids
-  observe({
-    # get_workflow_ids function (line 137) in db/R/query.dplyr.R takes a flag to check
-    # if we want to load all workflow ids.
-    # get_workflow_id function from query.dplyr.R
-    query <- isolate(shiny::parseQueryString(session$clientData$url_search))
-    all_ids <- get_workflow_ids(bety, query, all.ids=TRUE)
-    updateSelectizeInput(session, "all_workflow_id", choices = all_ids)
-  })
-  # Update all run ids
-  all_run_ids <- reactive({
-    # Retrieves all run ids for seleted workflow ids
-    # Returns ('workflow ',w_id,', run ',r_id)
-    req(input$all_workflow_id)
-    w_ids <- input$all_workflow_id
-    # Will return a list
-    run_id_list <- c()
-    for(w_id in w_ids){
-      # For all the workflow ids
-      r_ids <- get_run_ids(bety, w_id)
-      for(r_id in r_ids){
-        # Each workflow id can have more than one run ids
-        # ',' as a separator between workflow id and run id
-        list_item <- paste0('workflow ', w_id,', run ', r_id)
-        run_id_list <- c(run_id_list, list_item)
-      }
-    }
-    return(run_id_list)
-  })
-  # Update all run_ids ('workflow ',w_id,', run ',r_id)
-  observe({
-    updateSelectizeInput(session, "all_run_id", choices = all_run_ids())
-  })
-    
-  # Update variable names observeEvent on input$load 
-  observeEvent(input$load, {
-    req(input$all_run_id)
-    # All information about a model is contained in 'all_run_id' string
-    ids_DF <- parse_ids_from_input_runID(input$all_run_id)
-    var_name_list <- c()
-    for(row_num in 1:nrow(ids_DF)){
-      var_name_list <- c(var_name_list, var_names_all(bety, ids_DF$wID[row_num], ids_DF$runID[row_num]))
-    }
-    updateSelectizeInput(session, "variable_name", choices = var_name_list)
-  })
-  # Loads data for all workflow and run ids after the load button is pressed.
-  # All information about a model is contained in 'all_run_id' string
-  # Wrapper over 'load_data_single_run' in PEcAn.db::query.dplyr
-  # Model data different from observations data 
-  loadNewData <- eventReactive(input$load,{
-    req(input$all_run_id)
-    # Get IDs DF from 'all_run_id' string
-    ids_DF <- parse_ids_from_input_runID(input$all_run_id)
-    globalDF <- map2_df(ids_DF$wID, ids_DF$runID, ~load_data_single_run(bety, .x, .y))
-    return(globalDF)
-  })
-  
-  observeEvent(input$load,{
-    # Retrieves all site ids from multiple seleted run ids when load button is pressed
+
+  # Sidebar
+  source("server_files/sidebar_server.R", local = TRUE)
+
+  # Page 1: Select Data
+  source("server_files/select_data_server.R", local = TRUE)
+
+  # Page 2: Exploratory Plots
+  source("server_files/model_plots_server.R", local = TRUE)
+  source("server_files/model_data_plots_server.R", local = TRUE)
+
+  # Page 3: Benchmarking
+  observeEvent(input$load_model,{
     req(input$all_run_id)
     ids_DF <- parse_ids_from_input_runID(input$all_run_id)
-    site_id_list <- c()
-    for(row_num in 1:nrow(ids_DF)){
-      settings <- getSettingsFromWorkflowId(bety,ids_DF$wID[row_num])
-      site.id <- c(settings$run$site$id)
-      site_id_list <- c(site_id_list,site.id)
-    }
-    updateSelectizeInput(session, "all_site_id", choices=site_id_list)
-  })
-
-  # Update input id list as (input id, name)
-  observe({
-    req(input$all_site_id)
-    inputs_df <- getInputs(bety, c(input$all_site_id))
-    formats_1 <- dplyr::tbl(bety, 'formats_variables') %>%
-      dplyr::filter(format_id %in% inputs_df$format_id)
-    if (dplyr.count(formats_1) == 0) {
-      logger.warn("No inputs found. Returning NULL.")
-      return(NULL)
-    } else {
-      formats_sub <- formats_1 %>%
-        dplyr::pull(format_id) %>%
-        unique()
-      inputs_df <- inputs_df %>% dplyr::filter(format_id %in% formats_sub) # Only data sets with formats with associated variables will show up
-      updateSelectizeInput(session, "all_input_id", choices=inputs_df$input_selection_list)
-    }
-  })
-  # Renders ggplotly 
-  output$outputPlot <- renderPlotly({
-    # Error messages
-    validate(
-      need(input$all_workflow_id, 'Select workflow id'),
-      need(input$all_run_id, 'Select Run id'),
-      need(input$variable_name, 'Click the button to load data. Please allow some time')
-    )
-    # Load data
-    masterDF <- loadNewData()
-    # Convert from factor to character. For subsetting
-    masterDF$var_name <- as.character(masterDF$var_name)
-    # Convert to factor. Required for ggplot
-    masterDF$run_id <- as.factor(as.character(masterDF$run_id))
-    # Filter by variable name
-    df <- masterDF %>%
-      dplyr::filter(var_name == input$variable_name)
-    # Another way to make dynamic slider
-    # https://stackoverflow.com/questions/18700589/interactive-reactive-change-of-min-max-values-of-sliderinput
-    # output$slider <- renderUI({
-    #   sliderInput("smooth_n", "Value for smoothing:", min=0, max=nrow(df), value=80)
-    # })
-    updateSliderInput(session,"smooth_n", min=0, max=nrow(df))
-    # Meta information about the plot
-    title <- unique(df$title)
-    xlab <- unique(df$xlab)
-    ylab <- unique(df$ylab)
-    # ggplot function for scatter plots.
-    plt <- ggplot(df, aes(x=dates, y=vals, color=run_id))
-    # model_geom <- switch(input$plotType, scatterPlot = geom_point, lineChart = geom_line)
-    # plt <- plt + model_geom() 
-    # Toggle chart type using switch
-    switch(input$plotType,
-           "scatterPlot"  = {
-             plt <- plt + geom_point()
-           },
-           "lineChart"  = {
-             plt <- plt + geom_line()
-           }
-    )
-    # Check if user wants to load external data (==observations)
-    # Similar to using event reactive
-    if (input$load_data>0) {
-      # Input ID is of the form (input id, Name). Split by space and use the first element
-      inputs_df <- getInputs(bety,c(input$all_site_id))
-      inputs_df <- inputs_df %>% dplyr::filter(input_selection_list == input$all_input_id)
-      externalData <- loadObservationData(bety,inputs_df)
-      # If variable found in the uploaded file.
-      # TODO for now, actual observations can be plotted again a single model run (particular run id)
-      # Have to enhance to allow multiple run ids
-      if (input$variable_name %in% names(externalData)){
-        # No need for subsetting though as align data returns for now only the provided variable name
-        # externalData <- externalData %>% dplyr::select(posix,dplyr::one_of(input$variable_name))
-        var = input$variable_name
-        df = df %>% select(posix = dates, vals) 
-        colnames(df)[which(colnames(df) == "vals")] <- var 
-        aligned_data = PEcAn.benchmark::align_data(model.calc = df, obvs.calc = externalData, var =var, align_method = "mean_over_larger_timestep")
-        colnames(aligned_data)[grep("[.]m", colnames(aligned_data))] <- "model"
-        colnames(aligned_data)[grep("[.]o", colnames(aligned_data))] <- "observations"
-        colnames(aligned_data)[which(colnames(aligned_data) == "posix")] <- "Date"
-        
-        # Melt dataframe to plot two types of columns together
-        aligned_data <- reshape2::melt(aligned_data, "Date")
-        data_geom <- switch(input$data_geom, point = geom_point, line = geom_line)
-        plt <- ggplot(aligned_data, aes(x=Date, y=value, color=variable)) + data_geom()
-        output$outputNoVariableFound <- renderText({
-          paste0("Plotting data outputs.")
-        })
-      }
-      # Shiny output if variable not found
-      else {
-        output$outputNoVariableFound <- renderText({
-          paste0("Data related to variable not found in the observations uploaded. Select another variable")
-        })
-      }
-    }
-    plt <- plt + labs(title=title, x=xlab, y=ylab) + geom_smooth(n=input$smooth_n)
-    # Earlier code for smoothing, y labels, color and fill values
-    # Retaining if we want to use ggplot instead of ggplotly
-    # geom_smooth(aes(fill = "Spline fit")) +
-    # scale_y_continuous(labels=fancy_scientific) +
-    # scale_color_manual(name = "", values = "black") +
-    # scale_fill_manual(name = "", values = "grey50")
-    if(input$plotview){
-      plt<-ggplotly(plt)
+    button <- FALSE
+    print(nrow(ids_DF))
+    if(nrow(ids_DF) == 1){
+      source("server_files/benchmarking_server.R", local = TRUE)
+    }else if(nrow(ids_DF) > 1){
+      brr_message <- "Benchmarking currently only works when one run is selected."
     }else{
-      plt<-ggplot(data.frame(x = 0, y = 0), aes(x,y)) + annotate("text", x = 0, y = 0, label = "You chose to skip plotting
-proceed to benchmarking", size = 10, color = "grey")
+      brr_message <- "Cannot do benchmarking"
     }
-    # Not able to add icon over ggplotly
-    # add_icon()
   })
-  
-  
-  # Source the server code for all the benchmarking tabs in the app
-  source("bm.R", local = TRUE)
-  
-}) # Shiny server closes here  
-# To run the shiny app locally
-# runApp(port=6480, launch.browser=FALSE)
-# runApp(port=5658, launch.browser=FALSE)
+
+  }) # Shiny server closes here
diff --git a/shiny/workflowPlot/bm.R b/shiny/workflowPlot/server_files/benchmarking_server.R
similarity index 98%
rename from shiny/workflowPlot/bm.R
rename to shiny/workflowPlot/server_files/benchmarking_server.R
index dcf77f9b1c9..6e8e3204c61 100644
--- a/shiny/workflowPlot/bm.R
+++ b/shiny/workflowPlot/server_files/benchmarking_server.R
@@ -7,7 +7,7 @@ bm <- reactiveValues()
 ## Observe when the model run is loaded and check to see if it is registered 
 ## as a reference run. If not, create the record upon button click
 
-observeEvent(input$load,{
+observeEvent(input$load_model,{
   req(input$all_run_id)
   ids_DF <- parse_ids_from_input_runID(input$all_run_id)
   button <- FALSE
@@ -291,10 +291,11 @@ observeEvent(bm$load_results,{
       plot_list <- apply(
         result.out$bench.results[plots_used,c("variable", "metric")],
         1, paste, collapse = " ")
+      selection <- as.list(as.numeric(names(plot_list)))
+      names(selection) <- as.vector(plot_list)
       output$bm_plots <-  renderUI({
-        radioButtons("bench_plot", "Benchmark Plot",
-                     choiceNames = as.vector(plot_list), 
-                     choiceValues = as.numeric(names(plot_list)))
+        selectInput("bench_plot", "Benchmark Plot", multiple = FALSE,
+                     choices = selection)
       })
     }
   }
@@ -314,7 +315,6 @@ observeEvent(input$bench_plot,{
     filename = NA,
     draw.plot = TRUE
   )
-  output$blarg_message <- renderText({paste(input$bench_plot, var)})
   p <- do.call(fcn, args)
   output$bmPlot <- renderPlotly({
     plotly::ggplotly(p)
diff --git a/shiny/workflowPlot/server_files/model_data_plots_server.R b/shiny/workflowPlot/server_files/model_data_plots_server.R
new file mode 100644
index 00000000000..79ea31355ed
--- /dev/null
+++ b/shiny/workflowPlot/server_files/model_data_plots_server.R
@@ -0,0 +1,243 @@
+# Renders ggplotly
+
+output$modelDataPlot <- renderPlotly({
+  validate(
+    need(length(input$all_workflow_id) == 1, "Select only ONE workflow ID"),
+    need(length(input$all_run_id) == 1, "Select only ONE run ID"),
+    need(input$load_model > 0, 'Select Load Data'),
+    need(length(input$all_site_id) == 1, 'Select only ONE Site ID'),
+    need(length(input$all_input_id) == 1, 'Select only ONE Input ID'),
+    need(input$load_data > 0, 'Select Load External Data')
+  )
+  plt <- ggplot(data.frame(x = 0, y = 0), aes(x,y)) +
+    annotate("text", x = 0, y = 0, label = "You are ready to plot!",
+             size = 10, color = "grey")
+})
+
+# Update units every time a variable is selected
+observeEvent(input$var_name_modeldata, {
+  model.df <- load.model()
+  default.unit <- model.df %>% filter(var_name == input$var_name_modeldata) %>% pull(ylab) %>% unique()
+  updateTextInput(session, "units_modeldata", value = default.unit)
+})
+
+# Check that new units are parsible and can be used for conversion
+observeEvent(input$units_modeldata,{
+  if(udunits2::ud.is.parseable(input$units_modeldata)){
+    model.df <- load.model()
+    default.unit <- model.df %>% filter(var_name == input$var_name_modeldata) %>% pull(ylab) %>% unique()
+    if(udunits2::ud.are.convertible(default.unit, input$units_modeldata)){
+      output$unit_text2 <-  renderText({"Conversion possible"})
+    }else{
+      output$unit_text2 <-  renderText({"Units are parsible but conversion is not possible"})
+    }
+  }else{
+    output$unit_text2 <-  renderText({"Units are not parsible, please type units in udunits2 compatible format"})
+  }
+})
+
+
+
+observeEvent(input$ex_plot_modeldata,{
+  output$modelDataPlot <- renderPlotly({
+    input$ex_plot_modeldata
+    isolate({
+
+      var = input$var_name_modeldata
+
+      model_data <- dplyr::filter(load.model(), var_name == var)
+
+      updateSliderInput(session,"smooth_n_modeldata", min = 0, max = nrow(model_data))
+      title <- unique(model_data$title)
+      xlab  <- unique(model_data$xlab)
+      ylab  <- unique(model_data$ylab)
+
+      model_data <- model_data %>% dplyr::select(posix = dates, !!var := vals)
+      external_data <- load.model.data()
+      aligned_data = PEcAn.benchmark::align_data(
+        model.calc = model_data, obvs.calc = external_data,
+        var = var, align_method = "mean_over_larger_timestep") %>%
+        dplyr::select(everything(),
+                      model = matches("[.]m"),
+                      observations = matches("[.]o"),
+                      Date = posix)
+
+      print(head(aligned_data))
+      # Melt dataframe to plot two types of columns together
+      aligned_data <- tidyr::gather(aligned_data, variable, value, -Date)
+
+      unit <- ylab
+      if(input$units_modeldata != unit & udunits2::ud.are.convertible(unit, input$units_modeldata)){
+        aligned_data$value <- udunits2::ud.convert(aligned_data$value,unit,input$units_modeldata)
+        ylab <- input$units_modeldata
+      }
+
+
+      data_geom <- switch(input$plotType_modeldata, point = geom_point, line = geom_line)
+
+      plt <- ggplot(aligned_data, aes(x=Date, y=value, color=variable))
+      plt <- plt + data_geom()
+      plt <- plt + labs(title=title, x=xlab, y=ylab)
+      plt <- plt + geom_smooth(n=input$smooth_n_modeldata)
+      ply <- ggplotly(plt)
+
+
+    })
+  })
+  output$modelDataPlotStatic <- renderPlotly({
+    input$ex_plot_modeldata
+    isolate({
+
+      var = input$var_name_modeldata
+
+      model_data <- dplyr::filter(load.model(), var_name == var)
+
+      updateSliderInput(session,"smooth_n_modeldata", min = 0, max = nrow(model_data))
+      title <- unique(model_data$title)
+      xlab  <- unique(model_data$xlab)
+      ylab  <- unique(model_data$ylab)
+
+      model_data <- model_data %>% dplyr::select(posix = dates, !!var := vals)
+      external_data <- load.model.data()
+      aligned_data = PEcAn.benchmark::align_data(
+        model.calc = model_data, obvs.calc = external_data,
+        var = var, align_method = "mean_over_larger_timestep") %>%
+        dplyr::select(everything(),
+                      model = matches("[.]m"),
+                      observations = matches("[.]o"),
+                      Date = posix)
+
+      print(head(aligned_data))
+      # Melt dataframe to plot two types of columns together
+      aligned_data <- tidyr::gather(aligned_data, variable, value, -Date)
+
+      unit <- ylab
+      if(input$units_modeldata != unit & udunits2::ud.are.convertible(unit, input$units_modeldata)){
+        aligned_data$value <- udunits2::ud.convert(aligned_data$value,unit,input$units_modeldata)
+        ylab <- input$units_modeldata
+      }
+
+
+      data_geom <- switch(input$plotType_modeldata, point = geom_point, line = geom_line)
+
+      plt <- ggplot(aligned_data, aes(x=Date, y=value, color=variable))
+      plt <- plt + data_geom()
+      plt <- plt + labs(title=title, x=xlab, y=ylab)
+      plt <- plt + geom_smooth(n=input$smooth_n_modeldata)
+      ply <- ggplotly(plt)
+      ply <- plotly::config(ply, collaborate = F, doubleClick = F, displayModeBar = F, staticPlot = T)
+    })
+  })
+})
+
+observeEvent(input$model_data_toggle_plot,{
+  toggleElement("model_data_plot_interactive")
+  toggleElement("model_data_plot_static")
+})
+
+
+
+
+# observeEvent(input$ex_plot_modeldata,{
+#   output$modelDataPlot <- renderPlotly({
+#     annotate_text = sprintf("This is plot number %i", as.numeric(input$ex_plot_modeldata))
+#     plt <- ggplot(data.frame(x = 0, y = 0), aes(x,y)) +
+#       annotate("text", x = 0, y = 0, label = annotate_text,
+#                size = 10, color = "grey")
+#   })
+# })
+
+
+
+# observeEvent(input$ex_modelData_plot,{
+#
+# # Renders ggplotly
+# output$modelDataPlot <- renderPlotly({
+#   # Load data
+#   masterDF <- load.model()
+#   # Convert from factor to character. For subsetting
+#   masterDF$var_name <- as.character(masterDF$var_name)
+#   # Convert to factor. Required for ggplot
+#   masterDF$run_id <- as.factor(as.character(masterDF$run_id))
+#   # Filter by variable name
+#   df <- masterDF %>%
+#     dplyr::filter(var_name == input$variable_name)
+#   # Another way to make dynamic slider
+#   # https://stackoverflow.com/questions/18700589/interactive-reactive-change-of-min-max-values-of-sliderinput
+#   # output$slider <- renderUI({
+#   #   sliderInput("smooth_n", "Value for smoothing:", min=0, max=nrow(df), value=80)
+#   # })
+#   updateSliderInput(session,"smooth_n", min=0, max=nrow(df))
+#   # Meta information about the plot
+#   title <- unique(df$title)
+#   xlab <- unique(df$xlab)
+#   ylab <- unique(df$ylab)
+#   # ggplot function for scatter plots.
+#   plt <- ggplot(df, aes(x=dates, y=vals, color=run_id))
+#   # model_geom <- switch(input$plotType, scatterPlot = geom_point, lineChart = geom_line)
+#   # plt <- plt + model_geom()
+#   # Toggle chart type using switch
+#   switch(input$plotType,
+#          "scatterPlot"  = {
+#            plt <- plt + geom_point()
+#          },
+#          "lineChart"  = {
+#            plt <- plt + geom_line()
+#          }
+#   )
+#   # Check if user wants to load external data (==observations)
+#   # Similar to using event reactive
+#   if (input$load_data>0) {
+#     # Input ID is of the form (input id, Name). Split by space and use the first element
+#     inputs_df <- getInputs(bety,c(input$all_site_id))
+#     inputs_df <- inputs_df %>% dplyr::filter(input_selection_list == input$all_input_id)
+#     externalData <- loadObservationData(bety,inputs_df)
+#     # If variable found in the uploaded file.
+#     # TODO for now, actual observations can be plotted again a single model run (particular run id)
+#     # Have to enhance to allow multiple run ids
+#     if (input$variable_name %in% names(externalData)){
+#       # No need for subsetting though as align data returns for now only the provided variable name
+#       # externalData <- externalData %>% dplyr::select(posix,dplyr::one_of(input$variable_name))
+#       var = input$variable_name
+#       df = df %>% select(posix = dates, vals)
+#       colnames(df)[which(colnames(df) == "vals")] <- var
+#       aligned_data = PEcAn.benchmark::align_data(model.calc = df, obvs.calc = externalData, var =var, align_method = "mean_over_larger_timestep")
+#       colnames(aligned_data)[grep("[.]m", colnames(aligned_data))] <- "model"
+#       colnames(aligned_data)[grep("[.]o", colnames(aligned_data))] <- "observations"
+#       colnames(aligned_data)[which(colnames(aligned_data) == "posix")] <- "Date"
+#
+#       # Melt dataframe to plot two types of columns together
+#       aligned_data <- reshape2::melt(aligned_data, "Date")
+#       data_geom <- switch(input$data_geom, point = geom_point, line = geom_line)
+#       plt <- ggplot(aligned_data, aes(x=Date, y=value, color=variable)) + data_geom()
+#       output$outputNoVariableFound <- renderText({
+#         paste0("Plotting data outputs.")
+#       })
+#     }
+#     # Shiny output if variable not found
+#     else {
+#       output$outputNoVariableFound <- renderText({
+#         paste0("Data related to variable not found in the observations uploaded. Select another variable")
+#       })
+#     }
+#   }
+#   plt <- plt + labs(title=title, x=xlab, y=ylab) + geom_smooth(n=input$smooth_n)
+#   # Earlier code for smoothing, y labels, color and fill values
+#   # Retaining if we want to use ggplot instead of ggplotly
+#   # geom_smooth(aes(fill = "Spline fit")) +
+#   # scale_y_continuous(labels=fancy_scientific) +
+#   # scale_color_manual(name = "", values = "black") +
+#   # scale_fill_manual(name = "", values = "grey50")
+#   # if(input$plotview){
+#   plt<-ggplotly(plt)
+#   # }else{
+#   #   plt<-ggplot(data.frame(x = 0, y = 0), aes(x,y)) + annotate("text", x = 0, y = 0, label = "You chose to skip plotting
+#   #                                                            proceed to benchmarking", size = 10, color = "grey")
+#   # }
+#   # Not able to add icon over ggplotly
+#   # add_icon()
+# })
+#
+# })
+
+
diff --git a/shiny/workflowPlot/server_files/model_plots_server.R b/shiny/workflowPlot/server_files/model_plots_server.R
new file mode 100644
index 00000000000..e98be8fc413
--- /dev/null
+++ b/shiny/workflowPlot/server_files/model_plots_server.R
@@ -0,0 +1,118 @@
+# Renders ggplotly
+
+output$modelPlot <- renderPlotly({
+  validate(
+    need(input$all_workflow_id, 'Select workflow id'),
+    need(input$all_run_id, 'Select Run id'),
+    need(input$load_model > 0, 'Select Load Model Outputs')
+  )
+
+  plt <- ggplot(data.frame(x = 0, y = 0), aes(x,y)) +
+    annotate("text", x = 0, y = 0, label = "Ready to plot!",
+             size = 10, color = "grey")
+})
+
+# Update units every time a variable is selected
+observeEvent(input$var_name_model, {
+  model.df <- load.model()
+  default.unit <- model.df %>% filter(var_name == input$var_name_model) %>% pull(ylab) %>% unique()
+  updateTextInput(session, "units_model", value = default.unit)
+})
+
+# Check that new units are parsible and can be used for conversion
+observeEvent(input$units_model,{
+  parseable <- ifelse(udunits2::ud.is.parseable(input$units_model), "can", "cannot")
+  if(udunits2::ud.is.parseable(input$units_model)){
+    model.df <- load.model()
+    default.unit <- model.df %>% filter(var_name == input$var_name_model) %>% pull(ylab) %>% unique()
+    if(udunits2::ud.are.convertible(default.unit, input$units_model)){
+      output$unit_text <-  renderText({"Conversion possible"})
+    }else{
+      output$unit_text <-  renderText({"Units are parsible but conversion is not possible"})
+    }
+  }else{
+    output$unit_text <-  renderText({"Units are not parsible, please type units in udunits2 compatible format"})
+  }
+})
+
+
+observeEvent(input$ex_plot_model,{
+  req(input$units_model)
+
+  output$modelPlot <- renderPlotly({
+    input$ex_plot_model
+    isolate({
+      df <- dplyr::filter(load.model(), var_name == input$var_name_model)
+
+      updateSliderInput(session,"smooth_n_model", min = 0, max = nrow(df))
+
+      title <- unique(df$title)
+      xlab <- unique(df$xlab)
+      ylab <- unique(df$ylab)
+
+      unit <- ylab
+      if(input$units_model != unit & udunits2::ud.are.convertible(unit, input$units_model)){
+        df$vals <- udunits2::ud.convert(df$vals,unit,input$units_model)
+        ylab <- input$units_model
+      }
+
+      data_geom <- switch(input$plotType_model, point = geom_point, line = geom_line)
+
+      plt <- ggplot(df, aes(x = dates, y = vals, color = run_id))
+      plt <- plt + data_geom()
+      plt <- plt + labs(title=title, x=xlab, y=ylab)
+      plt <- plt + geom_smooth(n=input$smooth_n_model)
+      ply <- ggplotly(plt)
+    })
+  })
+
+  output$modelPlotStatic <- renderPlotly({
+    input$ex_plot_model
+    isolate({
+      df <- dplyr::filter(load.model(), var_name == input$var_name_model)
+
+      updateSliderInput(session,"smooth_n_model", min = 0, max = nrow(df))
+
+      title <- unique(df$title)
+      xlab <- unique(df$xlab)
+      ylab <- unique(df$ylab)
+
+      unit <- ylab
+      if(input$units_model != unit & udunits2::ud.are.convertible(unit, input$units_model)){
+        df$vals <- udunits2::ud.convert(df$vals,unit,input$units_model)
+        ylab <- input$units_model
+      }
+
+      data_geom <- switch(input$plotType_model, point = geom_point, line = geom_line)
+
+      plt <- ggplot(df, aes(x = dates, y = vals, color = run_id))
+      plt <- plt + data_geom()
+      plt <- plt + labs(title=title, x=xlab, y=ylab)
+      plt <- plt + geom_smooth(n=input$smooth_n_model)
+      ply <- ggplotly(plt)
+      ply <- plotly::config(ply, collaborate = F, doubleClick = F, displayModeBar = F, staticPlot = T)
+    })
+  })
+})
+
+observeEvent(input$model_toggle_plot,{
+  toggleElement("model_plot_static")
+  toggleElement("model_plot_interactive")
+})
+
+# masterDF <- loadNewData()
+# # Convert from factor to character. For subsetting
+# masterDF$var_name <- as.character(masterDF$var_name)
+# # Convert to factor. Required for ggplot
+# masterDF$run_id <- as.factor(as.character(masterDF$run_id))
+# plt <- callModule(testModule, "model", masterDF)
+# plt()
+
+
+
+
+
+# annotate_text = sprintf("This is plot number %i", as.numeric(input$ex_plot_model))
+# plt <- ggplot(data.frame(x = 0, y = 0), aes(x,y)) +
+#   annotate("text", x = 0, y = 0, label = annotate_text,
+#            size = 10, color = "grey")
diff --git a/shiny/workflowPlot/server_files/select_data_server.R b/shiny/workflowPlot/server_files/select_data_server.R
new file mode 100644
index 00000000000..9028ec85ac5
--- /dev/null
+++ b/shiny/workflowPlot/server_files/select_data_server.R
@@ -0,0 +1,36 @@
+observeEvent(input$load_model,{
+  req(input$all_run_id)
+  
+  df <- load.model()
+  # output$results_table <- DT::renderDataTable(DT::datatable(head(masterDF)))
+  
+  ids_DF <- parse_ids_from_input_runID(input$all_run_id)
+  README.text <- c()
+  
+  for(i in seq(nrow(ids_DF))){
+    
+    dfsub <- df %>% filter(run_id == ids_DF$runID[i])
+    
+    diff.m <- diff(dfsub$dates)
+    mode.m <- diff.m[which.max(tabulate(match(unique(diff.m), diff.m)))]
+    diff_units.m = units(mode.m)
+    
+    diff_message <- sprintf("timestep: %.2f %s", mode.m, diff_units.m)
+    wf.folder <- workflow(bety, ids_DF$wID[i]) %>% collect() %>% pull(folder)
+    
+    README.text <- c(README.text, 
+                     paste("SELECTION",i), 
+                     "============",
+                     readLines(file.path(wf.folder, 'run', ids_DF$runID[i], "README.txt")),
+                     diff_message,
+                     ""
+    )
+  }
+  
+  output$README <- renderUI({HTML(paste(README.text, collapse = '<br/>'))})
+  
+  output$dim_message <- renderText({sprintf("This data has %.0f rows, think about skipping exploratory plots if this is a large number...", dim(df)[1])})
+  
+})
+
+
diff --git a/shiny/workflowPlot/server_files/sidebar_server.R b/shiny/workflowPlot/server_files/sidebar_server.R
new file mode 100644
index 00000000000..4fdba4c61a8
--- /dev/null
+++ b/shiny/workflowPlot/server_files/sidebar_server.R
@@ -0,0 +1,140 @@
+# The sidebar is where both the model output and external data are loaded
+
+# Loading Model Output(s) -----------------------------------------------------#
+
+# Update workflow ids
+observe({
+  # get_workflow_ids function (line 137) in db/R/query.dplyr.R takes a flag to check
+  # if we want to load all workflow ids.
+  # get_workflow_id function from query.dplyr.R
+  all_ids <- get_workflow_ids(bety, query, all.ids=TRUE)
+  updateSelectizeInput(session, "all_workflow_id", choices = all_ids)
+  # Get URL prameters
+  query <- parseQueryString(session$clientData$url_search)
+  # Pre-select workflow_id from URL prams
+  updateSelectizeInput(session, "all_workflow_id", selected = query[["workflow_id"]])
+})
+
+# Update run ids
+all_run_ids <- reactive({
+  # Retrieves all run ids for seleted workflow ids
+  # Returns ('workflow ',w_id,', run ',r_id)
+  req(input$all_workflow_id)
+  w_ids <- input$all_workflow_id
+  # Will return a list
+  run_id_list <- c()
+  for(w_id in w_ids){
+    # For all the workflow ids
+    r_ids <- get_run_ids(bety, w_id)
+    for(r_id in r_ids){
+      # Each workflow id can have more than one run ids
+      # ',' as a separator between workflow id and run id
+      list_item <- paste0('workflow ', w_id,', run ', r_id)
+      run_id_list <- c(run_id_list, list_item)
+    }
+  }
+  return(run_id_list)
+})
+# Update all run_ids ('workflow ',w_id,', run ',r_id)
+observe({
+  updateSelectizeInput(session, "all_run_id", choices = all_run_ids())
+  # Get URL parameters
+  query <- parseQueryString(session$clientData$url_search)
+  # Make the run_id string with workflow_id
+  url_run_id <- paste0('workflow ', query[["workflow_id"]],', run ', query[["run_id"]])
+  # Pre-select run_id from URL params
+  updateSelectizeInput(session, "all_run_id", selected = url_run_id)
+})
+
+
+# Loads data for all workflow and run ids after the load button is pressed.
+# All information about a model is contained in 'all_run_id' string
+# Wrapper over 'load_data_single_run' in PEcAn.db::query.dplyr
+# Model data different from observations data
+load.model <- eventReactive(input$load_model,{
+  req(input$all_run_id)
+  # Get IDs DF from 'all_run_id' string
+  ids_DF <- parse_ids_from_input_runID(input$all_run_id)
+  globalDF <- map2_df(ids_DF$wID, ids_DF$runID, ~load_data_single_run(bety, .x, .y))
+  print("Yay the model data is loaded!")
+  print(head(globalDF))
+  globalDF$var_name <- as.character(globalDF$var_name)
+  globalDF$run_id <- as.factor(as.character(globalDF$run_id))
+  return(globalDF)
+})
+
+# Update all variable names
+observeEvent(input$load_model, {
+  req(input$all_run_id)
+  # All information about a model is contained in 'all_run_id' string
+  ids_DF <- parse_ids_from_input_runID(input$all_run_id)
+  var_name_list <- c()
+  for(row_num in 1:nrow(ids_DF)){
+    var_name_list <- c(var_name_list, var_names_all(bety, ids_DF$wID[row_num], ids_DF$runID[row_num]))
+  }
+  updateSelectizeInput(session, "var_name_model", choices = var_name_list)
+})
+
+observeEvent(input$load_model,{
+  # Retrieves all site ids from multiple seleted run ids when load button is pressed
+  req(input$all_run_id)
+  ids_DF <- parse_ids_from_input_runID(input$all_run_id)
+  site_id_list <- c()
+  for(row_num in 1:nrow(ids_DF)){
+    settings <- getSettingsFromWorkflowId(bety,ids_DF$wID[row_num])
+    site.id <- c(settings$run$site$id)
+    site_id_list <- c(site_id_list,site.id)
+  }
+  updateSelectizeInput(session, "all_site_id", choices=site_id_list)
+})
+# Update input id list as (input id, name)
+observe({
+  req(input$all_site_id)
+  inputs_df <- getInputs(bety, c(input$all_site_id))
+  formats_1 <- dplyr::tbl(bety, 'formats_variables') %>%
+    dplyr::filter(format_id %in% inputs_df$format_id)
+  if (dplyr.count(formats_1) == 0) {
+    logger.warn("No inputs found. Returning NULL.")
+    return(NULL)
+  } else {
+    formats_sub <- formats_1 %>%
+      dplyr::pull(format_id) %>%
+      unique()
+    inputs_df <- inputs_df %>% dplyr::filter(format_id %in% formats_sub) # Only data sets with formats with associated variables will show up
+    updateSelectizeInput(session, "all_input_id", choices=inputs_df$input_selection_list)
+  }
+})
+
+load.model.data <- eventReactive(input$load_data, {
+  req(input$all_input_id)
+
+  inputs_df <- getInputs(bety,c(input$all_site_id))
+  inputs_df <- inputs_df %>% dplyr::filter(input_selection_list == input$all_input_id)
+
+  input_id <- inputs_df$input_id
+  # File_format <- getFileFormat(bety,input_id)
+  File_format <- PEcAn.DB::query.format.vars(bety = bety, input.id = input_id)
+  start.year <- as.numeric(lubridate::year(inputs_df$start_date))
+  end.year <- as.numeric(lubridate::year(inputs_df$end_date))
+  File_path <- inputs_df$filePath
+  # TODO There is an issue with the db where file names are not saved properly.
+  # To make it work with the VM, uncomment the line below
+  # File_path <- paste0(inputs_df$filePath,'.csv')
+  site.id <- inputs_df$site_id
+  site <- PEcAn.DB::query.site(site.id,bety$con)
+  observations <- PEcAn.benchmark::load_data(
+    data.path = File_path, format = File_format, time.row = File_format$time.row,
+    site = site, start_year = start.year, end_year = end.year)
+  print("Yay the observational data is loaded!")
+  print(head(observations))
+  return(observations)
+})
+
+
+# Update all variable names
+observeEvent(input$load_data, {
+  model.df <- load.model()
+  obvs.df <- load.model.data()
+  updateSelectizeInput(session, "var_name_modeldata",
+                       choices = intersect(model.df$var_name, names(obvs.df)))
+})
\ No newline at end of file
diff --git a/shiny/workflowPlot/ui.R b/shiny/workflowPlot/ui.R
index 9121f806953..509b66e93f4 100644
--- a/shiny/workflowPlot/ui.R
+++ b/shiny/workflowPlot/ui.R
@@ -1,86 +1,68 @@
 library(shiny)
 library(plotly)
-# Helper allows to load functions and variables that could be shared both by server.R and ui.R 
-# source('helper.R')
+library(shinythemes)
+library(knitr)
+library(shinyjs)
+
+source("ui_utils.R", local = TRUE)
+
 # Define UI
-ui <- shinyUI(fluidPage(
-  # Application title
-  titlePanel("Workflow Plots"),
-  sidebarLayout(
-    sidebarPanel(
-      h3("Load Model Output"),
-      wellPanel(
-        p("Please select the workflow IDs to continue. You can select multiple IDs"),
-        selectizeInput("all_workflow_id", "Mutliple Workflow IDs", c(),multiple=TRUE),
-        p("Please select the run IDs. You can select multiple IDs"),
-        selectizeInput("all_run_id", "Mutliple Run IDs", c(),multiple=TRUE),
-        radioButtons("plotview", "Load initial plots?", choiceNames = c("Yes", "No"),
-                     choiceValues = c(TRUE, FALSE)),
-        actionButton("load", "Load Model outputs")
-      ),
-      
-      h3("Load External Data"),
-      wellPanel(
-        selectizeInput("all_site_id", "Select Site ID", c()),
-        # If loading multiple sites in future
-        # selectizeInput("all_site_id", "Select Site ID", c(), multiple=TRUE),
-        selectizeInput("all_input_id", "Select Input ID", c()),
-        actionButton("load_data", "Load External Data")
-      )
-    ),
-    mainPanel(
-      tabsetPanel(
-        tabPanel("Visualizations", 
-                 column(12, plotlyOutput("outputPlot")),
-                 column(12, wellPanel( 
-                   selectInput("variable_name", "Variable Name", ""),
-                   radioButtons("plotType", "Plot Type (for Model Outputs)", 
-                                c("Scatter Plot" = "scatterPlot", 
-                                  "Line Chart" = "lineChart"), 
-                                selected="scatterPlot"),
-                   radioButtons("data_geom", "Plot Type (for loaded data)", 
-                                c("Scatter Plot" = "point", 
-                                  "Line Chart" = "line"), 
-                                selected="point"),
-                   # uiOutput("slider"),
-                   sliderInput("smooth_n", "Value for smoothing:",
-                               min=0, max=100, value=80))
-                 ),
-                 verbatimTextOutput("outputNoVariableFound")
-        ),
-        tabPanel("Benchmarking Settings", 
-                 column(12, h3("Setup Reference Run")),
-                 column(12, 
-                        verbatimTextOutput("brr_message"),
-                        uiOutput("button_BRR")
-                 ),
-                 column(12,
-                        h3("Setup Benchmarks")),
-                 column(12, 
-                        uiOutput("results_message"),
-                        uiOutput("bm_inputs")
-                 ),
-                 column(12, h3("Calculate Benchmarks")),
-                 column(12, 
-                        verbatimTextOutput("calc_bm_message"),
-                        # verbatimTextOutput("report"),
-                        uiOutput("calc_bm_button"),
-                        uiOutput("inputs_df_table"),
-                        uiOutput("config_list_table"),
-                        uiOutput("reportvars"),
-                        uiOutput("reportmetrics"),
-                        uiOutput("print_bm_settings")
-                 )
-        ),
-        tabPanel("Benchmarking Scores", 
-                 DT::dataTableOutput("results_table")
-        ),
-        tabPanel("Benchmarking Plots",
-                 verbatimTextOutput("blarg_message"),
-                 uiOutput("bm_plots"),
-                 plotlyOutput("bmPlot")
-        )
-      )
-    )
-  )
-))
+ui <- fluidPage(theme = shinytheme("simplex"),
+                # Initializing shinyJs
+                useShinyjs(),
+                # Adding CSS to head
+                tags$head(
+                  tags$link(rel = "stylesheet", type = "text/css", href = "style.css")
+                ),
+                # Showing the animation
+                div( id = "loading-content",
+                     div(class = "plotlybars-wrapper",
+                         div( class="plotlybars",
+                              div(class="plotlybars-bar b1"),
+                              div(class="plotlybars-bar b2"),
+                              div(class="plotlybars-bar b3"),
+                              div(class="plotlybars-bar b4"),
+                              div(class="plotlybars-bar b5"),
+                              div(class="plotlybars-bar b6"),
+                              div(class="plotlybars-bar b7")
+                         ),
+                         div(class="plotlybars-text",
+                             p("Shiny is on its way!")
+                         )
+                     )
+                ),
+                # Hiding the application content till the page is ready
+                hidden(
+                  div(
+                    id = "app",
+                    sidebarLayout(
+                      source_ui("sidebar_UI.R"), # Sidebar
+                      mainPanel(navbarPage(title = NULL,
+                                           tabPanel(h4("Select Data"),
+                                                    # tabsetPanel(
+                                                    source_ui("select_data_UI.R")
+                                                    # )
+                                           ),
+                                           tabPanel(h4("Exploratory Plots"),
+                                                    tabsetPanel(
+                                                      source_ui("model_plots_UI.R"),
+                                                      source_ui("model_data_plots_UI.R")
+                                                    )
+                                           ),
+                                           tabPanel(h4("Benchmarking"),
+                                                    tabsetPanel(
+                                                      source_ui("benchmarking_settings_UI.R"),
+                                                      source_ui("benchmarking_scores_UI.R"),
+                                                      source_ui("benchmarking_plots_UI.R")
+                                                    )
+                                           ),
+                                           tabPanel(h4("Documentation"),
+                                                    withMathJax(includeMarkdown("markdown/workflowPlot_doc.Rmd"))
+                                           )
+                      )
+
+                      )
+                    )
+                  )
+                )
+                )
\ No newline at end of file
diff --git a/shiny/workflowPlot/ui_files/benchmarking_plots_UI.R b/shiny/workflowPlot/ui_files/benchmarking_plots_UI.R
new file mode 100644
index 00000000000..9b365456731
--- /dev/null
+++ b/shiny/workflowPlot/ui_files/benchmarking_plots_UI.R
@@ -0,0 +1,22 @@
+tabPanel("Plots",
+         uiOutput("bm_plots"),
+         div(
+           id = "plot-container",
+           div(
+             class = "plotlybars-wrapper",
+             div(
+               class = "plotlybars",
+               div(class = "plotlybars-bar b1"),
+               div(class = "plotlybars-bar b2"),
+               div(class = "plotlybars-bar b3"),
+               div(class = "plotlybars-bar b4"),
+               div(class = "plotlybars-bar b5"),
+               div(class = "plotlybars-bar b6"),
+               div(class = "plotlybars-bar b7")
+             ),
+             div(class = "plotlybars-text",
+                 p("Updating the plot. Hold tight!"))
+           ),
+           plotlyOutput("bmPlot")
+         )
+)
diff --git a/shiny/workflowPlot/ui_files/benchmarking_scores_UI.R b/shiny/workflowPlot/ui_files/benchmarking_scores_UI.R
new file mode 100644
index 00000000000..31c779fba95
--- /dev/null
+++ b/shiny/workflowPlot/ui_files/benchmarking_scores_UI.R
@@ -0,0 +1,3 @@
+tabPanel("Scores", 
+         DT::dataTableOutput("results_table")
+)
\ No newline at end of file
diff --git a/shiny/workflowPlot/ui_files/benchmarking_settings_UI.R b/shiny/workflowPlot/ui_files/benchmarking_settings_UI.R
new file mode 100644
index 00000000000..e4bf0083c04
--- /dev/null
+++ b/shiny/workflowPlot/ui_files/benchmarking_settings_UI.R
@@ -0,0 +1,24 @@
+tabPanel("Settings", 
+         column(12, h3("Setup Reference Run")),
+         column(12, 
+                verbatimTextOutput("brr_message"),
+                uiOutput("button_BRR")
+         ),
+         column(12,
+                h3("Setup Benchmarks")),
+         column(12, 
+                uiOutput("results_message"),
+                uiOutput("bm_inputs")
+         ),
+         column(12, h3("Calculate Benchmarks")),
+         column(12, 
+                verbatimTextOutput("calc_bm_message"),
+                # verbatimTextOutput("report"),
+                uiOutput("calc_bm_button"),
+                uiOutput("inputs_df_table"),
+                uiOutput("config_list_table"),
+                uiOutput("reportvars"),
+                uiOutput("reportmetrics"),
+                uiOutput("print_bm_settings")
+         )
+)
\ No newline at end of file
diff --git a/shiny/workflowPlot/ui_files/model_data_plots_UI.R b/shiny/workflowPlot/ui_files/model_data_plots_UI.R
new file mode 100644
index 00000000000..dd1c5e35aab
--- /dev/null
+++ b/shiny/workflowPlot/ui_files/model_data_plots_UI.R
@@ -0,0 +1,74 @@
+tabPanel(
+  "Model-Data Plots",
+  hidden(div(id = "model_data_plot_interactive", column(
+    12,
+    div(
+      id = "plot-container",
+      div(
+        class = "plotlybars-wrapper",
+        div(
+          class = "plotlybars",
+          div(class = "plotlybars-bar b1"),
+          div(class = "plotlybars-bar b2"),
+          div(class = "plotlybars-bar b3"),
+          div(class = "plotlybars-bar b4"),
+          div(class = "plotlybars-bar b5"),
+          div(class = "plotlybars-bar b6"),
+          div(class = "plotlybars-bar b7")
+        ),
+        div(class = "plotlybars-text",
+            p("Updating the plot. Hold tight!"))
+      ),
+      plotlyOutput("modelDataPlot")
+    )
+  ))),
+  div(id = "model_data_plot_static", column(
+    12,
+    div(
+      id = "plot-container",
+      div(
+        class = "plotlybars-wrapper",
+        div(
+          class = "plotlybars",
+          div(class = "plotlybars-bar b1"),
+          div(class = "plotlybars-bar b2"),
+          div(class = "plotlybars-bar b3"),
+          div(class = "plotlybars-bar b4"),
+          div(class = "plotlybars-bar b5"),
+          div(class = "plotlybars-bar b6"),
+          div(class = "plotlybars-bar b7")
+        ),
+        div(class = "plotlybars-text",
+            p("Updating the plot. Hold tight!"))
+      ),
+      plotlyOutput("modelDataPlotStatic")
+    )
+  )),
+  column(12, wellPanel(
+    actionButton("ex_plot_modeldata", "Generate Plot"),
+    div(actionButton("model_data_toggle_plot", "Toggle Plot"),
+        style = "float:right")
+  )),
+  column(
+    12,
+    wellPanel(
+      selectInput("var_name_modeldata", "Variable Name", ""),
+      textInput("units_modeldata", "Units",
+                placeholder = "Type units in udunits2 compatible format"),
+      verbatimTextOutput("unit_text2"),
+      radioButtons(
+        "plotType_modeldata",
+        "Plot Type (for Model Outputs)",
+        c("Scatter Plot" = "point", "Line Chart" = "line"),
+        selected = "point"
+      ),
+      sliderInput(
+        "smooth_n_modeldata",
+        "Value for smoothing:",
+        min = 0,
+        max = 100,
+        value = 80
+      )
+    )
+  )
+)
diff --git a/shiny/workflowPlot/ui_files/model_plots_UI.R b/shiny/workflowPlot/ui_files/model_plots_UI.R
new file mode 100644
index 00000000000..7ed8888d3bb
--- /dev/null
+++ b/shiny/workflowPlot/ui_files/model_plots_UI.R
@@ -0,0 +1,74 @@
+tabPanel(
+  "Model Plots",
+  hidden(div(id = "model_plot_interactive", column(
+    12,
+    div(
+      id = "plot-container",
+      div(
+        class = "plotlybars-wrapper",
+        div(
+          class = "plotlybars",
+          div(class = "plotlybars-bar b1"),
+          div(class = "plotlybars-bar b2"),
+          div(class = "plotlybars-bar b3"),
+          div(class = "plotlybars-bar b4"),
+          div(class = "plotlybars-bar b5"),
+          div(class = "plotlybars-bar b6"),
+          div(class = "plotlybars-bar b7")
+        ),
+        div(class = "plotlybars-text",
+            p("Updating the plot. Hold tight!"))
+      ),
+      plotlyOutput("modelPlot")
+    )
+  ))),
+  div(id = "model_plot_static", column(
+    12,
+    div(
+      id = "plot-container",
+      div(
+        class = "plotlybars-wrapper",
+        div(
+          class = "plotlybars",
+          div(class = "plotlybars-bar b1"),
+          div(class = "plotlybars-bar b2"),
+          div(class = "plotlybars-bar b3"),
+          div(class = "plotlybars-bar b4"),
+          div(class = "plotlybars-bar b5"),
+          div(class = "plotlybars-bar b6"),
+          div(class = "plotlybars-bar b7")
+        ),
+        div(class = "plotlybars-text",
+            p("Updating the plot. Hold tight!"))
+      ),
+      plotlyOutput("modelPlotStatic")
+    )
+  )),
+  column(12, wellPanel(
+    actionButton("ex_plot_model", "Generate Plot"),
+    div(actionButton("model_toggle_plot", "Toggle Plot"),
+        style = "float:right")
+  )),
+  column(
+    12,
+    wellPanel(
+      selectInput("var_name_model", "Variable Name", ""),
+      textInput("units_model", "Units",
+                placeholder = "Type units in udunits2 compatible format"),
+      verbatimTextOutput("unit_text"),
+      radioButtons(
+        "plotType_model",
+        "Plot Type (for Model Outputs)",
+        c("Scatter Plot" = "point", "Line Chart" = "line"),
+        selected = "point"
+      ),
+      sliderInput(
+        "smooth_n_model",
+        "Value for smoothing:",
+        min = 0,
+        max = 100,
+        value = 80
+      )
+    )
+  )
+)
diff --git a/shiny/workflowPlot/ui_files/select_data_UI.R b/shiny/workflowPlot/ui_files/select_data_UI.R
new file mode 100644
index 00000000000..873ad1b06e5
--- /dev/null
+++ b/shiny/workflowPlot/ui_files/select_data_UI.R
@@ -0,0 +1,6 @@
+# Select_Data
+
+tagList(
+  column(6, htmlOutput("README")),
+  column(6, verbatimTextOutput("dim_message"))
+)
diff --git a/shiny/workflowPlot/ui_files/sidebar_UI.R b/shiny/workflowPlot/ui_files/sidebar_UI.R
new file mode 100644
index 00000000000..505afa80afa
--- /dev/null
+++ b/shiny/workflowPlot/ui_files/sidebar_UI.R
@@ -0,0 +1,18 @@
+sidebarPanel(
+  h3("Load Model Output"),
+  wellPanel(
+    p("Please select the workflow IDs to continue. You can select multiple IDs"),
+    selectizeInput("all_workflow_id", "Mutliple Workflow IDs", c(), multiple=TRUE),
+    p("Please select the run IDs. You can select multiple IDs"),
+    selectizeInput("all_run_id", "Mutliple Run IDs", c(), multiple=TRUE),
+    actionButton("load_model", "Load Model outputs")
+  ),
+  h3("Load External Data"),
+  wellPanel(
+    selectizeInput("all_site_id", "Select Site ID", c()),
+    # If loading multiple sites in future
+    # selectizeInput("all_site_id", "Select Site ID", c(), multiple=TRUE),
+    selectizeInput("all_input_id", "Select Input ID", c()),
+    actionButton("load_data", "Load External Data")
+  )
+)
\ No newline at end of file
diff --git a/shiny/workflowPlot/ui_utils.R b/shiny/workflowPlot/ui_utils.R
new file mode 100644
index 00000000000..1c2630c2f75
--- /dev/null
+++ b/shiny/workflowPlot/ui_utils.R
@@ -0,0 +1,11 @@
+source_ui <- function(...) {
+  source(
+    file.path("ui_files", ...),
+    local = TRUE
+  )$value
+}
+
+load_anim_div <- function(plot_div) {
+  plot_var <- plot_div
+  source_ui("load_animation_div.R")
+}
\ No newline at end of file
diff --git a/shiny/workflowPlot/www/style.css b/shiny/workflowPlot/www/style.css
new file mode 100644
index 00000000000..e4d0d017911
--- /dev/null
+++ b/shiny/workflowPlot/www/style.css
@@ -0,0 +1,322 @@
+#loading-content {
+    position: absolute;
+    background: #ffffff;
+    opacity: 0.9;
+    z-index: 100;
+    text-align: center;
+    color: #FFFFFF;
+    top: 50%;
+    left: 50%;
+    height: 30%;
+    width: 50%;
+    margin: -15% 0 0 -25%;
+}
+
+.plotly.html-widget.html-widget-output.shiny-bound-output.js-plotly-plot {
+    z-index: 22;
+    position: relative;
+}
+
+.plotlybars {
+    padding: 0 10px;
+    vertical-align: bottom;
+    width: 100%;
+    height: 100%;
+    overflow: hidden;
+    position: relative;
+    box-sizing: border-box;
+}
+
+.plotlybars-wrapper {
+    width: 165px;
+    height: 100px;
+    margin: 0 auto;
+    left: 0;
+    right: 0;
+    position: absolute;
+    z-index: 1;
+}
+
+.plotlybars-text {
+    color: #2E86C1;
+    font-family: 'Open Sans', verdana, arial, sans-serif;
+    font-size: 80%;
+    text-align: center;
+    margin-top: 5px;
+}
+
+.plotlybars-bar {
+    background-color: #2874A6;
+    height: 100%;
+    width: 13.3%;
+    position: absolute;
+    -webkit-transform: translateZ(0);
+    transform: translateZ(0);
+    animation-duration: 2s;
+    animation-iteration-count: infinite;
+    animation-direction: normal;
+    animation-timing-function: linear;
+    -webkit-animation-duration: 2s;
+    -webkit-animation-iteration-count: infinite;
+    -webkit-animation-direction: normal;
+    -webkit-animation-timing-function: linear;
+}
+
+.b1 {
+    left: 0%;
+    top: 88%;
+    animation-name: b1;
+    -webkit-animation-name: b1;
+}
+
+.b2 {
+    left: 14.3%;
+    top: 76%;
+    animation-name: b2;
+    -webkit-animation-name: b2;
+}
+
+.b3 {
+    left: 28.6%;
+    top: 16%;
+    animation-name: b3;
+    -webkit-animation-name: b3;
+}
+
+.b4 {
+    left: 42.9%;
+    top: 40%;
+    animation-name: b4;
+    -webkit-animation-name: b4;
+}
+
+.b5 {
+    left: 57.2%;
+    top: 26%;
+    animation-name: b5;
+    -webkit-animation-name: b5;
+}
+
+.b6 {
+    left: 71.5%;
+    top: 67%;
+    animation-name: b6;
+    -webkit-animation-name: b6;
+}
+
+.b7 {
+    left: 85.8%;
+    top: 89%;
+    animation-name: b7;
+    -webkit-animation-name: b7;
+}
+
+@keyframes b1 {
+    0% {
+        top: 88%;
+    }
+    44% {
+        top: 0%;
+    }
+    94% {
+        top: 100%;
+    }
+    100% {
+        top: 88%;
+    }
+}
+
+@-webkit-keyframes b1 {
+    0% {
+        top: 88%;
+    }
+    44% {
+        top: 0%;
+    }
+    94% {
+        top: 100%;
+    }
+    100% {
+        top: 88%;
+    }
+}
+
+@keyframes b2 {
+    0% {
+        top: 76%;
+    }
+    38% {
+        top: 0%;
+    }
+    88% {
+        top: 100%;
+    }
+    100% {
+        top: 76%;
+    }
+}
+
+@-webkit-keyframes b2 {
+    0% {
+        top: 76%;
+    }
+    38% {
+        top: 0%;
+    }
+    88% {
+        top: 100%;
+    }
+    100% {
+        top: 76%;
+    }
+}
+
+@keyframes b3 {
+    0% {
+        top: 16%;
+    }
+    8% {
+        top: 0%;
+    }
+    58% {
+        top: 100%;
+    }
+    100% {
+        top: 16%;
+    }
+}
+
+@-webkit-keyframes b3 {
+    0% {
+        top: 16%;
+    }
+    8% {
+        top: 0%;
+    }
+    58% {
+        top: 100%;
+    }
+    100% {
+        top: 16%;
+    }
+}
+
+@keyframes b4 {
+    0% {
+        top: 40%;
+    }
+    20% {
+        top: 0%;
+    }
+    70% {
+        top: 100%;
+    }
+    100% {
+        top: 40%;
+    }
+}
+
+@-webkit-keyframes b4 {
+    0% {
+        top: 40%;
+    }
+    20% {
+        top: 0%;
+    }
+    70% {
+        top: 100%;
+    }
+    100% {
+        top: 40%;
+    }
+}
+
+@keyframes b5 {
+    0% {
+        top: 26%;
+    }
+    13% {
+        top: 0%;
+    }
+    63% {
+        top: 100%;
+    }
+    100% {
+        top: 26%;
+    }
+}
+
+@-webkit-keyframes b5 {
+    0% {
+        top: 26%;
+    }
+    13% {
+        top: 0%;
+    }
+    63% {
+        top: 100%;
+    }
+    100% {
+        top: 26%;
+    }
+}
+
+@keyframes b6 {
+    0% {
+        top: 67%;
+    }
+    33.5% {
+        top: 0%;
+    }
+    83% {
+        top: 100%;
+    }
+    100% {
+        top: 67%;
+    }
+}
+
+@-webkit-keyframes b6 {
+    0% {
+        top: 67%;
+    }
+    33.5% {
+        top: 0%;
+    }
+    83% {
+        top: 100%;
+    }
+    100% {
+        top: 67%;
+    }
+}
+
+@keyframes b7 {
+    0% {
+        top: 89%;
+    }
+    44.5% {
+        top: 0%;
+    }
+    94.5% {
+        top: 100%;
+    }
+    100% {
+        top: 89%;
+    }
+}
+
+@-webkit-keyframes b7 {
+    0% {
+        top: 89%;
+    }
+    44.5% {
+        top: 0%;
+    }
+    94.5% {
+        top: 100%;
+    }
+    100% {
+        top: 89%;
+    }
+}
diff --git a/tests/ebi-forecast.igb.illinois.edu.biocro.xml b/tests/ebi-forecast.igb.illinois.edu.biocro.xml
index 5be942a6cb4..51faecc20ea 100644
--- a/tests/ebi-forecast.igb.illinois.edu.biocro.xml
+++ b/tests/ebi-forecast.igb.illinois.edu.biocro.xml
@@ -11,6 +11,7 @@
       <dbname>bety</dbname>
       <write>FALSE</write>
     </bety>
+    <dbfiles>.pecan/dbfiles</dbfiles>
   </database>
 
   <pfts>
@@ -55,6 +56,5 @@
     <host>
       <name>localhost</name>
     </host>
-    <dbfiles>.pecan/dbfiles</dbfiles>
   </run>
 </pecan>
diff --git a/tests/pecan64.biocro.xml b/tests/pecan64.biocro.xml
index 91eb4ead8bb..32750b718e7 100644
--- a/tests/pecan64.biocro.xml
+++ b/tests/pecan64.biocro.xml
@@ -11,6 +11,7 @@
       <dbname>bety</dbname>
       <write>FALSE</write>
     </bety>
+    <dbfiles>pecan/dbfiles</dbfiles>
   </database>
 
   <pfts>
@@ -59,6 +60,5 @@
     <host>
       <name>localhost</name>
     </host>
-    <dbfiles>pecan/dbfiles</dbfiles>
   </run>
 </pecan>
diff --git a/web/01-introduction.php b/web/01-introduction.php
index 1f0f06fef85..746ecec4d20 100644
--- a/web/01-introduction.php
+++ b/web/01-introduction.php
@@ -80,7 +80,7 @@ function nextStep() {
 <br>
   <a href="https://pecanproject.github.io/pecan-documentation/master/" target="_blank">Documentation</a>
 <br>
-  <a href="https://gitter.im/PecanProject/pecan" target="_blank">Chat Room</a>
+  <a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE" target="_blank">Chat Room</a>
 <br>
   <a href="setups/submitissues.php" target="_blank">Bug Report</a>
 </p>
diff --git a/web/02-modelsite.php b/web/02-modelsite.php
index ccad8ba1d57..4691f4b0bd2 100644
--- a/web/02-modelsite.php
+++ b/web/02-modelsite.php
@@ -626,7 +626,7 @@ function goHome() {
 <p>
   <a href="https://pecanproject.github.io/pecan-documentation/master" target="_blank">Documentation</a>
   <br>
-  <a href="https://gitter.im/PecanProject/pecan" target="_blank">Chat Room</a>
+  <a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE" target="_blank">Chat Room</a>
   <br>
   <a href="https://github.com/PecanProject/pecan/issues/new" target="_blank">Bug Report</a>
 </p>
diff --git a/web/03-inputs.php b/web/03-inputs.php
index 42ca9a6c7eb..0fc0e63bafa 100644
--- a/web/03-inputs.php
+++ b/web/03-inputs.php
@@ -383,7 +383,6 @@ function mapsLoaded() {
         <input name="userok" type="hidden" value="on">
 <?php } ?>
 <?php foreach($_REQUEST as $key => $value){
-		file_put_contents('php://stderr', print_r('key top ' + $key, TRUE));
         if(is_array($value)) {
           foreach($value as $v) {
             echo "<input name=\"${key}[]\" id=\"${key}[]\" type=\"hidden\" value=\"${v}\"/>";
@@ -467,7 +466,7 @@ function mapsLoaded() {
 <p>
   <a href="https://pecanproject.github.io/pecan-documentation/master" target="_blank">Documentation</a>
   <br>
-  <a href="https://gitter.im/PecanProject/pecan" target="_blank">Chat Room</a>
+  <a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE" target="_blank">Chat Room</a>
   <br>
   <a href="https://github.com/PecanProject/pecan/issues/new" target="_blank">Bug Report</a>
 </p>
diff --git a/web/04-runpecan.php b/web/04-runpecan.php
index d53dc834abf..34eeb6f96bd 100644
--- a/web/04-runpecan.php
+++ b/web/04-runpecan.php
@@ -8,6 +8,7 @@
  * http://opensource.ncsa.illinois.edu/license.html
  */
 require("common.php");
+
 open_database();
 if ($authentication) {
   if (!check_login()) {
@@ -95,6 +96,10 @@
 if (isset($_REQUEST['variables'])) {
   $variables = $_REQUEST['variables'];
 }
+$parm_method = "uniform";
+if (isset($_REQUEST['parm_method'])) {
+  $parm_method = $_REQUEST['parm_method'];
+}
 $notes_xml = "";
 $notes_db = "";
 if (isset($_REQUEST['notes'])) {
@@ -244,6 +249,9 @@
 fwrite($fh, "      <user>${db_bety_username}</user>" . PHP_EOL);
 fwrite($fh, "      <password>${db_bety_password}</password>" . PHP_EOL);
 fwrite($fh, "      <host>${db_bety_hostname}</host>" . PHP_EOL);
+if (isset($db_bety_port)) {
+        fwrite($fh, "      <port>${db_bety_port}</port>" . PHP_EOL);
+}
 fwrite($fh, "      <dbname>${db_bety_database}</dbname>" . PHP_EOL);
 if ($db_bety_type == "mysql") {
 	fwrite($fh, "      <driver>MySQL</driver>" . PHP_EOL);
@@ -258,6 +266,9 @@
 	fwrite($fh, "      <user>${db_fia_username}</user>" . PHP_EOL);
 	fwrite($fh, "      <password>${db_fia_password}</password>" . PHP_EOL);
 	fwrite($fh, "      <host>${db_fia_hostname}</host>" . PHP_EOL);
+        if (isset($db_fia_port)) {
+                fwrite($fh, "      <port>${db_fia_port}</port>" . PHP_EOL);
+        }
 	fwrite($fh, "      <dbname>${db_fia_database}</dbname>" . PHP_EOL);
 	if ($db_fia_type == "mysql") {
 		fwrite($fh, "      <driver>MySQL</driver>" . PHP_EOL);
@@ -298,13 +309,29 @@
 
 if (!empty($runs)){
 	fwrite($fh, "  <ensemble>" . PHP_EOL);
-	fwrite($fh, "    <size>${runs}</size>" . PHP_EOL);
-	fwrite($fh, "    <variable>${variables}</variable>" . PHP_EOL);
+	fwrite($fh, "   <size>${runs}</size>" . PHP_EOL);
+	fwrite($fh, "   <variable>${variables}</variable>" . PHP_EOL);
+	fwrite($fh, "   <samplingspace>" . PHP_EOL);
+	fwrite($fh, "   <parameters>" . PHP_EOL);
+	fwrite($fh, "    <method>${parm_method}</method>" . PHP_EOL);
+	fwrite($fh, "   </parameters>" . PHP_EOL);
+	fwrite($fh, "   <met>" . PHP_EOL);
+	fwrite($fh, "    <method>sampling</method>" . PHP_EOL);
+    	fwrite($fh, " 	</met>" . PHP_EOL);
+	fwrite($fh, "   </samplingspace>" . PHP_EOL);
 	fwrite($fh, "  </ensemble>" . PHP_EOL);
 } else {
 	fwrite($fh, "  <ensemble>" . PHP_EOL);
 	fwrite($fh, "    <size>1</size>" . PHP_EOL);
 	fwrite($fh, "    <variable>NPP</variable>" . PHP_EOL);
+	fwrite($fh, "    <samplingspace>" . PHP_EOL);
+	fwrite($fh, "     <parameters>" . PHP_EOL);
+	fwrite($fh, "       <method>uniform</method>" . PHP_EOL);
+	fwrite($fh, "     </parameters>" . PHP_EOL);
+	fwrite($fh, "     <met>" . PHP_EOL);
+	fwrite($fh, "       <method>sampling</method>" . PHP_EOL);
+   	 fwrite($fh, "    </met>" . PHP_EOL);
+	fwrite($fh, "    </samplingspace>" . PHP_EOL);
 	fwrite($fh, "  </ensemble>" . PHP_EOL);
 }
 
@@ -425,6 +452,15 @@
     fwrite($fh, "    <data_hostname>" . toXML($hostoptions['data_hostname']) . "</data_hostname>" . PHP_EOL);
   }
 }
+if ($rabbitmq_host != "") {
+  $rabbitmq_uri = "amqp://" . $rabbitmq_username . ":" . $rabbitmq_password . "@" . $rabbitmq_host . ":" . $rabbitmq_port . "/" . urlencode($rabbitmq_vhost);
+  $rabbitmq_model_queue = $modeltype . "_" . $revision;
+
+  fwrite($fh, "    <rabbitmq>" . PHP_EOL);
+  fwrite($fh, "      <uri>" . $rabbitmq_uri . "</uri>" . PHP_EOL);
+  fwrite($fh, "      <queue>" . $rabbitmq_model_queue . "</queue>" . PHP_EOL);
+  fwrite($fh, "    </rabbitmq>" . PHP_EOL);
+}
 fwrite($fh, "  </host>" . PHP_EOL);
 
 if ($email != "") {
@@ -480,6 +516,46 @@
     $path .= "&offline=offline";
   }
   header("Location: ${path}");
+} else if ($rabbitmq_host != "") {
+
+  # create connection and queue
+  $connection = new AMQPConnection();
+  $connection->setHost($rabbitmq_host);
+  $connection->setPort($rabbitmq_port);
+  $connection->setVhost($rabbitmq_vhost);
+  $connection->setLogin($rabbitmq_username);
+  $connection->setPassword($rabbitmq_password);
+  $connection->connect();
+  $channel = new AMQPChannel($connection);
+  $exchange = new AMQPExchange($channel);
+
+  # create the queue
+  $queue = new AMQPQueue($channel);
+  $queue->setName($rabbitmq_queue);
+  $queue->setFlags(AMQP_DURABLE);
+  $queue->declareQueue();
+
+  # create the message
+  $message = '{"folder": "' . $folder . '", "workflowid": "' . $workflowid . '"}';
+
+  # send the message
+  $exchange->publish($message, $rabbitmq_queue);
+
+  # cleanup
+  $connection->disconnect();
+
+  #done
+  $path = "05-running.php?workflowid=$workflowid";
+  if ($pecan_edit) {
+    $path .= "&pecan_edit=pecan_edit";
+  }
+  if ($model_edit) {
+    $path .= "&model_edit=model_edit";
+  }
+  if ($offline) {
+    $path .= "&offline=offline";
+  }
+  header("Location: ${path}");
 } else {
   # start the actual workflow
   chdir($folder);
diff --git a/web/05-running.php b/web/05-running.php
index 84abcad8c15..f377c37d748 100644
--- a/web/05-running.php
+++ b/web/05-running.php
@@ -157,7 +157,7 @@ function refresh() {
 <p>
   <a href="https://pecanproject.github.io/pecan-documentation/master" target="_blank">Documentation</a>
   <br>
-  <a href="https://gitter.im/PecanProject/pecan" target="_blank">Chat Room</a>
+  <a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE" target="_blank">Chat Room</a>
   <br>
   <a href="https://github.com/PecanProject/pecan/issues/new" target="_blank">Bug Report</a>
 </p>
diff --git a/web/06-edit.php b/web/06-edit.php
index 3d1bd0773b2..d7fa2f2ac92 100644
--- a/web/06-edit.php
+++ b/web/06-edit.php
@@ -196,7 +196,7 @@ function endsWith(haystack, needle) {
 <p>
   <a href="https://pecanproject.github.io/pecan-documentation/master" target="_blank">Documentation</a>
   <br>
-  <a href="https://gitter.im/PecanProject/pecan" target="_blank">Chat Room</a>
+  <a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE" target="_blank">Chat Room</a>
   <br>
   <a href="https://github.com/PecanProject/pecan/issues/new" target="_blank">Bug Report</a>
 </p>
diff --git a/web/07-analysis.php b/web/07-analysis.php
index 8c5c81fffd5..0d646743688 100644
--- a/web/07-analysis.php
+++ b/web/07-analysis.php
@@ -235,6 +235,15 @@ function mapsLoaded() {
       <label>Variables<sup>*</sup></label></a>
       <input type="text" name="variables" id="variables" value="<?php echo "NPP"; ?>" onChange="validate();"/>
       <div class="spacer"></div>
+      <label>Sampling method for parameters<sup>*</sup></label>
+      <select name="parm_method" id="parm_method" onChange="validate();">
+      <option value="<?php echo "uniform"; ?>">Uniform</option>
+      <option value="<?php echo "halton"; ?>">Halton</option>
+      <option value="<?php echo "sobol"; ?>">Sobol</option>
+      <option value="<?php echo "torus"; ?>">Torus</option>
+      <option value="<?php echo "lhc"; ?>">Latin hypercube</option>
+     </select>
+      <div class="spacer"></div>
 
       <div class="spacer"></div>
       <label type="hidden">Sensitivity</label>
@@ -254,7 +263,7 @@ function mapsLoaded() {
 <p>
   <a href="https://pecanproject.github.io/pecan-documentation/master" target="_blank">Documentation</a>
   <br>
-  <a href="https://gitter.im/PecanProject/pecan" target="_blank">Chat Room</a>
+  <a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE" target="_blank">Chat Room</a>
   <br>
   <a href="https://github.com/PecanProject/pecan/issues/new" target="_blank">Bug Report</a>
 </p>
diff --git a/web/08-finished.php b/web/08-finished.php
index 23507722f62..8084bf0e96d 100644
--- a/web/08-finished.php
+++ b/web/08-finished.php
@@ -533,7 +533,7 @@ function startsWith(haystack, needle) {
 <p>
   <a href="https://pecanproject.github.io/pecan-documentation/master/" target="_blank">Documentation</a>
   <br>
-  <a href="https://gitter.im/PecanProject/pecan" target="_blank">Chat Room</a>
+  <a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE" target="_blank">Chat Room</a>
   <br>
   <a href="https://github.com/PecanProject/pecan/issues/new" target="_blank">Bug Report</a>
 </p>
diff --git a/web/checkfailed.php b/web/checkfailed.php
index 5a0150d22fd..5e5968231c0 100644
--- a/web/checkfailed.php
+++ b/web/checkfailed.php
@@ -80,7 +80,7 @@ function nextStep() {
 <p>
   <a href="https://pecan.gitbooks.io/pecan-documentation/content/" target="_blank">Documentation</a>
   <br>
-  <a href="https://gitter.im/PecanProject/pecan" target="_blank">Chat Room</a>
+  <a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE" target="_blank">Chat Room</a>
   <br>
   <a href="https://github.com/PecanProject/pecan/issues/new" target="_blank">Bug Report</a>
 </p>
diff --git a/web/common.php b/web/common.php
index 849e3ebb05f..73fa580fb04 100644
--- a/web/common.php
+++ b/web/common.php
@@ -12,7 +12,7 @@ function get_footer() {
   return "The <a href=\"http://pecanproject.org\">PEcAn project</a> is supported by the National Science Foundation
     (ABI #1062547, ABI #1458021, DIBBS #1261582, ARC #1023477, EF #1318164, EF #1241894, EF #1241891), NASA
     Terrestrial Ecosystems, Department of Energy (ARPA-E #DE-AR0000594 and #DE-AR0000598), the Energy Biosciences Institute, and an Amazon AWS in Education Grant.
-    <span style=\"float:right\">PEcAn Version 1.5.3</span>";
+    <span style=\"float:right\">PEcAn Version 1.6.0</span>";
 }
 
 function whoami() {
diff --git a/web/config.example.php b/web/config.example.php
index 07234f6c1fd..dd1ced9c3d3 100644
--- a/web/config.example.php
+++ b/web/config.example.php
@@ -3,6 +3,7 @@
 # Information to connect to the BETY database
 $db_bety_type="pgsql";
 $db_bety_hostname="localhost";
+$db_bety_port=5432;
 $db_bety_username="bety";
 $db_bety_password="bety";
 $db_bety_database="bety";
diff --git a/web/curl.php b/web/curl.php
new file mode 100644
index 00000000000..12fea4456cd
--- /dev/null
+++ b/web/curl.php
@@ -0,0 +1,66 @@
+<?php
+require("common.php");
+open_database();
+
+// runid
+if (!isset($_REQUEST['workflowid'])) {
+  die("Need a workflowid.");
+}
+$workflowid=$_REQUEST['workflowid'];
+
+// get run information
+$stmt = $pdo->prepare("SELECT * FROM workflows WHERE workflows.id=?");
+if (!$stmt->execute(array($workflowid))) {
+  die('Invalid query: ' . error_database());
+}
+$workflow = $stmt->fetch(PDO::FETCH_ASSOC);
+$stmt->closeCursor();
+$start = substr($workflow['start_date'], 0, 4);
+$end = substr($workflow['end_date'], 0, 4);
+$folder = $workflow['folder'];
+$notes = htmlspecialchars($workflow['notes']);
+$params = $workflow['params'];
+if ($params == '') {
+  die('No parameters found, was this not launched from web interface?');
+}
+eval('$array = ' . $params . ';');
+
+$pft=$array['pft'];
+
+
+$stmt = $pdo->prepare("SELECT model_name, revision FROM models WHERE id=?;");
+if (!$stmt->execute(array($array['modelid']))) {
+  die('Invalid query: ' . error_database());
+}
+$model = "";
+while ($row = @$stmt->fetch(PDO::FETCH_ASSOC)) {
+    $model = "${row['model_name']} (v${row['revision']})";
+}
+$stmt->closeCursor();
+
+
+echo "<pre>\n";
+echo "# model       : ${model}\n";
+echo "# site        : ${array['sitename']}\n";
+echo "# pft         : ${pft[0]}\n";
+echo "# time range  : ${array['start']} - ${array['end']}\n";
+echo "curl -v -X POST \\\n";
+echo "    -F 'hostname=${array['hostname']}' \\\n";
+echo "    -F 'modelid=${array['modelid']}' \\\n";
+echo "    -F 'sitegroupid=1' \\\n";
+echo "    -F 'siteid=${array['siteid']}' \\\n";
+echo "    -F 'sitename=${array['sitename']}' \\\n";
+echo "    -F 'pft[]=${pft[0]}' \\\n";
+echo "    -F 'start=${array['start']}' \\\n";
+echo "    -F 'end=${array['end']}' \\\n";
+foreach($array as $key => $value) {
+    if (substr($key, 0, 6) === "input_" && $value !== "-1") {
+        echo "    -F '${key}=${value}' \\\n";
+    }
+}
+echo "    -F 'email=' \\\n";
+echo "    -F 'notes=' \\\n";
+echo "    'http://localhost:6480/pecan/04-runpecan.php'\n";
+echo "</pre>";
+
+close_database();
diff --git a/web/history.php b/web/history.php
index c769adf1196..1f8888a26e3 100644
--- a/web/history.php
+++ b/web/history.php
@@ -96,6 +96,7 @@ function filter() {
         row += '  <div class="cell">' + workflow.attr("started_at") + '</div>';
         row += '  <div class="cell">' + workflow.attr("finished_at") + '</div>';
 <?php if (check_login() && (get_page_acccess_level() <= $min_delete_level)) { ?>
+        row += '  <div class="cell"><a href="curl.php?workflowid=' + workflow.attr("id") + '">CURL</a></div>';
         row += '  <div class="cell"><a href="delete.php?workflowid=' + workflow.attr("id") + '">DELETE</a></div>';
 <?php } ?>
         row += '</div>';
@@ -158,6 +159,7 @@ function filter() {
           <div class="header">Started</div>
           <div class="header">Finished</div>
 <?php if (check_login() && (get_page_acccess_level() <= $min_delete_level)) { ?>
+          <div class="header">Curl</div>
           <div class="header">Delete</div>
 <?php } ?>
         </div>
diff --git a/web/setups/page.template.php b/web/setups/page.template.php
index 9abe180a4e8..ec25b9378c9 100644
--- a/web/setups/page.template.php
+++ b/web/setups/page.template.php
@@ -54,7 +54,7 @@
       <p>
         <a href="https://pecan.gitbooks.io/pecan-documentation/content/" target="_blank">Documentation</a>
       <br>
-        <a href="https://gitter.im/PecanProject/pecan" target="_blank">Chat Room</a>
+        <a href="https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLTYyZTZiZWQ4NGE1YWU3YWIyMTVmZjEyYzA3OWJhYTZmOWQwMDkwZGU0Mjc4Nzk0NGYwYTIyM2RiZmMyNjg5MTE" target="_blank">Chat Room</a>
       <br>
         <a href="submitissues.php" target="_blank">Bug Report</a>
       </p>
diff --git a/web/workflow.R b/web/workflow.R
index 90990c2616b..1c802e95a4d 100755
--- a/web/workflow.R
+++ b/web/workflow.R
@@ -34,7 +34,7 @@ options(error=quote({
 # Open and read in settings file for PEcAn run.
 args <- commandArgs(trailingOnly = TRUE)
 if (is.na(args[1])){
-  settings <- PEcAn.settings::read.settings("pecan.xml")
+  settings <- PEcAn.settings::read.settings("pecan.xml") 
 } else {
   settings.file = args[1]
   settings <- PEcAn.settings::read.settings(settings.file)
@@ -66,7 +66,7 @@ statusFile <- file.path(settings$outdir, "STATUS")
 if (length(which(commandArgs() == "--continue")) == 0 && file.exists(statusFile)) {
   file.remove(statusFile)
 }
-  
+
 # Do conversions
 settings <- PEcAn.utils::do_conversions(settings)
 
@@ -80,7 +80,7 @@ if (PEcAn.utils::status.check("TRAIT") == 0){
   settings <- PEcAn.settings::read.settings(file.path(settings$outdir, 'pecan.TRAIT.xml'))
 }
 
-  
+
 # Run the PEcAn meta.analysis
 if(!is.null(settings$meta.analysis)) {
   if (PEcAn.utils::status.check("META") == 0){
@@ -89,17 +89,17 @@ if(!is.null(settings$meta.analysis)) {
     PEcAn.utils::status.end()
   }
 }
-  
+
 # Write model specific configs
 if (PEcAn.utils::status.check("CONFIG") == 0){
   PEcAn.utils::status.start("CONFIG")
-  settings <- PEcAn.utils::runModule.run.write.configs(settings)
+  settings <- PEcAn.workflow::runModule.run.write.configs(settings)
   PEcAn.settings::write.settings(settings, outputfile='pecan.CONFIGS.xml')
   PEcAn.utils::status.end()
 } else if (file.exists(file.path(settings$outdir, 'pecan.CONFIGS.xml'))) {
   settings <- PEcAn.settings::read.settings(file.path(settings$outdir, 'pecan.CONFIGS.xml'))
 }
-    
+
 if ((length(which(commandArgs() == "--advanced")) != 0) && (PEcAn.utils::status.check("ADVANCED") == 0)) {
   PEcAn.utils::status.start("ADVANCED")
   q();
@@ -157,13 +157,13 @@ if("benchmarking" %in% names(settings) & "benchmark" %in% names(settings$benchma
   results <- papply(settings, function(x) calc_benchmark(x, bety))
   PEcAn.utils::status.end()
 }
-  
+
 # Pecan workflow complete
 if (PEcAn.utils::status.check("FINISHED") == 0) {
   PEcAn.utils::status.start("FINISHED")
   PEcAn.remote::kill.tunnel(settings)
   db.query(paste("UPDATE workflows SET finished_at=NOW() WHERE id=", settings$workflow$id, "AND finished_at IS NULL"), params=settings$database$bety)
-
+  
   # Send email if configured
   if (!is.null(settings$email) && !is.null(settings$email$to) && (settings$email$to != "")) {
     sendmail(settings$email$from, settings$email$to,