Merge pull request #41 from micokoch/br-v1.0.0

docs/source/index.md

@@ -6,36 +6,7 @@ This project is under active development.
 
 **The Consortium of Infectious Disease Modeling Hubs** is a collaboration of research teams that have built and maintained predictive modeling hubs for infectious disease applications. Working together, we have developed software for groups that are running collaborative modeling hub efforts. This website documents the requirements for using the infrastructure that the Consortium has set up.  
 
-The following sections of this page provide an outline of the different resources created by this project.
-
-## Tools for building and hosting modeling hubs
-
-The following subsections provide pointers to resources developed by the Consortium to make designing, launching, and maintaining hubs easier.
-
-### Template hubs
-
-The [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) provided by the consortium may be cloned directly to start a new hub. Unlike the example hubs below, these repositories do not have any data in them, they just provide a skeletal structure of a hub. Currently, we only host a single [template hub](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate).
-
-### Example hubs
-
-We have created some [example Hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=) that provide minimal working examples of hubs. These repositories could be used for ideas of how to set up configuration files for new projects. They are also used as use-cases for testing the software described below.
-
-- The [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub) is designed to be similar to the [US CDC FluSight Hospitalization Forecasting exercise](https://github.com/cdcepi/Flusight-forecast-data) from 2022-2023.
-- The [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub) is designed to be similar to the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub) and the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe).
-- The [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub) is designed to be similar to the [US COVID-19 Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub)
-
-### Schema files for hub configuration
-
-To take advantage of the infrastructure designed by the Consortium, a hub must contain JSON configuration files in a [specific location and format](hub-config). The schemas that define the structure and formats of the configuration files live in their own [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas). The schemas are versioned, and every hub must point to a specific version of the schemas that they are using.
-
-## Software for modeling hubs
-
-The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models. 
-
-- [hubUtils](https://infectious-disease-modeling-hubs.github.io/hubUtils/) is an R package with utility functions for working with data from modelings hubs.
-- [hubEnsembles](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles) is an R package with functionality to build simple ensembles of data from modeling hubs.
-
-
+The [overview](overview/who-we-are.md) section provides an introduction to the project, and the [getting started](overview/getting-started.md) section outlines how to set up a working hub, as well as the different resources created by this project.  
 
 
 
@@ -48,6 +19,8 @@ The main benefit of setting up a hub using the structure outlined in this docume
 overview/who-we-are.md
 overview/scope.md
 overview/definitions.md
+overview/getting-started.md
+overview/software.md
 ```
 
 ```{toctree}

docs/source/overview/getting-started.md

@@ -0,0 +1,32 @@
+# Getting started  
+
+The following subsections provide pointers to resources developed by the Consortium to make designing, launching, and maintaining hubs easier.  
+
+The simplest way to set up a modeling hub is to directly clone one from the [template hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=) or to use one of the [example hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=), which are based on prior use cases. The template hubs provide a skeletal structure of a hub without any data in them, whereas the example hubs provide minimal working examples of hubs and could be used for ideas of how to set up configuration files for new projects.    
+
+## [Template hubs](https://github.com/Infectious-Disease-Modeling-Hubs?q=&type=template&language=&sort=)  
+
+The [`hubTemplate`](https://github.com/Infectious-Disease-Modeling-Hubs/hubTemplate) repository (under development) provides a skeleton structure for groups wishing to build and maintain a new modeling hub. This repository may be cloned to start a new repository for a modeling hub.  
+
+## [Example hubs](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=)  
+
+The [example Hub repositories](https://github.com/Infectious-Disease-Modeling-Hubs?q=example&type=all&language=&sort=) provide minimal working examples of hubs that can be used for ideas of how to set up configuration files for new projects. They are also used as use-cases for testing the [software for modeling hubs](software.md). 
+
+### 1. [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub)  
+The [Simple Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-simple-forecast-hub) is designed to be similar to the [US CDC FluSight Hospitalization Forecasting exercise](https://github.com/cdcepi/Flusight-forecast-data) from 2022-2023.  
+
+### 2. [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub)  
+The [Complex Forecast Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub) is designed to be similar to the [US COVID-19 Forecast Hub](https://github.com/reichlab/covid19-forecast-hub) and the [European COVID-19 Forecast Hub](https://github.com/covid19-forecast-hub-europe/covid19-forecast-hub-europe).  
+
+### 3. [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub)  
+The [Complex Scenario Hub Example](https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-scenario-hub) is designed to be similar to the [US COVID-19 Scenario Modeling Hub](https://github.com/midas-network/covid19-scenario-modeling-hub)  
+
+
+## [Schema files](https://github.com/Infectious-Disease-Modeling-Hubs/schemas)  
+
+To take advantage of the infrastructure designed by the Consortium, a hub must contain JSON configuration files in a [specific location and format](hub-config). The schemas that define the structure and formats of the configuration files live in their own [schemas repository](https://github.com/Infectious-Disease-Modeling-Hubs/schemas). The schemas are versioned, and every hub must point to a specific version of the schemas that they are using.  
+
+## [Software for modeling hubs](software.md)  
+
+The main benefit of setting up a hub using the structure outlined in this documentation is that it enables you to use a wide array of tools designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
+

docs/source/overview/software.md

@@ -0,0 +1,18 @@
+# Software  
+
+To assist users in building a hub, we have developed a software suite with specific functions and uses outlined below. These tools are designed to support common modeling hub tasks, like loading model output data, plotting the model output data, building ensembles using the data, and in some cases evaluating the predictions made by different models.  
+
+## [`hubUtils`](https://infectious-disease-modeling-hubs.github.io/hubUtils/)  
+
+The goal of `hubUtils` is to provide a set of utility functions for downloading, plotting, and scoring forecast and truth data from Infectious Disease Modeling Hubs. You can find instructions to download and use the package [here](https://infectious-disease-modeling-hubs.github.io/hubUtils/).  
+
+## [`hubEnsembles`](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles)  
+
+`hubEnsembles` is an R package with functionality to build simple ensembles of data from modeling hubs. Different ensembles can be built using for instance the mean, median, and mode. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubEnsembles).  
+
+## [`hubValidations`](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations)  
+
+The `hubValidations` repository facilitates the implementation of general validation rules that are enforced on submissions in the form of pull requests to hub repositories. You can find the complete package and instructions for use [here](https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations).  
+
+
+