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Wip features#67

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rvyuha wants to merge 137 commits intomasterBig-Life-Lab/bllflow:masterfrom WIP-featuresBig-Life-Lab/bllflow:WIP-featuresCopy head branch name to clipboard

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Commits on Apr 1, 2019

• Merge pull request #28 from Big-Life-Lab/small-cells

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Commits on Apr 19, 2019

• Example of using centering, rcs and Fine and Grey modelling using pbc data

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• [feature] linting and add getwd()

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Commits on May 13, 2019

• [Refactor] Added travis settings

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• [Refactor] Merged Stacey's model branch

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• [Feature] Added basic Model Reference creation

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• [Refactor] Added example to vignette

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• [feature] example vignette for CreateBLLModelObject

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• Merge remote-tracking branch 'origin/create-reference' into create-reference

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• [Refactor] Column name change

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Commits on May 21, 2019

• [Feature] Function Skeleton

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Commits on May 27, 2019

• Merge remote-tracking branch 'origin/master' into create-reference

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• [Feature] Cleaner CreateBLLModelObject function structure with additional args

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• [Refactor] Revieved the comments of CreateBLLModelObject

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Commits on May 28, 2019

• [Bug] Fixed check() errors

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• [Bug] Fixed model example rmd not being pkgdown properly

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• [Bug] pkgdown function fix

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Commits on May 31, 2019

• [feature] add vignette to e_model_development.Rmd

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Commits on Jun 4, 2019

• Modify fine and grey example to use rcs2 function

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• Revert commit- will move to new branch

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• Fine and Grey baseline risk and other minor chagnes

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Commits on Jun 25, 2019

• [Feature] Implemented calculateMean param

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• Merge remote-tracking branch 'origin/baseline-risk' into create-reference

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• [Feature] Added baseline

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Commits on Jul 3, 2019

• [Feature] Recipe use Example

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• [Refactor] Better comments

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Commits on Jul 8, 2019

• [Feature] Proposed Implementation of the operations

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• [Refactor] Function name fix

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Commits on Jul 9, 2019

• [Feature] Updated Proof of concept

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Commits on Jul 11, 2019

• [Feature] Added a sample run of modules

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• [Feature] Module sequence error trapping

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• [Feature] TestThat merge

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• [Feature] Master Merge

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• [Bug] Fixed missing comma

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Commits on Jul 17, 2019

• [Feature] Function Object created

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Commits on Jul 22, 2019

• [Feature] Created arg specific functions

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Commits on Aug 6, 2019

• [Refactor] Changed function special character from - to ::

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Commits on Aug 19, 2019

• [Feature] Wrapper function skeleton

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Commits on Aug 20, 2019

• [Feature] Created bllFlow meanImpute

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• [Feature] Added a testing viggnette

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Commits on Sep 9, 2019

• [Feature] Modification on main function loop

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• .

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Commits on Sep 16, 2019

• Merge branch 'recode-with-table' into derived-variable-creation

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• [Feature] Set up recursive function for Function variables

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Commits on Sep 17, 2019

• [Feature] Got the function call working

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Commits on Sep 18, 2019

• [Feature] Recoded Packyears function

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Commits on Sep 23, 2019

• [Feature] Finished packyear recode

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Commits on Sep 24, 2019

• [Feature] PackYears function

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Commits on Sep 26, 2019

• [Feature] Added ability to pass custom functions

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Commits on Oct 1, 2019

• [Feature] Dplyr function calling

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Commits on Oct 3, 2019

• Merge branch 'master' into derived-variable-creation

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• Merge remote-tracking branch 'origin/master' into derived-variable-creation

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• [Feature] Added vignette to test some simple functionallity

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Commits on Oct 7, 2019

• [Feature] Added recusive support for multiple function variables

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Commits on Oct 10, 2019

• [Refactor] Prepping for multi data

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Commits on Oct 15, 2019

• [Feature] List bllFlow creation support

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• [Feature] Template generation

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• [Bug] Fixed non character reading

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• [Refactor] Added better warnings for derived variable creation

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• [Bug] Reverting unsported changes

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Commits on Oct 22, 2019

• [Fix] Addressed merge issues

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• Merge branch 'new-format-update' into step-function-recoding

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• [Feature] Building recipy using steps

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• [Feature] Passed variables as arguments

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Commits on Oct 23, 2019

• [Feature] Reading specific columns

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Commits on Oct 28, 2019

• [Feature] Parsed out variables

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• [Feature] Only specified columns are read

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• [Bug] Fixed funcCellnon character argument

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• [Feature] Added ability to specify number of rows to read

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• [Bug] Fixed null column creation

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• Merge branch 'derived-variable-creation' into dev

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• Merge branch 'importing-data' into dev

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Commits on Oct 29, 2019

• [Feature] Added directory for MSW and modified read data to take variables

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Commits on Oct 31, 2019

• [Feature] Added variable extraction functions

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Commits on Nov 4, 2019

• [Bug] Fixed different functions on same variable in same cycle

  rvyuha

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• [Feature] Got long table working as well as summary table

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Commits on Nov 8, 2019

• add role (#65)

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Commits on Nov 12, 2019

• [Feature] Readded ReadData nrow argument

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Commits on Nov 18, 2019

• [Feature] Skeleton for recipy get and set

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• [Feature] Partial snake_case variable and function name conversion

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Commits on Jan 9, 2020

• [Feature] snake_case_update and test removal

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• [Feature] Added step_z

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• [Feature] Fixed z_score bugs and added testing vignette

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Commits on Jan 15, 2020

• [Feature] Removed list handling added modules

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Commits on Jan 28, 2020

• [Feature] Harrell rcs wrapper function

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Commits on Jan 29, 2020

• [Feature] Added bllflow run_module and apply_missing_tagged_na new function

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Commits on Feb 4, 2020

• [Feature] Added module handling for

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Commits on Feb 6, 2020

• [Feature] Added proper run_module bllflow return

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Commits on Feb 7, 2020

• [Feature] Role selection for table one

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Commits on Feb 10, 2020

• [Bug] Fixed non tibble vars select

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• [Bug] Fixed white space issue

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Commits on Feb 11, 2020

• [Bug] Accounted for multiple roles

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• [Bug] levels mismatch fix

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Commits on Feb 12, 2020

• [Feature] Added labels to tableOne

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Commits on Feb 13, 2020

• [Feature] Additional params for CreateTableOne are passed to tableOne

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Commits on Feb 18, 2020

• [Test] Testing tableone added features

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Commits on Feb 19, 2020

• [Feature] Slight Bloat reduction and commenting out of old/depricated function

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• .

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Commits on Feb 25, 2020

• [Feature] Added sample config file

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• [Feature] Config rec with table

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• [Bug] Fixed modules not being read and multi rec not working

  rvyuha

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• [Feature] config data combination

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  0b31a41

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• [Feature] Custom function skeleton

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Commits on Feb 26, 2020

• [Feature] Added steps back due to complications with bllflow-recipes

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• [Feature] Added missing export

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Commits on Feb 27, 2020

• [Feature] Fixed z

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• [Feature] fixed NA.rm

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• [Bug] Removed print

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Commits on Feb 28, 2020

• [Bug] Reverted bllflow class change back to BLLFlow

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• [Feature] Removed the need for tableoneTest as a way of applying value labels

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• [Bug] Added tableone function reference

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Commits on Feb 29, 2020

• [Bug] Removed tableoneTEST reference

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Commits on Mar 2, 2020

• [Feature] Added basic formatting from variables in case variable is not in var details and added missing label for tableone print

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• [Feature] added labels to kableone print

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Commits on Mar 3, 2020

• [Feature] Added additional params to bllflow::kableone (missingLabel, valLabel, varLabel)

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• [Bug] Fixed trying to add labels to non existant variables anywhwere

  rvyuha

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• [Feature] Added bllflow object return to avoid accidental NULL return

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Commits on Mar 9, 2020

• [Feature] Test updated bllflow

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• [Feature] Updated RData config reading to resave data in default location

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Commits on Mar 11, 2020

• [Feature] Added bllflow scrambling of data

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• [Feature] Updated argument for data_name

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Commits on Mar 24, 2020

• [Feature] Updated examples

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Commits on Mar 25, 2020

• [Test] Testing derived/recoded combo

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• [Bug] Fixed derived and rec on same variable

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• [Test] Default for rec and derived vars

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• [Bug] Fixed rec and derived for default years

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Commits on Mar 26, 2020

• [Feature] Strata scrambling

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Commits on Jun 8, 2020

• [Bug] Fixed && usage causing all var selection

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Commits on Jun 25, 2020

• [Feature] Reintroduced summary_data_long

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Commits on Jul 22, 2020

• [Feature] Initial PR edits

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• [Refactor] Updated namespace

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• [Bug] Fixed broken example

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Commits on Jul 24, 2020

• [Refactor] Fixed linter and spelling errors

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Commits on Jul 28, 2020

• [Bug] Fixed adding arguments to formula based steps

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Commits on Jul 29, 2020

• [Fix] Minor fix for roles

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Commits on Aug 4, 2020

• [Refactor] Moved the WIP functions

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• [Refactor] Adding missing snippit of depricated

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