A function that will create extra files required for the study package

[cebarboza]

Function must contain this, but other elements could be added:

• Test
• renv/ Latest version for this month
• renv/ installs all darwin analytical packages
• LICENSE
• README.rmd
• extras/CodeToRun.R
• extras/pullFromATLAS.R
• option: pullFromDeck.R
• Delete hello.R
• R/createCohorts.R
• R/runDiagnostics.R
• R/runStudy.R
• R/runObjective1.R
• R/runObjective2.R
• R/pullFromATLAS.R
• ...
• Tests for all default R files
• extras/shiny
  • PhenotypeR
  • Shiny Modules
  • OmopViewer
• inst/cohorts
• inst/concept_sets

[cebarboza]

Hi @laacri @ariannaa7 probably we can divide thuis in sub-issues.

I see a function studyGenerics::insertStructure() that will first add required files to the project in one go.

Also you may grasp an idea of the contents of an actual off-the-shelf study.

I am thinking we can divide this in more simple functions:

studyGenerics::installPackages()

• This function takes a list argument that defaults to all "darwin", "phenotypeR", "drug_exposure_diagnostics", "darwinShinyModles" and will try to install all requirements for those in the renv.

install.packages("omopgenerics")
usethis::use_package("omopgenerics")

studyGenerics::insertDocs():

usethis::use_news_md()
usethis::use_apl2_license()
usethis::use_readme_rmd()

studyGenerics::insertTests():

• takes the 'objectives' parameter and insertes a test file for every file.

usethis::use_testthat()
usethis::use_test("objective1")
(...)

studyGenerics::insertStudyFiles():

R/runDiagnostics.R
R/runStudy.R
R/objective1.R
(...)
dir.create(inst/cohorts)
dir.create(inst/concept_sets)
dir.create(extras)
extras/CodeToRun.R
extras/pullFromATLAS.R

CONTENTS:

runStudy.R:

#' Documentation
runStudy() {
   createLogger()*
   assertCdmName()
   takeCdmSnapShot()*
   createResultsDir()
   createCohorts()**
   exportAttrition()*
   if (obj_1) {
      runObjective1()
      exportResult()
   }
   (...)
   zipStudyResults
}

runDiagnostics.R:

#' Documentation
runDiagnostics() {
   createLogger()*
   assertCdmName()
   takeCdmSnapShot()*
   createResultsDir()
   createCohorts()**
   if (diagnostics) {
      phenotypeR::Diagnostics()
      exportResult()
   }
   if (drug_exposure_diagnostics) {
      drugExposureDiagnostics::check()
      exportResult()
   }
   (...)
   zipStudyResults
}

* To be created
** From a study package such as onconet