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Create a Study Package

Source: vignettes/new_study_package.Rmd
new_study_package.Rmd

Use insertStructure() to set up a new OMOP study package with common folders, starter scripts, tests, and package dependencies.

Before you start

Create an empty R package and make sure you have internet access. The setup installs the standard study-package dependencies.

1. Create an empty package

Create a package with usethis, or use File > New Project in RStudio.

usethis::create_package(
  path = "~/P1C1001"
)

2. Initialize the environment

Inside the new package, initialize renv and install studyGenerics.

renv::init()

renv::install("mi-erasmusmc/studyGenerics")

3. Insert the study structure

Run insertStructure() from the package directory. n_obj sets the number of objective scripts to create.

studyGenerics::insertStructure(
  path = ".",
  n_obj = 3
)

The package will include:

studyPackage/
├── R/
│   ├── createCohorts.R
│   ├── runStudy.R
│   ├── runDiagnostics.R
│   ├── utils.R
│   ├── globals.R
│   ├── merge.R
│   └── objective1.R, ..., objective<n_obj>.R
├── inst/
│   ├── cohorts/
│   └── concept_sets/
├── extras/
│   ├── CodeToRun.R
│   └── pullConceptSetsFromAtlas.R
├── man/
├── tests/
│   └── testthat/test-*.R
├── LICENSE.md
├── NEWS.md
└── README.Rmd

4. Next steps

Add concept sets to inst/concept_sets/, develop the study code in R/, then generate documentation with devtools::document() and check the package with devtools::check().