Create a Study Package • studyGenerics

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

Create the study package

Choose a new, empty directory and supply it explicitly. The example uses a temporary directory so it does not write to the current working directory or a home directory. Make sure you have internet access because the setup installs the standard study-package dependencies. n_obj sets the number of objective scripts to create.

study_path <- file.path(tempdir(), "P1-C1-001")
dir.create(study_path)

studyGenerics::insertStructure(
  studyName = "P1-C1-001",
  path = study_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

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().