Creates initial directory for an OMOP CDM network study

Usage

initStudy(
  directory,
  diagnostics = TRUE,
  study = TRUE,
  studyTitle = NULL,
  studyLeads = NULL,
  studyDescription = NULL,
  repository = NULL,
  organisation = NULL,
  private = TRUE
)

Arguments

directory: Path to a directory that will be used as the root folder for the study. If it does not exist, it will be created. The directory must be empty if it already exists.
diagnostics: A single TRUE or FALSE value. If TRUE (the default), the function creates the `diagnosticsCode/` and `diagnosticsShiny/` folders using the package templates. If FALSE, these diagnostics folders are not created.
study: A single TRUE or FALSE value. If TRUE (the default), the function creates the `studyCode/` and `studyShiny/` folders using the package templates. If FALSE, these study folders are not created.
studyTitle: Character string with the study title. If NULL (default), uses the directory basename.
studyLeads: Character string with study leads. If NULL (default), leaves a placeholder.
studyDescription: Character string with study description. If NULL (default), leaves a placeholder.
repository: Optional GitHub repository name. If provided, creates a GitHub repository and links it to the study. Requires the gh and gert packages and GitHub authentication (for example via GITHUB_PAT).
organisation: Optional GitHub organisation name. If NULL (default), creates repository under your personal account. Only used when repository is provided.
private: Logical. If TRUE (default), creates a private GitHub repository. Only used when repository is provided.

Value

Project directory will be created

Examples

# Create a study called "SampleStudy" in a temporary directory
study_root <- file.path(tempdir(), "SampleStudy")
initStudy(study_root)
#> ✔ /tmp/Rtmp9w46L2/SampleStudy prepared as root folder for study.
#> ✔ /tmp/Rtmp9w46L2/SampleStudy/diagnosticsCode prepared for study diagnostics code
#> ✔ /tmp/Rtmp9w46L2/SampleStudy/diagnosticsShiny prepared for diagnostics shiny app
#> ✔ /tmp/Rtmp9w46L2/SampleStudy/studyCode prepared for study study code
#> ✔ /tmp/Rtmp9w46L2/SampleStudy/studyShiny prepared for study shiny app

# Inspect the top-level contents
list.files(study_root)
#> [1] "INSTRUCTIONS.md"  "README.md"        "diagnosticsCode"  "diagnosticsShiny"
#> [5] "studyCode"        "studyShiny"      

# Create another study with custom metadata
study_root2 <- file.path(tempdir(), "DiabetesStudy")
initStudy(study_root2,
          studyTitle = "Diabetes Prevalence Study",
          studyLeads = "Dr. Smith, Dr. Jones")
#> ✔ /tmp/Rtmp9w46L2/DiabetesStudy prepared as root folder for study.
#> ✔ /tmp/Rtmp9w46L2/DiabetesStudy/diagnosticsCode prepared for study diagnostics code
#> ✔ /tmp/Rtmp9w46L2/DiabetesStudy/diagnosticsShiny prepared for diagnostics shiny app
#> ✔ /tmp/Rtmp9w46L2/DiabetesStudy/studyCode prepared for study study code
#> ✔ /tmp/Rtmp9w46L2/DiabetesStudy/studyShiny prepared for study shiny app

if (FALSE) { # \dontrun{
# Create study with GitHub integration (requires GITHUB_PAT)
# Set PAT for current session:
Sys.setenv(GITHUB_PAT = "your_token_here")

study_root3 <- file.path(tempdir(), "GitHubStudy")
initStudy(
  directory = study_root3,
  repository = "my-omop-study",
  organisation = "oxford-pharmacoepi",
  private = TRUE
)
} # }