studyGenerics

studyGenerics provides small, tested functions for common tasks in OMOP-CDM study packages developed at the Erasmus MC Department of Medical Informatics.

Installation

You can install studyGenerics from CRAN or the latest development version from GitHub with:

# CRAN download
install.packages("studyGenerics")

# install.packages("remotes")
remotes::install_github("mi-erasmusmc/studyGenerics")

Create a study package

Create the standard study-package folders, scripts, tests, and documentation. Use n_obj to set the number of objective scripts.

studyGenerics::insertStructure(
  studyName = "P1-C1-001",
  path = "/path/to/P1-C1-001",
  n_obj = 3
)

It adds the following files and folders to an existing study package:

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

Download concept sets from ATLAS

Use pullConceptsAtlas() to save ATLAS concept-set definitions in an explicit output directory. It requires access to the ATLAS WebAPI.

studyGenerics::pullConceptsAtlas(
  conceptSetList = c(12345),
  conceptSetType = "example",
  outputDir = file.path(tempdir(), "concept_sets"),
  baseUrl = "https://atlas.darwin-eu.org/WebAPI"
)

Manage study files

Use the shared functions to validate data-partner names and create, archive, or extract study results.

studyGenerics::arrangeCdmNames(labels)

studyGenerics::createResultsDir(
  outputDir,
  dbname
)

studyGenerics::zipStudyFiles(
  resultsDirName,
  outputDir,
  dbname
)

studyGenerics::unZipStudyFiles(
  path,
  pattern,
  negate,
  recursive,
  outputDir
)

Updating summarised results

Use updateColumnValues() to replace values in a summarised-result column, for example when preparing clearer cohort labels for presentation.

studyGenerics::updateColumnValues(
  summarised_result = summarised_result,
  names_map = c(
    "old_cohort_name" = "Clear cohort name"
  ),
  variable = "group_level"
)

Prepare dependencies for offline installation

Save packages from renv.lock to renv/cellar, then use that cellar to restore the environment on a machine without internet access.

# Save packages in an explicit cellar directory
studyGenerics::packageCellar(path = file.path(tempdir(), "cellar"))

# Restore packages into an explicit library directory
studyGenerics::installCellar(
  path = file.path(tempdir(), "cellar"),
  library = file.path(tempdir(), "library")
)

Version control workflow

Configure GITHUB_PAT in .Renviron, then create an issue and branch, open a pull request, and return to the latest develop branch.

# Create a GitHub issue and check out a branch named after it
studyGenerics::issueOpen(
  title = "Add study outcome",
  body = "Describe the planned change.",
  newBranch = TRUE
)

# After committing and pushing the branch, create a pull request to develop
studyGenerics::pullRequest(
  title = "Add study outcome",
  body = "Describe the implemented change.",
  base = "develop"
)

# After the pull request is merged, return to the latest develop branch
studyGenerics::devCheckout()