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Contributing

Source: CONTRIBUTING.md

Keep statistical behavior documented and tested. Preserve caller-owned inputs. Update deterministic tests and documentation when model behavior or result fields change.

PheWAS is an optional suggested package for the interoperability example and comparison tests. DESCRIPTION pins the upstream revision through Remotes. Install development dependencies with remotes::install_deps() so that this GitHub dependency is resolved. Normal phewasFlow use requires only the runtime dependencies; comparison tests skip when PheWAS is unavailable.

When changing model wrappers or the PheWAS revision, run the shared-data comparison as well as the package tests. Record versions, numerical agreement, and measured runtime. Keep generated tables in an ignored output directory, and describe the simulation and limits when reporting any result. Do not infer superiority from agreement or from one timing run.

Use the installation and dependency commands in the README, reinstall the current source so parallel workers use it, then run:

testthat::test_local()
rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning")

Do not commit individual-level health data, fitted model objects, site-specific paths, credentials, or generated analysis results.

Regenerate function documentation with roxygen2::roxygenise() after changing documented interfaces. Preview the package website with pkgdown::build_site(preview = FALSE); it uses the Fritsche Lab palette and links back to the lab website. The site is generated into ignored docs/.

Before a public release:

  1. Keep the MIT license declaration and copyright statement consistent across DESCRIPTION, LICENSE, and LICENSE.md.
  2. Run the package checks, including vignettes and the simulated workflows.
  3. Review git ls-files and the contents of the source tarball. Publish from Git or the checked tarball; a copy of a working directory can include ignored private inputs and local workflows.
  4. Confirm repository and support URLs, update the version and citation metadata, and review generated outputs before sharing them.

Archive releases and maintain citations

Use CITATION.cff as the metadata source for GitHub and Zenodo. Keep its title, authors, version, license, and project URLs consistent with DESCRIPTION and inst/CITATION. Add authors and ORCIDs only when verified.

For the first archived release:

  1. Connect the maintainer’s GitHub account to Zenodo and enable this repository. Organization repositories may require organization access approval.
  2. Set the release version in DESCRIPTION and CITATION.cff, add the actual date-released to CITATION.cff, and check the citation returned by citation("phewasFlow") after reinstalling the package.
  3. Publish the checked GitHub release and wait for Zenodo to archive it.
  4. Record the assigned DOI in CITATION.cff (doi) and inst/CITATION (the doi argument to bibentry), and link it from the README citation section. Use the DOI for the matching release and update the citation year to match its release date. Do not pair a previous release’s DOI with a new version; obtain the matching DOI when archiving each release.

Keep scholarly citation requests in the documentation and citation files. Do not add citation conditions to the standard MIT license text.

Only the source, documentation, and synthetic examples belong in this repository. Git ignore rules do not remove previously tracked files or clean Git history.