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AGENTS.md

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Repository Guidelines

Project Structure & Module Organization

  • R/ holds hand-written analyses (*.b.R) and generated bases (*.h.R); helper utilities live alongside.
  • jamovi/*.a|u|r.yaml define options, UI, and results; jamovi/0000.yaml anchors shared references.
  • tests/testthat/ contains unit and integration coverage; mirror feature names as test-<feature>.R.
  • Documentation lives in man/, vignettes/, and the pkgdown site under docs/; metadata is in DESCRIPTION and NAMESPACE.
  • Reusable datasets and fixtures belong in data/ (compressed .rda) or data-raw/ for generation scripts.

Build, Test, and Development Commands

  • Rscript -e "devtools::document()" regenerates roxygen documentation before commits touching R/.
  • Rscript -e "devtools::test()" runs the full testthat suite; prefer focused files via testthat::test_file().
  • Rscript -e "devtools::check()" mirrors CI; use before release or structural changes.
  • Rscript -e "pkgdown::build_site()" refreshes the docs site; run after editing vignettes/ or roxygen examples.
  • Fast iterations: Rscript -e "rcmdcheck::rcmdcheck(args = c('--no-manual'))" catches failures without rebuilding the manual.

Coding Style & Naming Conventions

  • Follow tidyverse style: 2-space indents, <- for assignment, snake_case objects, and ≤100-character lines.
  • Name analysis pairs as analysis.b.R and analysis.h.R; align option names with YAML definitions verbatim.
  • Use roxygen2 tags above exported functions; prefer dplyr pipelines over deeply nested loops when practical.
  • Keep comments concise and functional; avoid describing obvious assignments.

Testing Guidelines

  • Write tests in tests/testthat/test-<feature>.R; organize helpers in helper-*.R.
  • Cover edge cases (single-level factors, missing values, seed-controlled simulations) and ensure deterministic snapshots.
  • Validate tables with expect_equal() or snapshot tests; assert plot objects via expect_s3_class() and layer checks.

Commit & Pull Request Guidelines

  • Commits use imperative verbs (Add, Fix, Refactor) and focus on a single concern; avoid "WIP" labels.
  • PRs require a summary, linked issues (Fixes #NNN), and screenshots for UI/plot updates; call out breaking changes explicitly.
  • Update documentation and tests in the same PR when behaviour shifts; note follow-up tasks in TODO.md if deferred.

Security & Configuration Tips

  • Never commit PHI/PII; anonymize inputs and rely on illustrative datasets in inst/extdata/.
  • Respect CI parity: run devtools::check() on macOS or Linux when possible to match GitHub Actions expectations.