Changelog

Source: NEWS.md

polylinkR 0.5.0

Major Changes

• Comprehensive documentation enhancement with pkgdown site
• Created 5 detailed vignettes:
  • Basic workflow tutorial with Anatolia_EF_CLR dataset
  • Controlling for confounders and covariates
  • Using recombination rates from Bherer et al. 2017
  • Parallel processing for performance optimization
  • Input formats and parameters reference
• Added professional pkgdown configuration with Bootstrap 5
• Added hex logo to package

Technical Improvements

• Removed tdigest dependency (not on CRAN) - replaced with base R stats::quantile()
• Added GitHub Actions workflows:
  • R-CMD-check with multi-OS matrix
  • pkgdown auto-deployment to GitHub Pages
  • test-coverage with Codecov integration
• Removed Travis CI (superseded by GitHub Actions)
• Fixed pkgdown reference index for all exported functions

Package Infrastructure

• 72 comprehensive tests covering core functionality
• Runnable vignettes demonstrating workflows
• Fixed R CMD check issues:
  • Added missing NAMESPACE imports for stats, utils, methods
  • Added globalVariables for data.table NSE column references
  • Fixed data file organization and documentation
  • Removed stale documentation artifacts
• Fixed code issues:
  • Removed false plot() method claims from documentation
  • Fixed missing closing parenthesis in plR_permute.R
  • Fixed .create_seed() to return integer values

Notes

Version 0.5.0 represents a significant documentation milestone. The package implements gene-based pathway enrichment with linkage-preserving permutation nulls. All core statistical algorithms are frozen and validated against the reference implementation.

The pkgdown site is available at: https://acad-uofa.github.io/PolyLinkR/