Changes in version 4.0.2 (2026-02-26)                  

Changed

  - Updated import.vcf INFO-field tests to be robust to upstream
    vcfR::vcfR2tidy() schema additions (e.g., VariantKey) and avoid CRAN
    failures.

                 Changes in version 4.0.1 (2026-01-23)                  

Changed

  - Updated Paul Boutros email to @sbpdiscovery.org

                 Changes in version 4.0.0 (2025-08-20)                  

Changed

  - Refactored all main functions for gains in RAM efficiency and
    runtime
  - Introduced a breaking change to the output of import.vcf. The
    outputed list object has a different naming scheme and different
    data formats. Previous data formats are still supported by setting
    long.format to TRUE, however the naming scheme is still changed.
  - Introduced a breaking change to apply.polygenic.score. The expected
    default vcf.data input format has changed. The previous input format
    is still supported by setting vcf.long.format to TRUE from the
    default FALSE.

Added

  - Added support for more efficient storage and manipulation of
    imported VCF data. The default output of import.vcf now returns VCF
    data in a split format. A data.table object contains VCF data from
    fixed fields (CHROM, POS, ID, REF, ALT). A matrix object contains
    sample-specific genotypes in allele-format in a sample (columns) by
    variant (rows) matrix.

                        Changes in version 3.1.0                        

Changed

  - Fixed regression of combine.vcf.with.pgs() function that prevented
    it from handling multiple rsIDs on the same line.
  - Fixed bug caused by the case of a sample-specific missing variant at
    a multiallelic site
  - Use updated R CMD check CI/CD action with renv dependency management

Added

  - Added new contributor
  - Added minimum sample size check for grouped density curves
  - Added new plotting function create.pgs.boxplot
  - Added option for user to provide custom PGS source column(s) for
    plotting functions
  - Added option to assess.pgs.vcf.allele.match to condition the
    handling of ambiguous strand flips on the total number of
    unambiguous strand flips.
  - Added new function analyze.pgs.binary.predictiveness which given a
    PGS and phenotypes runs a logistic regression and returns statistics
    (OR, p-value, AUC) describing how well the PGS predicts the
    phenotype. It also automatically plots a receiver-operator-curve.

                        Changes in version 3.0.2                        

Changed

  - ApplyPolygenicScore released on CRAN! Updated README with CRAN
    links.

                 Changes in version 3.0.1 (2025-03-05)                  

Added

  - Added hemizygous allele handling to dosage calculation
  - Added toggle to hexbinplot at sample size threshold in
    create.pgs.with.continuous.phenotype.plot

Changed

  - Updated INDEL effect switch reporting by strand flip checker
  - Updated data structuring for automated statistical analysis in
    apply.polygenic.score

                        Changes in version 3.0.0                        

Added

  - Added handling of overlapping deletion allele notation
  - Added secondary PGS/VCF variant matching method using rsID after
    first attempt with genomic coordinates
  - Added checks for rsID as an optional column in input PGS weight
    files
  - Added functionality to assess allele matches and correct strand
    flips

                        Changes in version 2.0.0                        

Changed

  - Renamed functions starting with reserved vocabulary for S3 generic
    methods merge. -> combine.

                        Changes in version 1.0.0                        

  - First release

                        Changes in version 0.1.0                        

  - INITIAL FEATURES