Changes in version 29-06-2021 - First build Changes in version 28-04-2024 - Updated vcf2diem functionality to optionally require homozygous individuals for both most frequent alleles. Changes in version 28-03-2022 - First public release. - Updated citation. Changes in version 23-09-2024 - Updated vignette authorship, and a link to a reference. - Fixed error message formatting in CheckDiemFormat. - Added rank2map and smoothPolarizedGenotypes. - Improved memory handling in diem. - Fixed exit bug in diem when number of iterations reaches maxIterations. Changes in version 21-03-2023 - Added vcf2diem to convert SNP in vcf format to diem genotypes. - Added myotis vcf dataset with documentation. - Added vignette Importing data for genome polarisation. - Updated CITATION. Changes in version 20-01-2025 - Updated vcf2diem to allow a user-defined minimum number of homozygous individuals, and to allow subsetting the conversion to ChosenInds. - Updated documentation. Changes in version 19-10-2022 - Updated README file. - Added user-choice of colours in plotPolarized. - Updated CITATION. - Added efficient correction for other markers in likelihood calculation. Changes in version 19-04-2023 - Added link to bug reports page. - Fixed bug in vcf2diem for multiallelic SNPs. Changes in version 18-03-2026 - Fixed a bug in vcf2diem where diploid genotypes were incorrectly recoded as haploid. Changes in version 16-07-2024 - Updated reference to vignette Understanding genome polarisation output files. - Modified importPolarized to accept multiple files and a logical vector indicating which sites to import. The file processing is parallelised. - Added functions plotDeFinetti and plotMarkerAxis. - Modified plotPolarized to show colored tick marks for individuals and to accept selected graphical parameters. - Fixed bug in vcf2diem when requireHomozygous = TRUE. - Added ChosenSites argument in diem that allows to select sites for identifying a barrier to geneflow. Polarity is calculated for all sites, but only ChosenSites influence the likelihood in each EM iteration. - Updated vignettes to reflect new functionality. Changes in version 14-06-2024 - Fixed bug in vcf2diem for multiallelic markers where REF allele is rare. - Improved user-flexibility in reporting verbose EM search in diem. As a consequence ModelOfDiagnostic is no longer exported. - Added vignette Understanding genome polarisation output files. - Removed warnings when generating random null polarities. - Hybrid indices and the 4-genomic state count matrix I4 are now calculated from the polarised genomes for all individuals. As a result, diem now requires ploidies for all individuals in the input files listed in the files argument. - Set default ploidy = FALSE in diem that assumes all individuals are diploid across all compartments. Changes in version 13-01-2026 - Added test for rank2map. - Updated documentation. - Fixed bug in diem finalizing step when using a subset of individuals. - Removed row names from the diem output files. Changes in version 12-01-2022 - Added user choice of null polarities in the diem argument markerPolarity. - Added FAQ to vignette. - Added functions importPolarized and plotPolarized. Changes in version 11-12-2025 - Integrated BED-format support into internal functions. - Fixed bug in rank2map when a chromosome had only one site. - Added default value of 0.5 to hybridIndex when there are no data. - Added ploidy-aware hybrid index calculation to hybridIndex. - Modified vcf2diem to write all sites into one file when chunk = 1L, allow minimum number of required genotyped individuals per site, and subset sampleNames.txt to ChosenInds only. - Added check for the changePolarity argument in importPolarized. - Added internal function resolveChosenInds. - Updated README. Changes in version 11-09-2025 - Added iris plots to the plotPolarized. - Updated internal function markerAxis to avoid plotting multiple tick labels over one another. - Updated plotMarkerAxis to check the expected user input. - Added variantSites function that selects sites with required number of homozygous genotypes in a subset of individuals. - Removed function shorthand \(x) syntax. - Updated plotPolarized to unlist and unname the values in HI. - Updated documentation. Changes in version 11-07-2023 - Modified vcf2diem so that markers without homozygous genotypes or markers with only one heterozygous genotype are removed as non-informative for genome polarisation. - Updated vignette Importing data for genome polarisation. - Fixed formatting in vcf2diem documentation. Changes in version 09-10-2025 - Added hybridIndex function that returns a numeric vector suitable for plotting. - Modified vcf2diem to optionally output site location in BED format. - Updated DESCRIPTION (Title, Description, BugReports, URL). - Updated documentation. Changes in version 09-07-2021 - Updated hybrid index calculation for consistency with diploid/haploid individuals. - Added tolerance for unknown genotypes encoded either as _ or U. - Added vignette diemr: Diagnostic index expectation maximisation in R. - Added a NEWS.md file to track changes to the package. - Added README.md with quick start analysis instructions. - Added default ChosenInds to include all individuals to diem. Changes in version 09-03-2026 - Set default major alleles to all alleles in vcf2diem. - Removed support for vcfR objects in vcf2diem. - Added conversion of haploid genotypes in vcf2diem. Changes in version 02-12-2024 - Updated rank2mapChr internal function to be more efficient. It now uses the Inchworm algorithm by Stuart J.E. Baird. - Modified rank2map to allow also a data.frame in the inclucedSites argument. - Added vcf2diem obligatory output of sample names. - Changed smoothPolarizedGenotypes to return a weighted mode, added corresponding internal functions truncatedLaplace and unbiasedWeightedStateChoice. Changes in version 02-12-2021 - Added examples to documentation. Changes in version 02-02-2023 - Fixed potential infinite loop error in halting condition of diem. Changes in version 01-12-2021 - Added ploidy flexibility across compartments and across individuals. - Updated documentation.