NEWS

diemr 29-06-2021

Updated vcf2diem functionality to optionally require homozygous individuals for both most frequent alleles.

Updated vcf2diem to allow a user-defined minimum number of homozygous individuals, and to allow subsetting the conversion to ChosenInds.
Updated documentation.

Fixed a bug in vcf2diem where diploid genotypes were incorrectly recoded as haploid.

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.

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.

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.

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.

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.

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.

Updated hybrid index calculation for consistency with diploid/haploid individuals.

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.