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CheckDiemFormat.rank2map and
smoothPolarizedGenotypes.diem.diem when number of iterations
reaches maxIterations.importPolarized to accept multiple files and a
logical vector indicating which sites to import. The file processing is
parallelised.plotDeFinetti and
plotMarkerAxis.plotPolarized to show colored tick marks for
individuals and to accept selected graphical parameters.vcf2diem when
requireHomozygous = TRUE.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.vcf2diem for multiallelic markers where
REF allele is rare.diem. As a consequence ModelOfDiagnostic is no
longer exported.diem now requires ploidies for all individuals in the input
files listed in the files argument.ploidy = FALSE in diem that
assumes all individuals are diploid across all compartments.vcf2diem functionality to optionally require
homozygous individuals for both most frequent alleles.vcf2diem so that markers without homozygous
genotypes or markers with only one heterozygous genotype are removed as
non-informative for genome polarisation.vcf2diem documentation.vcf2diem for multiallelic SNPs.vcf2diem to convert SNP in vcf format to diem
genotypes.myotis vcf dataset with documentation.diem.plotPolarized.markerPolarity.importPolarized and
plotPolarized._ or U.NEWS.md file to track changes to the
package.README.md with quick start analysis
instructions.ChosenInds to include all individuals to
diem.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.