NEWS.md

In diemr: Genome Polarization via Diagnostic Index Expectation Maximization

diemr 1.5.2, released 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.

diemr 1.5.1, released 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.

diemr 1.5, released 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.

diemr 1.4.3, released 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.

diemr 1.4.2, released 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.

diemr 1.4.1, released 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.

diemr 1.4, released 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.

diemr 1.3, released 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.

diemr 1.2.3, released 28-04-2024

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

diemr 1.2.2, released 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.

diemr 1.2.1, released 19-04-2023

• Added link to bug reports page.
• Fixed bug in vcf2diem for multiallelic SNPs.

diemr 1.2, released 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.

diemr 1.1.1, released 02-02-2023

• Fixed potential infinite loop error in halting condition of diem.

diemr 1.1, released 19-10-2022

• Updated README file.
• Added user-choice of colours in plotPolarized.
• Updated CITATION.
• Added efficient correction for other markers in likelihood calculation.

diemr 1.0, released 28-03-2022

• First public release.
• Updated citation.

diemr 0.3, build 12-01-2022

• Added user choice of null polarities in the diem argument markerPolarity.
• Added FAQ to vignette.
• Added functions importPolarized and plotPolarized.

diemr 0.2.1, build 02-12-2021

• Added examples to documentation.

diemr 0.2, build 01-12-2021

• Added ploidy flexibility across compartments and across individuals.
• Updated documentation.

diemr 0.1.2, build 09-07-2021

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

diemr 0.1.1, build 09-07-2021

• 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.

diemr 0.1, build 29-06-2021

• First build

diemr documentation built on Dec. 11, 2025, 5:07 p.m.