Movatterモバイル変換

diemr 1.5.2, released11-12-2025

• Integrated BED-format support into internal functions.
• Fixed bug inrank2map when a chromosome had only onesite.
• Added default value of 0.5 tohybridIndex when thereare no data.
• Added ploidy-aware hybrid index calculation tohybridIndex.
• Modifiedvcf2diem to write all sites into one file whenchunk = 1L, allow minimum number of required genotypedindividuals per site, and subsetsampleNames.txt toChosenInds only.
• Added check for thechangePolarity argument inimportPolarized.
• Added internal functionresolveChosenInds.
• Updated README.

diemr 1.5.1, released09-10-2025

• AddedhybridIndex function that returns a numericvector suitable for plotting.
• Modifiedvcf2diem to optionally output site location inBED format.
• Updated DESCRIPTION (Title, Description, BugReports, URL).
• Updated documentation.

diemr 1.5, released11-09-2025

• Added iris plots to theplotPolarized.
• Updated internal functionmarkerAxis to avoid plottingmultiple tick labels over one another.
• UpdatedplotMarkerAxis to check the expected userinput.
• AddedvariantSites function that selects sites withrequired number of homozygous genotypes in a subset of individuals.
• Removed function shorthand\(x) syntax.
• UpdatedplotPolarized to unlist and unname the valuesinHI.
• Updated documentation.

diemr 1.4.3, released20-01-2025

• Updatedvcf2diem to allow a user-defined minimum numberof homozygous individuals, and to allow subsetting the conversion toChosenInds.
• Updated documentation.

diemr 1.4.2, released02-12-2024

• Updatedrank2mapChr internal function to be moreefficient. It now uses theInchworm algorithm by StuartJ.E. Baird.
• Modifiedrank2map to allow also a data.frame in theinclucedSites argument.
• Addedvcf2diem obligatory output of sample names.
• ChangedsmoothPolarizedGenotypes to return a weightedmode, added corresponding internal functionstruncatedLaplace andunbiasedWeightedStateChoice.

diemr 1.4.1, released23-09-2024

• Updated vignette authorship, and a link to a reference.
• Fixed error message formatting inCheckDiemFormat.
• Addedrank2map andsmoothPolarizedGenotypes.
• Improved memory handling indiem.
• Fixed exit bug indiem when number of iterationsreachesmaxIterations.

diemr 1.4, released16-07-2024

• Updated reference to vignetteUnderstanding genomepolarisation output files.
• ModifiedimportPolarized to accept multiple files and alogical vector indicating which sites to import. The file processing isparallelised.
• Added functionsplotDeFinetti andplotMarkerAxis.
• ModifiedplotPolarized to show colored tick marks forindividuals and to accept selected graphical parameters.
• Fixed bug invcf2diem whenrequireHomozygous = TRUE.
• AddedChosenSites argument indiem thatallows to select sites for identifying a barrier to geneflow. Polarityis calculated for all sites, but onlyChosenSites influencethe likelihood in each EM iteration.
• Updated vignettes to reflect new functionality.

diemr 1.3, released14-06-2024

• Fixed bug invcf2diem for multiallelic markers whereREF allele is rare.
• Improved user-flexibility in reporting verbose EM search indiem. As a consequenceModelOfDiagnostic is nolonger exported.
• Added vignetteUnderstanding genome polarisation outputfiles.
• Removed warnings when generating random null polarities.
• Hybrid indices and the 4-genomic state count matrix I4 are nowcalculated from the polarised genomes for all individuals. As a result,diem now requires ploidies for all individuals in the inputfiles listed in thefiles argument.
• Set defaultploidy = FALSE indiem thatassumes all individuals are diploid across all compartments.

diemr 1.2.3, released28-04-2024

• Updatedvcf2diem functionality to optionally requirehomozygous individuals for both most frequent alleles.

diemr 1.2.2, released11-07-2023

• Modifiedvcf2diem so that markers without homozygousgenotypes or markers with only one heterozygous genotype are removed asnon-informative for genome polarisation.
• Updated vignetteImporting data for genomepolarisation.
• Fixed formatting invcf2diem documentation.

diemr 1.2.1, released19-04-2023

• Added link to bug reports page.
• Fixed bug invcf2diem for multiallelic SNPs.

diemr 1.2, released21-03-2023

• Addedvcf2diem to convert SNP in vcf format to diemgenotypes.
• Addedmyotis vcf dataset with documentation.
• Added vignetteImporting data for genomepolarisation.
• Updated CITATION.

diemr 1.1.1, released02-02-2023

• Fixed potential infinite loop error in halting condition ofdiem.

diemr 1.1, released19-10-2022

• Updated README file.
• Added user-choice of colours inplotPolarized.
• Updated CITATION.
• Added efficient correction for other markers in likelihoodcalculation.

diemr 1.0, released28-03-2022

• First public release.
• Updated citation.

diemr 0.3, build 12-01-2022

• Added user choice of null polarities in the diem argumentmarkerPolarity.
• Added FAQ to vignette.
• Added functionsimportPolarized andplotPolarized.

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 acrossindividuals.
• Updated documentation.

diemr 0.1.2, build 09-07-2021

• Updated hybrid index calculation for consistency withdiploid/haploid individuals.

diemr 0.1.1, build 09-07-2021

• Added tolerance for unknown genotypes encoded either as_ orU.
• Added vignettediemr: Diagnostic index expectationmaximisation in R.
• Added aNEWS.md file to track changes to thepackage.
• AddedREADME.md with quick start analysisinstructions.
• Added defaultChosenInds to include all individuals todiem.

diemr 0.1, build 29-06-2021

• First build