NEWS
diemr 29-06-2021
diemr 28-04-2024
- Updated
vcf2diem functionality to optionally require homozygous individuals for both most frequent alleles.
diemr 28-03-2022
- First public release.
- Updated citation.
diemr 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 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 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 19-04-2023
- Added link to bug reports page.
- Fixed bug in
vcf2diem for multiallelic SNPs.
diemr 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 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 12-01-2022
- Added user choice of null polarities in the diem argument
markerPolarity.
- Added FAQ to vignette.
- Added functions
importPolarized and plotPolarized.
diemr 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 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.
diemr 02-12-2021
- Added examples to documentation.
diemr 02-02-2023
- Fixed potential infinite loop error in halting condition of
diem.
diemr 01-12-2021
- Added ploidy flexibility across compartments and across individuals.
- Updated documentation.