diemr 1.4.2
- 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, release
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