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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

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.
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