BIGpopA 2.1.0

• New vcf_to_dosage() converts a VCF (.vcf / .vcf.gz) or vcfR object into allele-B dosages for any ploidy, as an id + markers table or an individuals x markers matrix.
• New ped_to_dosage() converts a PLINK .ped file (diploid) into allele dosages. A .map file is optional and only supplies marker names. The counted allele is the alphabetically/numerically last allele at each marker, or can be supplied to code a second file like a first one.
• find_parentage(), validate_pedigree(), allele_freq_poly() and solve_composition_poly() now accept genotypes as a TXT/TSV/CSV file, a VCF file or vcfR object, a PLINK .ped file, a data.frame / data.table, or a matrix. VCF input is converted with vcf_to_dosage() using the function’s ploidy; .ped input requires ploidy = 2.
• When the reference panel is a .ped file, allele_freq_poly() stores the counted allele per marker and solve_composition_poly() uses it to code a validation .ped file consistently.
• allele_freq_poly() and solve_composition_poly() also accept a data.frame with an id / ID column; existing matrix and row-named data.frame inputs are unchanged.
• Genotype read errors in find_parentage() and validate_pedigree() now include the underlying error message.
• Column names id, male_parent, female_parent and sex are now matched ignoring case, spaces and dots (e.g. ID, Male_Parent, FEMALE PARENT) in check_ped(), validate_pedigree(), find_parentage() and genotype tables.
• Fixed solve_composition_poly() failing when Y contains a single animal.
• Removed the ped, groups, mia, sire and dam arguments from solve_composition_poly(). They relied on internal helpers that were not carried over from BIGr and always failed. The function now takes Y, X and ploidy.

BIGpopA 2.0.0

• find_parentage() and validate_pedigree() now support any ploidy through a new ploidy argument (default 2). Genotypes may be coded as allele-B dosage (0, 1, …, ploidy).
• Even ploidy uses a generalized polysomic gamete-range Mendelian test; it is exact for autopolyploids and conservative for allopolyploids (correct trios are never wrongly flagged).
• Odd ploidy (e.g. triploid), where balanced gametes are undefined, automatically falls back to a model-free opposite-homozygote exclusion evaluated on homozygous-informative markers only.
• Diploid results (ploidy = 2) are unchanged from previous versions.

BIGpopA 1.0.6

• Added a “BIGpopA Tutorial” vignette demonstrating the pedigree cleaning, validation, parentage assignment, and breed/line composition workflow

BIGpopA 1.0.5

• Updated package title and example on function descriptions to pass CRAN review

BIGpopA 1.0.4

• Removed LICENSE file to pass CRAN automated tests

BIGpopA 1.0.3

• Fixed typo on repo name and patched find_parentage
• Removed /dev from repository
• Added words to WORDLIST

BIGpopA 1.0.2

• Renamed package to BIGpopA and made repo public

popR 1.0.2

• Initial release of BIGpopA as a standalone package.
• BIGpopA contains pedigree validation and breed/line composition functions previously found in BIGr, where they will no longer be maintained going forward.
• These functions are the backbone of the pedigree and composition modules in the familia Shiny app.

Functions included

• check_ped() — checks and corrects common pedigree errors (duplicate rows, conflicting trios, missing parents, cycles, inconsistent sex roles)
• find_parentage() — assigns most likely parent(s) to progeny using Mendelian error rates or homozygous mismatch rates
• validate_pedigree() — validates parent-offspring trios against SNP genotype data and outputs a corrected pedigree
• allele_freq_poly() — computes allele frequencies for diploid and polyploid reference populations
• solve_composition_poly() — estimates genome-wide breed/line composition using quadratic programming