NEWS

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BIGpopA 2.2.0 (2026-10-12)

• validate_pedigree() and find_parentage(): founders_file now also accepts a character vector of ids or a data.frame (first column), in addition to a file path. All inputs can now be supplied from memory.
• validate_pedigree(): removed the suggested replacement parents (best_male_candidate, best_male_candidate_error_pct, best_female_candidate, best_female_candidate_error_pct) from full_results and the per-status tables. Use find_parentage(method = "fill_pedigree") on corrected_pedigree to fill in missing parents.
• validate_pedigree(): new marker_summary element in the returned list gives, for every marker, the number of trios tested, the number with a Mendelian mismatch and the mismatch percentage, sorted worst first. It covers all trios with both parents known and genotyped, and helps spot markers (e.g. paralogous or miscalled) that cause many failures.
• find_parentage(): new method = "fill_pedigree" fills in missing parents of a pedigree. progeny_file must have id, male_parent and female_parent columns (e.g. validate_pedigree()$corrected_pedigree); parents coded 0/NA/empty are unknown. A known male searches only females, a known female only males, and rows with both unknown get the full pair search (skip founders with the new founders_file). Rows with both parents known are skipped. Results gain search_mode and known_parent_error_pct, and a known parent without genotypes gets status = "known_parent_no_genotype".
• find_parentage(): new top_n argument reports the best top_n candidates per progeny, ranked by Mendelian error (ties broken by markers tested). Rank 1 stays in the base columns and ranks 2 to top_n are added as suffix columns (male_parent_2, female_parent_2, mendelian_error_pct_2, markers_tested_2 for best_pair; best_match_2 and the same error/marker columns for the other methods). The default top_n = 1 keeps the previous output, including show_ties.
• find_parentage(): new tied_candidates column gives the number of candidates (pairs for best_pair) that share each progeny's lowest error. Values above 1 mean the best assignment is ambiguous, including for the single-parent methods, which previously did not report ties.
• validate_pedigree(): fixed corrected_pedigree for low_markers_remove_female_parent, which also set the male parent to 0. Low-marker trios now remove only the identified parent(s).
• New assign_composition_line() turns the output of solve_composition_poly() into the composition table used by Familia: percentages per reference population and a Predicted line, labelled Undetermined when the highest proportion is below assign_threshold (default 50). solve_composition_poly() is unchanged.
• validate_pedigree(): new marker_trio_table = FALSE argument. When TRUE the result includes marker_trio_table, a marker-by-trio table with one column per trio (id_male_parent_female_parent) giving each marker's status: match, mismatch_male, mismatch_female, mismatch_both, mismatch_combination (each parent compatible alone but not the pair), untestable (odd ploidy) or missing_* named after the individuals without a call (e.g. missing_male, missing_male_female, missing_progeny).

BIGpopA 2.1.1

• validate_pedigree(): a trio that fails the Mendelian error threshold while neither parent fails the single-parent homozygous check now gets recommended_correction = "unresolved" instead of "keep_both". This happens, for example, with a recorded self whose offspring carries alleles the parent lacks: the pedigree is wrong, but the faulty parent cannot be identified. These trios are left unchanged in corrected_pedigree for manual review.
• validate_pedigree() plot: bars are coloured by trio error first, so no trio above the threshold is shown as Pass. Unresolved trios are shown in grey ("Fail - Parents Unresolved"), and the legend wraps onto two rows so all labels are visible.

BIGpopA 2.1.0 (2026-10-05)

• 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 (2026-08-21)

• 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 (2026-07-16)

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

BIGpopA 1.0.5 (2026-06-24)

• 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

• 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