BIGpopA 2.2.0

• 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).

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