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New features
validate_pedigree() returns a marker_summary element with the number of trios tested, the number with a Mendelian mismatch and the mismatch percentage for every marker, sorted worst first.
validate_pedigree() has a new marker_trio_table argument. When TRUE, the result includes a marker-by-trio table with the status of each marker in each trio.
find_parentage() has a new method = "fill_pedigree" that fills in missing parents of a pedigree. A known male searches only females, a known female searches only males, and rows with both parents unknown get the full pair search.
find_parentage() has a new top_n argument that reports the best top_n candidates per progeny, and a tied_candidates column that flags ambiguous assignments. The default keeps the previous output.
founders_file accepts a file path, a character vector of ids or a data.frame, so all inputs can be supplied from memory.
New assign_composition_line() turns the output of solve_composition_poly() into a composition table with percentages per reference population and a predicted line, with Undetermined below the assignment threshold (default 50).
Changes
validate_pedigree() no longer returns best_male_candidate, best_male_candidate_error_pct, best_female_candidate and best_female_candidate_error_pct. Use find_parentage(method = "fill_pedigree") on corrected_pedigree instead. This is the only removed output, and Familia does not use it.
Bug fixes
validate_pedigree() now removes only the identified parent in corrected_pedigree for low_markers_remove_female_parent. It previously also set the male parent to 0.
Documentation and tests
New user guide in docs/, plus updated vignette sections and help pages.
New tests for the founders input, genotype input, hard cases, marker_summary, marker_trio_table and assign_composition_line().