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2.2.0 - #7
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2.2.0#7
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official CRAN version 2.1 submission
New top_n argument (best N candidates per progeny) and a tied_candidates column that flags ambiguous assignments. New method = "fill_pedigree" fills missing parents of a 3-column pedigree, with a founders_file option. It errors if the input isn't such a pedigree. validate_pedigree(): New marker_summary with per-marker mismatch counts. Suggested replacement parents (best_*_candidate) removed. recommended_correction and corrected_pedigree unchanged. Tests: oracle-based tests for find_parentage() passed (957). The marker_summary tests passed (25). Not re-run since the suggested-parent removal. Docs: .Rd, vignette, README, NEWS.md, cran-comments.md and DESCRIPTION (2.2.0) updated.
…line and marker_trio_table
find_parentage(): add fill_pedigree method, top_n, tied_candidates and founders_file. validate_pedigree(): add marker_summary and the marker_trio_table argument. Remove the best_*_candidate columns, which find_parentage(method = "fill_pedigree") replaces. validate_pedigree(): fix low_markers_remove_female_parent so it removes only the female parent. Add assign_composition_line() with an assignment threshold (default 50). Update tests, docs, vignette, NEWS and cran-comments.md.
upgrade from strawberry project
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Release 2.2.0 of BIGpopA, prepared for CRAN submission.
New features
validate_pedigree(): new marker_summary element (per-marker Mendelian mismatch counts) and new marker_trio_table argument (marker-by-trio status table).
find_parentage(): new method = "fill_pedigree", new top_n argument and new tied_candidates column.
founders_file accepts a file path, a character vector or a data.frame, so all inputs can be supplied from memory.
New assign_composition_line() for the composition table used by Familia.
Changes and fixes
Removed the four best_*_candidate columns from validate_pedigree(). find_parentage(method = "fill_pedigree") replaces them.
Fixed corrected_pedigree for low_markers_remove_female_parent, which also set the male parent to 0.
Documentation and tests
New user guide in docs/.
Updated vignette, NEWS.md and cran-comments.md.
New tests for the founders input, the genotype input, the hard cases, marker_summary, marker_trio_table and assign_composition_line().
Notes
Removed stray files (_to_delete/, tracked .DS_Store).
Familia does not use the removed columns, so there are no reverse dependency problems.