NEWS.md

In BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids

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

BIGpopA documentation built on July 17, 2026, 1:07 a.m.