Package: Familia 2.2.0

Familia: 'shiny' Application for Population Structure and Ancestry Assessments

Provides a 'shiny' web application developed by the Breeding Insight team to support pedigree validation and ancestry assessment of plant and animal populations. The app integrates Mendelian error analysis, parentage assignment and genetic composition/ancestry methods to help researchers evaluate genomic relationships through an accessible, web-based interface without requiring command-line tools. Pedigree validation, Mendelian error analysis and parentage assignment build on the 'BIGpopA' package (<https://CRAN.R-project.org/package=BIGpopA>) and support diploid and polyploid data. Genotypes can be uploaded as dosage tables, VCF files, or 'PLINK' .ped files. Ancestry estimation uses the sparse non-negative matrix factorization method of Frichot et al. (2014) <doi:10.1534/genetics.113.160572> as implemented in the 'LEA' package by Frichot and Francois (2015) <doi:10.1111/2041-210X.12382>. Line and breed composition are estimated using the breed composition regression method of Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>, extended to polyploid species by Sandercock et al. (2025) <doi:10.1002/tpg2.70067>.

Authors:Josue Chinchilla-Vargas [aut, cre], Alexander M. Sandercock [aut], Breeding Insight Team [aut]