Package: BIGpopA
Title: Pedigree Validation Genetic Composition of Diploids & Polyploids
Version: 2.2.0
Authors@R: c(person(given='Josue',
                    family='Chinchilla-Vargas',
                    email='josue.chinchilla@ufl.edu',
                    role=c('cre','aut')),
             person(given='Alexander',
                    family='Sandercock',
                    role=c('aut')),
             person('University', "of Florida",
                    role=c('cph'),
                    comment = "Breeding Insight"))
Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>
Description: Tools for pedigree quality control and genomic breed/line
        composition estimation in diploid and polyploid breeding
        populations. 'BIGpopA' provides functions to check and correct
        common pedigree errors, assign parentage from SNP genotype data
        using Mendelian error rates, validate parent-offspring trios,
        and estimate genome-wide breed or line composition using
        quadratic programming. Pedigree validation and parentage
        assignment support any ploidy, using a polysomic Mendelian test
        for even ploidy and a homozygosity-based check for odd ploidy.
        Genotypes can be supplied as dosage tables, VCF files, or
        'PLINK' .ped files. For more details about the included
        'breedTools' functions, see Funkhouser et al. (2017)
        <doi:10.2527/tas2016.0003>.
License: Apache License (>= 2)
URL: https://CRAN.R-project.org/package=BIGpopA,
        https://github.com/Breeding-Insight/BIGpopA
BugReports: https://github.com/Breeding-Insight/BIGpopA/issues
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.4.0)
Imports: dplyr, janitor, quadprog, data.table, ggplot2
Suggests: covr, knitr (>= 1.10), rmarkdown, scales, testthat (>=
        3.0.0), vcfR (>= 1.15.0), withr
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libicu-dev
Repository: https://breeding-insight.r-universe.dev
Date/Publication: 2026-10-12 20:35:48 UTC
RemoteUrl: https://github.com/breeding-insight/bigpopa
RemoteRef: HEAD
RemoteSha: ca36034f20aec4bc46ba0a324901f7b564588e79
NeedsCompilation: no
Packaged: 2026-10-12 23:26:53 UTC; root
Author: Josue Chinchilla-Vargas [cre, aut],
  Alexander Sandercock [aut],
  University of Florida [cph] (Breeding Insight)