Package: Familia
Title: 'shiny' Application for Population Structure and Ancestry
        Assessments
Version: 1.0.3
Authors@R: 
    c(
              person("Josue", "Chinchilla-Vargas",
                    role = c("aut","cre"),
                    email = "josue.chinchilla@ufl.edu"),
              person(c("Alexander", "M."), "Sandercock",
                    role = "aut"),
              person("Breeding Insight Team",
                    role = "aut"))
Description: 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>). 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>.
License: Apache License (>= 2)
Encoding: UTF-8
Depends: R (>= 4.4.0)
biocViews:
Imports: BIGpopA, bs4Dash, config, curl, data.table, dplyr, DT,
        ggplot2, golem, httr, openxlsx, RColorBrewer, scales, shiny,
        shinydisconnect, shinyjs, shinyWidgets, tibble, tidyr, vcfR (>=
        1.15.0), withr, zip
Suggests: LEA, spelling, testthat
Language: en-US
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-07-20 18:57:02 UTC; josue.chinchilla
Author: Josue Chinchilla-Vargas [aut, cre],
  Alexander M. Sandercock [aut],
  Breeding Insight Team [aut]
Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>
Repository: CRAN
Date/Publication: 2026-07-29 18:30:17 UTC
Built: R 4.6.0; ; 2026-07-29 19:49:19 UTC; unix
