# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "Familia" in publications use:'
type: software
license: Apache-2.0
title: 'Familia: ''shiny'' Application for Population Structure and Ancestry Assessments'
version: 2.2.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.Familia
abstract: 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) <https://doi.org/10.1534/genetics.113.160572>
  as implemented in the 'LEA' package by Frichot and Francois (2015) <https://doi.org/10.1111/2041-210X.12382>.
  Line and breed composition are estimated using the breed composition regression
  method of Funkhouser et al. (2017) <https://doi.org/10.2527/tas2016.0003>, extended
  to polyploid species by Sandercock et al. (2025) <https://doi.org/10.1002/tpg2.70067>.
authors:
- family-names: Chinchilla-Vargas
  given-names: Josue
  email: josue.chinchilla@ufl.edu
- family-names: Sandercock
  given-names: Alexander M.
- name: Breeding Insight Team
preferred-citation:
  type: manual
  title: 'Familia: ''shiny'' Application for Population Structure and Ancestry Assessments'
  authors:
  - family-names: Chinchilla-Vargas
    given-names: Josue
    email: josue.chinchilla@ufl.edu
  - family-names: Sandercock
    given-names: Alexander M.
  - name: Breeding Insight Team
  year: '2026'
  notes: R package version 2.2.0
  url: https://CRAN.R-project.org/package=Familia
repository: https://cran.r-universe.dev
repository-code: https://github.com/Breeding-Insight/Familia
commit: 9e3fc3f11be1a7e2be7fda412158eb7c5392e4ed
url: https://github.com/Breeding-Insight/Familia
date-released: '2026-10-28'
contact:
- family-names: Chinchilla-Vargas
  given-names: Josue
  email: josue.chinchilla@ufl.edu