R Observatory: Metrics for Familia version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Familia

1.0.3

'shiny' Application for Population Structure and Ancestry Assessments

0packages depend

112downloads / year

0.5%test coverage

13/13checks pass

Overview

About

Maintained by Josue Chinchilla-VargasFirst published 2026-07-301 releasesCRAN page ↗

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.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("Familia", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-familia

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-Familia

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 2.9 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.01

0.5%

Coverage · measured lines

100%

Documentation · exports

22

Dependencies · direct

Check history

OK2026-08-05
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
10 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-30
6 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 593 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

112

CRAN downloads in the past year

Rank #24,614 · ~0/day · ~9/mo

Releases R versions

Daily download trend is not available in this view yet.

11230 days

11290 days

1121 year

Compare downloads with other packages →

Also on3 r2u

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4.0

Imports (22)

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

LinkingTo (0)

none

Suggests (3)

LEA spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Josue Chinchilla-Vargas

Author, Maintainer

Authors (3)

Josue Chinchilla-Vargas

Author, Maintainer

Breeding Insight Team

Author

Alexander M. Sandercock

Author

Listed in earlier versions (1)

Alexander M.

no longer listed · 1.0.3

Package Timeline

1 release. R releases are shown for context.

1.0.3Latest
2026-07-30 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-30
Total releases: 1 / 1 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.4.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Familia")

Format

Chinchilla-Vargas, J., Breeding Insight Team, & Sandercock, A. M. (2026). Familia: 'shiny' Application for Population Structure and Ancestry Assessments (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.Familia

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for Familia version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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