R Observatory: Metrics for Familia version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Familia

2.0.0Package record

'shiny' Application for Population Structure and Ancestry Assessments

0packages depend

812downloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Josue Chinchilla-VargasCRAN page ↗GitHub ↗Issues ↗

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. 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.

Changes in 2.0.0

Added a **Ploidy** selector to the Find Parentage and Validate Pedigree tabs, passed through to 'BIGpopA' so pedigree validation and parentage assignment now support any ploidy. Even ploidy uses the full polysomic Mendelian test; odd ploidy (e.g. triploid) uses a homozygosity-based check. Default is 2 (diploid).
Updated the in-app Instructions and Help panels to document the Ploidy option and to generalize genotype dosage coding to 0, 1, ..., ploidy.
Requires 'BIGpopA' (>= 2.0.0).

From NEWS.md in the release

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("Breeding-Insight/Familia")

Development version from Breeding-Insight/Familia. Installs pak first if it is not already available.

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

CRAN check page ↗

Slowest check: 2.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OKNow
OK12 OK2026-08-05
NOTE10 OK, 1 NOTE2026-08-01
OK6 OK2026-07-30

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.0

READMEYes · 639 wordsVignettesNoNEWSYes · 100% structured · mentions 2.0.0Citation fileYes · software entry onlyWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 100%1 run in a plain check (under a condition)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

812

CRAN downloads in the past year

Rank #14,987 · ~2/day · ~68/mo

Releases R versions

Daily download trend is not available in this view yet.

17930 days

81290 days

8121 year

Compare downloads with other packages →

Also on24 r2u

How downloads are counted

Repository

breeding-insight/familia ↗Organization: Breeding-Insight

0Stars

1Forks

2Open PRs

5Releases

112Commits

6Commit identities

112 commits · Last activity 2026-08-24

Responsiveness

How these are sampled

PRs merged (all time): 87%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Forks over time

2026-08-25 · 02026-10-17 · 1

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/breeding-insight/familia on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Installing Familia adds 96 packages (49 with compiled code, 84 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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 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.

How these are counted

Code & Tests

People & History

People (3)

Josue Chinchilla-Vargas

Author, Maintainer since 1.0.3 (2026)

Breeding Insight Team

Author

Alexander M. Sandercock

Author

Listed in earlier versions (1)

Alexander M.

no longer listed · 1.0.3 to 2.0.0

Releases (2)

Pick two releases to compare their code metrics.

2.0.0Latest
record
2026-08-24 · current release · diff ↗
1.0.3
record
2026-07-29
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-29
Total releases: 2 / 1 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.4.0
Download size: 627 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("Familia")

The package provides a citation file, so citation() returns the authors' own entry.

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 2.0.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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