R Observatory: Metrics for BIGpopA version 1.0.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BIGpopA

1.0.6

Pedigree Validation Genetic Composition of Diploids & Polyploids

1packages depend

495downloads / year

94.2%test coverage

13/13checks pass

Overview

About

Maintained by Josue Chinchilla-VargasFirst published 2026-06-242 releasesCRAN page ↗GitHub ↗

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. Supports both diploid and polyploid species. For more details about the included 'breedTools' functions, see Funkhouser et al. (2017) doi:10.2527/tas2016.0003.

Install

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

install.packages("BIGpopA", 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/BIGpopA")

Development version from Breeding-Insight/BIGpopA. 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-bigpopa

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-BIGpopA

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

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-BIGpopA

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.7 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 1.49

94.2%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-25
8 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 179 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 60%
Documented parameters: 100%
Return-value docs: 100%
References docs: 40%

Downloads

495

CRAN downloads in the past year

Rank #22,060 · ~1/day · ~41/mo

Releases R versions

Daily download trend is not available in this view yet.

20330 days

49590 days

4951 year

Compare downloads with other packages →

Also on21 r2u11 autocran

Repository

GitHub ↗ breeding-insight/bigpopa

0Stars

1Forks

0Open issues

0Open PRs

6Releases

73Commits

2Contributors

73 commits · Last activity 2026-07-20

Forks over time

2026-07-07 · 02026-07-09 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/breeding-insight/bigpopa on 2026-08-09.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4.0

Imports (5)

dplyr janitor quadprog data.table ggplot2

LinkingTo (0)

none

Suggests (5)

covr knitr rmarkdown scales testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Familia

Code & Tests

People & History

People (3)

Maintainer (1)

Josue Chinchilla-Vargas

Maintainer, Author

Authors (2)

Josue Chinchilla-Vargas

Maintainer, Author

Alexander Sandercock

Author

Copyright holders (1)

University of Florida

Copyright holder

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

1.0.6Latest
2026-07-17 · current release · diff ↗
1.0.5
2026-06-24
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-24
Total releases: 2 / 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("BIGpopA")

Format

Chinchilla-Vargas, J., Sandercock, A., & of Florida, U. (2026). BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids (Version 1.0.6) [Computer software]. https://doi.org/10.32614/CRAN.package.BIGpopA

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 BIGpopA version 1.0.6 [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.

Report a problem with this page →