R Observatory: Metrics for statgenGWAS version 1.0.13

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

statgenGWAS

1.0.13

Genome Wide Association Studies

3packages depend

10Kdownloads / year

90.5%test coverage

13/13checks pass

Overview

About

Maintained by Bart-Jan van RossumFirst published 2020-01-1913 releasesCRAN page ↗GitHub ↗

Fast single trait Genome Wide Association Studies (GWAS) following the method described in Kang et al. (2010), doi:10.1038/ng.548. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.

Install

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

install.packages("statgenGWAS", 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("Biometris/statgenGWAS")

Development version from Biometris/statgenGWAS. 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-statgengwas

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-statgenGWAS

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-statgenGWAS

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

Health

CRAN checks

13OK

Slowest check: 7.4 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.00

90.5%

Coverage · measured lines

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 5 earlier snapshots

NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 121 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 50%

Downloads

10K

CRAN downloads in the past year

Rank #5,458 · ~27/day · ~835/mo

Releases R versions

Daily download trend is not available in this view yet.

32930 days

1.4K90 days

10K1 year

Compare downloads with other packages →

Also on645 r2u17 autocran54 c2d4u

Repository

GitHub ↗ biometris/statgengwas

15Stars

6Forks

4Open issues

0Open PRs

0Releases

390Commits

3Contributors

geneticsgwascranr-package

390 commits · Last activity 2026-07-16 · 0% stars, 30d

Stars over time

2025-07-18 · 132026-07-07 · 15

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/biometris/statgengwas on 2026-08-16.

Continuous integration (2)

GitHub ActionsGitLab CI

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (2)

EditorConfigRStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6

Imports (7)

data.table ggplot2 LMMsolvermethodsrlang Rcpp sommer

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (6)

knitr rmarkdown officer tinytest snpStats vcfR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

statgenMPP statgenIBD statgenQTLxT

Code & Tests

Datasets

People & History

People (11)

Maintainer (1)

Bart-Jan van Rossum

Author, Maintainer

Authors (2)

Bart-Jan van Rossum

Author, Maintainer

Willem Kruijer

Author

Contributors (9)

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Contributor

Show 1 more contributors

Fred van Eeuwijk

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.13Latest
2026-02-19 · current release · diff ↗
1.0.12
2025-07-01 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.11
2025-03-31 · diff ↗
1.0.10
2024-11-15 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.9
2022-10-13 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.8
2022-02-16 · diff ↗
1.0.7
2021-07-29 · diff ↗
1.0.6
2021-07-26 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.5
2020-09-29 · diff ↗
R
R 4.0.0 released · 2020-04-24

Show 5 earlier events

1.0.4
2020-03-02 · diff ↗
1.0.3
2020-01-27 · diff ↗
1.0.2
2020-01-20 · diff ↗
1.0.1
2020-01-19
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-01-19
Total releases: 13 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6
Bundled data: 1.8 MB / 3 files
Download size: 2.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("statgenGWAS")

Format

van Rossum, B., Boer, M., Bustos-Korts, D., Kruijer, W., Malosetti, M., Millet, E., Paulo, J., Verouden, M., Wehrens, R., Zheng, C., & van Eeuwijk, F. (2026). statgenGWAS: Genome Wide Association Studies (Version 1.0.13) [Computer software]. https://doi.org/10.32614/CRAN.package.statgenGWAS

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 statgenGWAS version 1.0.13 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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