R Observatory: Metrics for gemma2 version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gemma2

0.1.3

GEMMA Multivariate Linear Mixed Model

1packages depend

2.8Kdownloads / year

95.7%test coverage

11/13checks pass

Overview

About

Maintained by Frederick BoehmFirst published 2019-10-012 releasesCRAN page ↗GitHub ↗

Fits a multivariate linear mixed effects model that uses a polygenic term, after Zhou & Stephens (2014) (https://www.nature.com/articles/nmeth.2848). Of particular interest is the estimation of variance components with restricted maximum likelihood (REML) methods. Genome-wide efficient mixed-model association (GEMMA), as implemented in the package 'gemma2', uses an expectation-maximization algorithm for variance components inference for use in quantitative trait locus studies.

Install

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

install.packages("gemma2", 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("fboehm/gemma2")

Development version from fboehm/gemma2. 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-gemma2

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-gemma2

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-gemma2

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 24.3 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.39

95.7%

Coverage · measured lines

100%

Documentation · exports

2

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 178 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 89%
References docs: 0%

Downloads

2.8K

CRAN downloads in the past year

Rank #15,412 · ~8/day · ~230/mo

Releases R versions

Daily download trend is not available in this view yet.

14930 days

67690 days

2.8K1 year

Compare downloads with other packages →

Also on102 r2u22 autocran

Repository

GitHub ↗ fboehm/gemma2

14Stars

2Forks

0Open issues

0Open PRs

2Releases

151Commits

1Contributors

geneticsem-algorithmmixed-models

151 commits · Last activity 2020-10-24 · +7.7% stars, 30d

Stars over time

2025-01-01 · 122026-08-20 · 14

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/fboehm/gemma2 on 2026-08-16.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

methodsMatrix

LinkingTo (0)

none

Suggests (5)

covr testthat knitr rmarkdown readr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

qtl2pleio

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Frederick Boehm

Author, Maintainer

Authors (1)

Frederick Boehm

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.1.3Latest
2020-10-24 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.1
2019-10-01
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-10-01
Total releases: 2 / 7 yrs
License: MIT + file LICENSE OSI
Download size: 470 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("gemma2")

Format

Boehm, F. (2020). gemma2: GEMMA Multivariate Linear Mixed Model (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.gemma2

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 gemma2 version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, 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 →