R Observatory: Metrics for lme4GS version 0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

lme4GS

0.1

'lme4' for Genomic Selection

0packages depend

2.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Paulino Perez RodriguezFirst published 2025-04-081 releasesCRAN page ↗

Flexible functions that use 'lme4' as computational engine for fitting models used in Genomic Selection (GS). GS is a technology used for genetic improvement, and it has many advantages over phenotype-based selection. There are several statistical models that adequately approach the statistical challenges in GS, such as in linear mixed models (LMMs). The 'lme4' is the standard package for fitting linear and generalized LMMs in the R-package, but its use for genetic analysis is limited because it does not allow the correlation between individuals or groups of individuals to be defined. The 'lme4GS' package is focused on fitting LMMs with covariance structures defined by the user, bandwidth selection, and genomic prediction. The new package is focused on genomic prediction of the models used in GS and can fit LMMs using different variance-covariance matrices. Several examples of GS models are presented using this package as well as the analysis using real data. For more details see Caamal-Pat et.al. (2021) doi:10.3389/fgene.2021.680569.

Install

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

install.packages("lme4GS", 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-lme4gs

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-lme4GS

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-lme4GS

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

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 20%
Documented parameters: 83%
Return-value docs: 100%
References docs: 33%

Downloads

2.2K

CRAN downloads in the past year

Rank #20,638 · ~6/day · ~183/mo

Releases R versions

Daily download trend is not available in this view yet.

12830 days

53990 days

2.2K1 year

Compare downloads with other packages →

Also on112 r2u25 autocran

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (4)

R >= 3.6.3lme4methodsMatrix

Imports (0)

none

LinkingTo (0)

none

Suggests (1)

BGLR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Paulino Perez Rodriguez

Author, Maintainer

Authors (2)

Paulino Perez Rodriguez

Author, Maintainer

Diana Yanira Caamal Pat

Author

Contributors (1)

Erick Javier Suarez Sanchez

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-04-08
Total releases: 1 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.6.3
Bundled data: 167 KB / 2 files
Download size: 181 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("lme4GS")

Format

Perez Rodriguez, P., Caamal Pat, D. Y., & Suarez Sanchez, E. J. (2025). lme4GS: 'lme4' for Genomic Selection (Version 0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.lme4GS

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 lme4GS version 0.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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