plmmr

4.3.0

Penalized Linear Mixed Models for Correlated Data

0packages depend

2.5Kdownloads / year

0.0%test coverage

12/13checks pass

Overview

About

Maintained by Patrick J. BrehenyFirst published 2024-10-117 releasesCRAN page ↗GitHub ↗

Fits penalized linear mixed models that correct for unobserved confounding factors. 'plmmr' infers and corrects for the presence of unobserved confounding effects such as population stratification and environmental heterogeneity. It then fits a linear model via penalized maximum likelihood. Originally designed for the multivariate analysis of single nucleotide polymorphisms (SNPs) measured in a genome-wide association study (GWAS), 'plmmr' eliminates the need for subpopulation-specific analyses and post-analysis p-value adjustments. Functions for the appropriate processing of 'PLINK' files are also supplied. For examples, see the package homepage https://pbreheny.github.io/plmmr/.

Install

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

install.packages("plmmr", 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("pbreheny/plmmr")

Development version from pbreheny/plmmr. 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-plmmr

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-plmmr

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-plmmr

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

Health

CRAN checks

1WARNING12OK

Failing flavors

WARNING r-oldrel-macos-arm64

Slowest check: 4.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

0.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

WARNING2026-06-09
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
11 OK · 0 NOTE · 1 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-04-27
11 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-04-22
13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
12 OK · 0 NOTE · 1 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-03-10
13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 141 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.5K

CRAN downloads in the past year

Rank #13,596 · ~7/day · ~209/mo

Releases R versions

Daily download trend is not available in this view yet.

25930 days

77090 days

2.5K1 year

Compare downloads with other packages →

Also on584 r2u11 autocran

Repository

GitHub ↗ pbreheny/plmmr

10Stars

0Forks

4Open issues

0Open PRs

0Releases

1,003Commits

10Contributors

1,003 commits · Last activity 2026-07-03

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/pbreheny/plmmr on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Automation and maintenance (1)

Dependabot

Lint, format, editor (3)

lintrAirRStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.4.0bigalgebra bigmemory

Imports (7)

biglasso data.table glmnetMatrixncvregparallelutils

LinkingTo (4)

BH bigmemory Rcpp RcppArmadillo

Suggests (10)

bigsnpr bigstatsrgraphicsgrDevicesknitrMASSrmarkdown R.utils tinytest withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Patrick J. Breheny

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author · added in 4.2.2

Package Timeline

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

4.3.0Latest
2026-06-11 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
4.2.3
2026-01-26 · diff ↗
4.2.2
2026-01-21 · diff ↗
R
R 4.5.0 released · 2025-04-11
4.2.1
2025-03-03 · diff ↗
4.2.0
2025-02-19 · diff ↗
4.1.0
2024-10-24 · diff ↗
4.0.0
2024-10-11
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-10-11
Total releases: 7 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.4.0
Bundled data: 5.8 KB / 1 file
Download size: 2.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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