R Observatory: Metrics for mrMLM version 5.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mrMLM

5.0.1Package record

Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for GWAS

1packages depend

4.9Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Yuan-Ming ZhangCRAN page ↗

Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes, and all the nonzero effects were further identified by likelihood ratio test for significant QTL. The program may run on a desktop or laptop computers. If marker genotypes in association mapping population are almost homozygous, these methods in this software are very effective. If there are many heterozygous marker genotypes, the IIIVmrMLM software is recommended. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018, doi:10.1093/bib/bbw145), and Li M, Zhang YW, Zhang ZC, Xiang Y, Liu MH, Zhou YH, Zuo JF, Zhang HQ, Chen Y, Zhang YM (2022, doi:10.1016/j.molp.2022.02.012).

Install

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

install.packages("mrMLM", 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-mrmlm

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-mrMLM

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-mrMLM

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) MultiManhattan.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item{LogTimes}{Magnification of {-log10(P-value)}; the default is
       |                                          ^
checkRd: (-1) MultiManhattan.Rd:35: Lost braces; missing escapes or markup?
    35 |     \item{LODTimes}{Magnification of {LOD score}; the default is 1.2.}
       |                                      ^

CRAN check page ↗

Slowest check: 5.1 min · r-devel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-04-22
ERROR13 NOTE, 1 ERROR2026-04-18
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 5.0.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 18includes a package overview page
Examples that run: 92%11 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 0%
Help pages citing references: 6%

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #6,785 · ~13/day · ~407/mo

Releases R versions

Daily download trend is not available in this view yet.

41730 days

1.3K90 days

4.9K1 year

Compare downloads with other packages →

Also on357 r2u7 autocran1.1K conda_forge

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing mrMLM adds 22 packages (13 with compiled code, 26 MB of source tarballs). Heaviest: TH.data 8.2 MB, data.table 5.7 MB, Rcpp 1.8 MB.

Depends (2)

R >= 3.5.0lars

Imports (10)

Rcppmethodsforeach ncvreg coin(>= 1.1-0)sampling data.table doParallel sbl BEDMatrix

LinkingTo (2)

Rcpp RcppEigen

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

mrMLM.GUI

How these are counted

Code & Tests

Datasets

People & History

People (4)

Yuan-Ming Zhang

Author, Maintainer · added in 5.0

Pei Li

Author · added in 5.0

Jing-Tian Wang

Author · added in 5.0

Ya-Wen Zhang

Author · added in 5.0

Maintainer since 1.0 (2016)

Listed in earlier versions (9)

Show 8 of 9 peopleHide 8 people

Wenlong Ren

no longer listed · 1.0 to 2.1

Shibo Wang

no longer listed · 1.0 to 2.1

Yuanming Zhang

no longer listed · 1.0 to 2.1

Bo Huang

no longer listed · 1.2 to 2.1

Yuanli Ni Shibo Wang

no longer listed · 1.3

Yuanli Ni

no longer listed · 2.0 to 2.1

Yangjun Wen

no longer listed · 2.0 to 2.1

Ren Wen-Long

no longer listed · 3.0 to 3.1

Releases (13)

Pick two releases to compare their code metrics.

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
5.0.1Latest
record
2022-03-27 · current release · diff ↗
5.0
record
2022-03-18 · diff ↗
R
R 4.1.0 released · 2021-05-18
4.0.2
record
2020-10-08 · diff ↗
4.0.1
record
2020-09-29 · diff ↗ ·
added 2 exports
pattern:^[[:alpha:]]+, MultiManhattan
R
R 4.0.0 released · 2020-04-24
4.0
record
2019-10-22 · diff ↗
R
R 3.6.0 released · 2019-04-26
3.1
record
2018-08-26 · diff ↗ ·
added 9 exports
mrMLMFun, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS, ReadData, inputData, DoData
R
R 3.5.0 released · 2018-04-23
3.0
record
2018-03-12 · diff ↗

Show 9 earlier eventsHide 9 earlier events

R
R 3.4.0 released · 2017-04-21
2.1
record
2017-02-09 · diff ↗
2.0
record
2016-12-20 · diff ↗
1.3
record
2016-07-16 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.2
record
2016-04-07 · diff ↗
1.1
record
2016-03-06 · diff ↗
1.0
record
2016-02-26
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-02-26
Total releases: 13 / 10 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 107 KB / 6 files
Download size: 645 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mrMLM")

Format

Zhang, Y., Li, P., Wang, J., & Zhang, Y. (2022). mrMLM: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for GWAS (Version 5.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.mrMLM

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 mrMLM version 5.0.1 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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