R Observatory: Metrics for mppR version 1.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mppR

1.5.0

Multi-Parent Population QTL Analysis

0packages depend

2.8Kdownloads / year

25.1%test coverage

13/13checks pass

Overview

About

Maintained by Vincent GarinFirst published 2018-07-016 releasesCRAN page ↗GitHub ↗

Analysis of experimental multi-parent populations to detect regions of the genome (called quantitative trait loci, QTLs) influencing phenotypic traits measured in unique and multiple environments. The population must be composed of crosses between a set of at least three parents (e.g. factorial design, 'diallel', or nested association mapping). The functions cover data processing, QTL detection, and results visualization. The implemented methodology is described in Garin, Wimmer, Mezmouk, Malosetti and van Eeuwijk (2017) doi:10.1007/s00122-017-2923-3, in Garin, Malosetti and van Eeuwijk (2020) <doi: 10.1007/s00122-020-03621-0>, and in Garin, Diallo, Tekete, Thera, ..., and Rami (2024) <doi: 10.1093/genetics/iyae003>.

Install

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

install.packages("mppR", 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("vincentgarin/mppR")

Development version from vincentgarin/mppR. 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-mppr

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-mppR

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-mppR

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

Health

CRAN checks

13OK

Slowest check: 8.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

25.1%

Coverage · measured lines

97%

Documentation · exports

12

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 118 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 100%
Return-value docs: 97%
References docs: 37%

Downloads

2.8K

CRAN downloads in the past year

Rank #14,971 · ~8/day · ~236/mo

Releases R versions

Daily download trend is not available in this view yet.

17330 days

69290 days

2.8K1 year

Compare downloads with other packages →

Also on119 r2u20 autocran

Repository

GitHub ↗ vincentgarin/mppr

2Stars

1Forks

4Open issues

0Open PRs

1Releases

211Commits

3Contributors

211 commits · Last activity 2024-03-11

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/vincentgarin/mppr on 2026-08-16.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (12)

dplyr ggplot2graphicsgrDevicesigraphMatrixmethodsnlmeparallelqtlstatsutils

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Vincent Garin

Author, Maintainer

Authors (2)

Vincent Garin

Author, Maintainer

Valentin Wimmer

Author

Contributors (3)

Dietrich Borchardt

Contributor, Data contributor

Marcos Malosetti

Contributor, Thesis advisor

Fred van Eeuwijk

Contributor, Thesis advisor

Package Timeline

6 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
1.5.0Latest
2024-02-22 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.4.0
2023-01-05 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.3.0
2021-05-15 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2.1
2020-02-11 · diff ↗
1.2.0
2019-05-31 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.10
2018-07-01
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-07-01
Total releases: 6 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Bundled data: 834 KB / 8 files
Download size: 2.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mppR")

Format

Garin, V., Borchardt, D., Malosetti, M., Wimmer, V., & van Eeuwijk, F. (2024). mppR: Multi-Parent Population QTL Analysis (Version 1.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.mppR

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 mppR version 1.5.0 [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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