R Observatory: Metrics for qtl2pleio version 1.4.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

qtl2pleio

1.4.4

Testing Pleiotropy in Multiparental Populations

0packages depend

3.5Kdownloads / year

51.3%test coverage

13/13checks pass

Overview

About

Maintained by Frederick J BoehmFirst published 2019-11-055 releasesCRAN page ↗GitHub ↗

We implement an adaptation of Jiang & Zeng's (1995) doi:10.1093/genetics/140.3.1111 likelihood ratio test for testing the null hypothesis of pleiotropy against the alternative hypothesis, two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995) and that in Tian et al. (2016) doi:10.1534/genetics.115.183624 in that our test accommodates multiparental populations.

Install

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

install.packages("qtl2pleio", 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/qtl2pleio")

Development version from fboehm/qtl2pleio. 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-qtl2pleio

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-qtl2pleio

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-qtl2pleio

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

Health

CRAN checks

13OK

Slowest check: 7.6 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.40

51.3%

Coverage · measured lines

96%

Documentation · exports

9

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
OK2026-04-29
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
8 OK · 5 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 664 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 93%
References docs: 13%

Downloads

3.5K

CRAN downloads in the past year

Rank #7,327 · ~10/day · ~296/mo

Releases R versions

Daily download trend is not available in this view yet.

23730 days

1.2K90 days

3.5K1 year

Compare downloads with other packages →

Also on398 r2u24 autocran

Repository

GitHub ↗ fboehm/qtl2pleio

6Stars

2Forks

11Open issues

0Open PRs

9Releases

663Commits

4Contributors

quantitative-traitquantitative-geneticsmultiparental-populations

663 commits · Last activity 2026-05-29 · 0% stars, 30d

Stars over time

2024-10-08 · 52026-07-07 · 6

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/fboehm/qtl2pleio on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Dockerfile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Research and citation (3)

codemeta.jsonJOSS paperZenodo

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2

Imports (9)

dplyr gemma2 ggplot2 magrittrMASSRcpp rlang tibbleparallel

LinkingTo (2)

Rcpp RcppEigen

Suggests (9)

covr mvtnorm knitr rmarkdown testthat broman devtools qtl2 parallelly

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Frederick J Boehm

Author, Maintainer

Authors (1)

Frederick J Boehm

Author, Maintainer

Package Timeline

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

1.4.4Latest
2026-04-26 · current release · diff ↗
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
1.4.3
2020-12-02 · diff ↗
1.4.1
2020-10-29 · diff ↗
1.3.0
2020-06-30 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2.3
2019-11-05
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-11-05
Total releases: 5 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.2
Download size: 124 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("qtl2pleio")

The authors publish a JOSS paper, so they have said how they want this cited. Run citation() and use what it gives you.

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 qtl2pleio version 1.4.4 [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.

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