R Observatory: Metrics for qtl2pattern version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

qtl2pattern

1.2.1

Pattern Support for 'qtl2' Package

0packages depend

2.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Brian S YandellFirst published 2021-09-223 releasesCRAN page ↗GitHub ↗

Routines in 'qtl2' to study allele patterns in quantitative trait loci (QTL) mapping over a chromosome. Useful in crosses with more than two alleles to identify how sets of alleles, genetically different strands at the same locus, have different response levels. Plots show profiles over a chromosome. Can handle multiple traits together. See https://github.com/byandell/qtl2pattern.

Install

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

install.packages("qtl2pattern", 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("byandell/qtl2pattern")

Development version from byandell/qtl2pattern. 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-qtl2pattern

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-qtl2pattern

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-qtl2pattern

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

Health

CRAN checks

13OK

Slowest check: 2.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

11

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
WARNING2026-06-08
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 91%
Return-value docs: 100%
References docs: 10%

Downloads

2.8K

CRAN downloads in the past year

Rank #16,145 · ~8/day · ~231/mo

Releases R versions

Daily download trend is not available in this view yet.

13430 days

65390 days

2.8K1 year

Compare downloads with other packages →

Also on121 r2u22 autocran

Repository

GitHub ↗ byandell/qtl2pattern

1Stars

1Forks

0Open issues

0Open PRs

0Releases

229Commits

7Contributors

229 commits · Last activity 2026-08-10

Stars over time

2019-05-03 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

Checks run against github.com/byandell/qtl2pattern on 2026-08-16.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (11)

dplyr tidyr stringr ggplot2 assertthat qtl2 qtl2fst fst rlangstatsgraphics

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown qtl2ggplot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Brian S Yandell

Author, Maintainer

Authors (1)

Brian S Yandell

Author, Maintainer

Package Timeline

3 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
R
R 4.3.0 released · 2023-04-21
1.2.1Latest
2023-03-11 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.0
2022-01-24 · diff ↗
1.0.17
2021-09-22
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-22
Total releases: 3 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("qtl2pattern")

Format

Brian S Yandell. (2023). qtl2pattern: Pattern Support for 'qtl2' Package (Version 1.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.qtl2pattern

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 qtl2pattern version 1.2.1 [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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