R Observatory: Metrics for polyqtlR version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

polyqtlR

0.1.1

QTL Analysis in Autopolyploid Bi-Parental F1 Populations

0packages depend

3.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Peter BourkeFirst published 2020-12-168 releasesCRAN page ↗

Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in autopolyploid bi-parental F1 populations. For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated. Significance thresholds, exploring QTL allele effects and visualising results are provided. For more background and to reference the package see doi:10.1093/bioinformatics/btab574.

Install

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

install.packages("polyqtlR", 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-polyqtlr

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-polyqtlR

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-polyqtlR

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

Health

CRAN checks

13OK

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

13

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
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 79%
Documented parameters: 100%
Return-value docs: 84%
References docs: 3%

Downloads

3.3K

CRAN downloads in the past year

Rank #12,936 · ~9/day · ~279/mo

Releases R versions

Daily download trend is not available in this view yet.

15830 days

77690 days

3.3K1 year

Compare downloads with other packages →

Also on449 r2u21 autocran50 c2d4u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (13)

abind doParallel foreachgrDevicesgraphicsHmisc knitrnlmeRColorBrewer Rcpp reshape2statsutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

igraph mappoly polymapR rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Peter Bourke

Author, Maintainer

Authors (1)

Peter Bourke

Author, Maintainer

Contributors (5)

Contributor

Contributor

Contributor

Contributor

Contributor

Package Timeline

8 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
0.1.1Latest
2024-01-09 · current release · diff ↗
0.1.0
2024-01-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.0.9
2022-02-02 · diff ↗
0.0.8
2022-01-20 · diff ↗
0.0.7
2021-12-09 · diff ↗
0.0.6
2021-06-23 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.0.5
2021-03-11 · diff ↗
0.0.4
2020-12-16
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-12-16
Total releases: 8 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.5 MB / 14 files
Download size: 4.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("polyqtlR")

Format

Bourke, P., Hackett, C., Maliepaard, C., Voorrips, R., Willemsen, J., & van Geest, G. (2024). polyqtlR: QTL Analysis in Autopolyploid Bi-Parental F1 Populations (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.polyqtlR

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 polyqtlR version 0.1.1 [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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