R Observatory: Metrics for polyqtlR version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

polyqtlR

0.1.1Package record

QTL Analysis in Autopolyploid Bi-Parental F1 Populations

0packages depend

3.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Peter BourkeCRAN 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. 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-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). 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

13OK

CRAN check page ↗

Slowest check: 4.3 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 4 earlier changesHide 4 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 40 (1 internal)includes a package overview page
Examples that run: 79%19 run in a plain check · 5 never run
Exported functions with examples: 96%
Documented parameters: 100%
Return-value docs: 84%
Help pages citing references: 3%

Vignettes (1)

How to use polyqtlR

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #11,409 · ~10/day · ~295/mo

Releases R versions

Daily download trend is not available in this view yet.

35330 days

94690 days

3.5K1 year

Compare downloads with other packages →

Also on416 r2u8 autocran127 c2d4u

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing polyqtlR adds 59 packages (30 with compiled code, 56 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Peter Bourke

Author, Maintainer since 0.0.4 (2020)

Contributor

Contributor

Contributor

Contributor

Contributor

Releases (8)

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
0.1.1Latest
record
2024-01-09 · current release · diff ↗
0.1.0
record
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
record
2022-02-02 · diff ↗
0.0.8
record
2022-01-20 · diff ↗
0.0.7
record
2021-12-09 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 1 export
maxL_IBD
0.0.6
record
2021-06-23 · diff ↗ ·
added 1 export
check_cofactors
R
R 4.1.0 released · 2021-05-18
0.0.5
record
2021-03-11 · diff ↗ ·
added 3 exports
findPeak, findSupport, visualisePairing
0.0.4
record
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

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("polyqtlR")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btab574.

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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