polymapR

1.1.7

Linkage Analysis in Outcrossing Polyploids

4packages depend

5.7Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Peter BourkeFirst published 2017-12-0518 releasesCRAN page ↗

Creation of linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) doi:10.1093/bioinformatics/bty371. Since version 1.1.0, both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) doi:10.1007/s00122-021-03834-x.

Install

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

install.packages("polymapR", 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-polymapr

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-polymapR

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-polymapR

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 45.1 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
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
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 70%
Documented parameters: 99%
Return-value docs: 70%
References docs: 0%

Downloads

5.7K

CRAN downloads in the past year

Rank #9,981 · ~16/day · ~479/mo

Releases R versions

Daily download trend is not available in this view yet.

29230 days

1K90 days

5.7K1 year

Compare downloads with other packages →

Also on391 r2u21 c2d4u

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (9)

doParallel foreachgraphicsgrDevicesigraph knitr MDSMapstatsutils

LinkingTo (0)

none

Suggests (8)

ggplot2 Hmisc RColorBrewer reshape2 rmarkdown polyRAD updog mappoly

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

mappoly polyRAD polyqtlR segtest

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Peter Bourke

Author, Maintainer

Authors (2)

Peter Bourke

Author, Maintainer

Geert van Geest

Author

Contributors (2)

Yanlin Liao

Contributor · added in 1.1.0

Roeland Voorrips

Contributor · added in 1.0.20

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.7Latest
2025-10-17 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.6
2024-05-31 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.5
2024-01-08 · diff ↗
1.1.4
2023-11-04 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.3
2023-03-13 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.2
2021-03-09 · diff ↗
1.1.1
2020-12-17 · diff ↗
1.1.0
2020-07-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.20
2019-12-12 · diff ↗

Show 12 earlier events

R
R 3.6.0 released · 2019-04-26
1.0.19
2019-02-01 · diff ↗
1.0.18
2018-11-01 · diff ↗
1.0.17
2018-08-24 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.16
2018-04-13 · diff ↗
1.0.15
2018-04-13 · diff ↗
1.0.14
2018-03-27 · diff ↗
1.0.13
2018-02-13 · diff ↗
1.0.12
2017-12-14 · diff ↗
1.0.11
2017-12-05
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-12-05
Total releases: 18 / 9 yrs
License: GPL
Minimum R: ≥ 3.5.0
Bundled data: 2.9 MB / 42 files
Download size: 4.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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Agricultural Science

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