R Observatory: Metrics for polymapR version 1.1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

polymapR

1.1.7Package record

Linkage Analysis in Outcrossing Polyploids

0packages dependsuggested by 4

4.9Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Peter BourkeCRAN 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. 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-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). 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

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘p4_functions.Rd’ ‘r4_functions.Rd’ ‘r6_functions.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 26.9 min · r-devel-linux-x86_64-debian-clang

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.7

READMENoVignettesYes · 2 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 73 (1 internal)includes a package overview page
Examples that run: 70%33 run in a plain check · 14 never run
Exported functions with examples: 94%
Documented parameters: 99%
Return-value docs: 70%
Help pages citing references: 0%

Vignettes (2)

How to use polymapR HTML
Using genotype probabilities in polymapR HTML

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #7,930 · ~13/day · ~406/mo

Releases R versions

Daily download trend is not available in this view yet.

47730 days

1.1K90 days

4.9K1 year

Compare downloads with other packages →

Also on205 r2u2 autocran53 c2d4u

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing polymapR adds 110 packages (61 with compiled code, 90 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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

0direct

0indirect

Suggested by 4

Suggests, most downloaded first

mappoly polyRAD segtest polyqtlR

How these are counted

Code & Tests

Datasets

People & History

People (4)

Peter Bourke

Author, Maintainer since 1.0.11 (2017)

Geert van Geest

Author

Yanlin Liao

Contributor · added in 1.1.0

Roeland Voorrips

Contributor · added in 1.0.20

Releases (18)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.7Latest
record
2025-10-17 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.6
record
2024-05-31 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.5
record
2024-01-08 · diff ↗ ·
removed 1 export
plot_linkage_df
1.1.4
record
2023-11-04 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.3
record
2023-03-13 · diff ↗ ·
removed 1 export
merge_marker_assignments
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.2
record
2021-03-09 · diff ↗
1.1.1
record
2020-12-17 · diff ↗
1.1.0
record
2020-07-16 · diff ↗ ·
removed 3 exports
marker_binning_list, orient_and_merge_maps, split_linkage_info

added 6 exports
check_maxP, convert_polyRAD, convert_updog, gp_overview, linkage.gp, screen_for_duplicate_individuals.gp
R
R 4.0.0 released · 2020-04-24
1.0.20
record
2019-12-12 · diff ↗ ·
removed 1 export
createMap

added 1 export
compare_maps

Show 12 earlier eventsHide 12 earlier events

R
R 3.6.0 released · 2019-04-26
1.0.19
record
2019-02-01 · diff ↗
1.0.18
record
2018-11-01 · diff ↗ ·
removed 2 exports
leftstr, rightstr
1.0.17
record
2018-08-24 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.16
record
2018-04-13 · diff ↗
1.0.15
record
2018-04-13 · diff ↗ ·
added 1 export
write.TSNPM
1.0.14
record
2018-03-27 · diff ↗
1.0.13
record
2018-02-13 · diff ↗
1.0.12
record
2017-12-14 · diff ↗
1.0.11
record
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

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("polymapR")

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

It points to 10.1093/bioinformatics/bty371.

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 polymapR version 1.1.7 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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