R Observatory: Metrics for MDSMap version 1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MDSMap

1.3Package record

High Density Genetic Linkage Mapping using Multidimensional Scaling

1packages depend

4.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Bram BoskampCRAN page ↗

Estimate genetic linkage maps for markers on a single chromosome (or in a single linkage group) from pairwise recombination fractions or intermarker distances using weighted metric multidimensional scaling. The methods are suitable for autotetraploid as well as diploid populations. Options for assessing the fit to a known map are also provided. Methods are discussed in detail in Preedy and Hackett (2016) doi:10.1007/s00122-016-2761-8.

Install

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

install.packages("MDSMap", 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-mdsmap

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-MDSMap

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-MDSMap

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: 3.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3

READMENoVignettesYes · 1 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 24includes a package overview page
Examples that run: 86%12 run in a plain check · 2 never run
Exported functions with examples: 44%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 33%

Vignettes (1)

MDSMap: High Density Linkage Maps using Multi-Dimensional Scaling PDF

How these are measured

Downloads

4.3K

CRAN downloads in the past year

Rank #9,482 · ~12/day · ~358/mo

Releases R versions

Daily download trend is not available in this view yet.

34530 days

1K90 days

4.3K1 year

Compare downloads with other packages →

Also on94 r2u3 autocran56 c2d4u

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing MDSMap adds 108 packages (60 with compiled code, 84 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.2.0

Imports (4)

smacof princurve rgl reshape

LinkingTo (0)

none

Suggests (2)

qtl R.rsp

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

polymapR

How these are counted

Code & Tests

Datasets

People & History

People (3)

Bram Boskamp

Maintainer · added in 1.3

Christine A. Hackett

Author · added in 1.1

Katharine F. Preedy

Author

Maintainer since 1.0 (2017)

Listed in earlier versions (2)

Hackett

no longer listed · 1.3

Preedy

no longer listed · 1.3

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.3Latest
record
2025-04-28 · current release · diff ↗
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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.1
record
2018-08-09 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0
record
2017-11-29
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-11-29
Total releases: 3 / 9 yrs
License: GPL-3 | file LICENSE OSI
Minimum R: ≥ 3.2.0
Download size: 697 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MDSMap")

Format

Boskamp, B., Hackett, C. A., & Preedy, K. F. (2025). MDSMap: High Density Genetic Linkage Mapping using Multidimensional Scaling (Version 1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.MDSMap

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 MDSMap version 1.3 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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