R Observatory: Metrics for pedtools version 2.11.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pedtools

2.11.0

Creating and Working with Pedigrees and Marker Data

20packages depend

7.7Kdownloads / year

56.6%test coverage

13/13checks pass

Overview

About

Maintained by Magnus Dehli VigelandFirst published 2019-10-1127 releasesCRAN page ↗GitHub ↗

A comprehensive collection of tools for creating, manipulating and visualising pedigrees and genetic marker data. Pedigrees can be read from text files or created on the fly with built-in functions. A range of utilities enable modifications like adding or removing individuals, breaking loops, and merging pedigrees. An online tool for creating pedigrees interactively, based on 'pedtools', is available at https://magnusdv.shinyapps.io/quickped. 'pedtools' is the hub of the 'pedsuite', a collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite' is given in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).

Install

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

install.packages("pedtools", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("magnusdv/pedtools")

Development version from magnusdv/pedtools. Installs pak first if it is not already available.

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-pedtools

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-pedtools

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-pedtools

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

Health

CRAN checks

13OK

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.16

56.6%

Coverage · measured lines

100%

Documentation · exports

2

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 239 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 92%
Return-value docs: 91%
References docs: 0%

Downloads

7.7K

CRAN downloads in the past year

Rank #4,018 · ~21/day · ~644/mo

Releases R versions

Daily download trend is not available in this view yet.

45130 days

2.1K90 days

7.7K1 year

Compare downloads with other packages →

Also on244 r2u15 autocran

Repository

GitHub ↗ magnusdv/pedtools

28Stars

6Forks

1Open issues

0Open PRs

25Releases

885Commits

1Contributors

pedigreespedsuite

License GPL-3.0 · 885 commits · Last activity 2026-06-29 · 0% stars, 30d

Stars over time

2025-04-22 · 252026-07-07 · 28

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/magnusdv/pedtools on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2

Imports (2)

kinship2 pedmut

LinkingTo (0)

none

Suggests (4)

kableExtra knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

20direct

1indirect

dvir forrel ibdsim2 paramlink2 pedFamilias pedbuildr pedprobr pedsuite ribd segregatr verbalisr KLINK KinMixLite forensicolors ibdfindr ibdsegments mispitools numberofalleles relMix simDNAmixtures

Code & Tests

People & History

People (1)

Maintainer (1)

Magnus Dehli Vigeland

Author, Maintainer

Authors (1)

Magnus Dehli Vigeland

Author, Maintainer

Package Timeline

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

2.11.0Latest
2026-06-19 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.10.0
2026-02-01 · diff ↗
2.9.0
2025-10-28 · diff ↗
2.8.2
2025-07-13 · diff ↗
2.8.1
2025-04-29 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.8.0
2025-01-25 · diff ↗
2.7.1
2024-09-08 · diff ↗
2.7.0
2024-06-28 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.6.0
2024-03-31 · diff ↗
2.5.0
2023-11-05 · diff ↗
2.4.0
2023-10-02 · diff ↗
2.3.1
2023-08-24 · diff ↗
2.2.0
2023-05-25 · diff ↗

Show 19 earlier events

R
R 4.3.0 released · 2023-04-21
2.1.1
2023-01-05 · diff ↗
2.0.0
2022-11-03 · diff ↗
1.3.0
2022-06-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.0
2022-03-30 · diff ↗
1.1.0
2021-12-08 · diff ↗
1.0.1
2021-06-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.9.7
2021-02-10 · diff ↗
0.9.6
2020-11-14 · diff ↗
0.9.5
2020-08-04 · diff ↗
0.9.4
2020-06-18 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.9.3
2020-03-21 · diff ↗
0.9.2
2020-02-03 · diff ↗
0.9.1
2019-12-02 · diff ↗
0.9.0
2019-10-11
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-10-11
Total releases: 27 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2
Download size: 305 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pedtools")

Format

Vigeland, M. D. (2026). pedtools: Creating and Working with Pedigrees and Marker Data (Version 2.11.0) [Computer software]. https://doi.org/10.32614/CRAN.package.pedtools

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 pedtools version 2.11.0 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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