R Observatory: Metrics for statgenIBD version 1.0.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

statgenIBD

1.0.11

Calculation of IBD Probabilities

1packages depend

4.5Kdownloads / year

85.0%test coverage

11/13checks pass

Overview

About

Maintained by Bart-Jan van RossumFirst published 2021-08-1612 releasesCRAN page ↗GitHub ↗

For biparental, three and four-way crosses Identity by Descent (IBD) probabilities can be calculated using Hidden Markov Models and inheritance vectors following Lander and Green (https://www.jstor.org/stable/29713) and Huang (doi:10.1073/pnas.1100465108). One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.

Install

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

install.packages("statgenIBD", 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("Biometris/statgenIBD")

Development version from Biometris/statgenIBD. 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-statgenibd

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-statgenIBD

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-statgenIBD

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 7.4 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

85.0%

Coverage · measured lines

100%

Documentation · exports

8

Dependencies · direct

Check history

NOTE2026-04-22
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 84 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 78%
Documented parameters: 100%
Return-value docs: 100%
References docs: 8%

Downloads

4.5K

CRAN downloads in the past year

Rank #10,932 · ~12/day · ~374/mo

Releases R versions

Daily download trend is not available in this view yet.

21030 days

89390 days

4.5K1 year

Compare downloads with other packages →

Also on567 r2u20 autocran74 c2d4u

Repository

GitHub ↗ biometris/statgenibd

0Stars

2Forks

0Open issues

0Open PRs

1Releases

282Commits

3Contributors

crangeneticsibdhmmr-package

282 commits · Last activity 2026-05-05

Forks over time

2025-06-30 · 12026-07-07 · 2

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/biometris/statgenibd on 2026-08-16.

Continuous integration (2)

GitHub ActionsGitLab CI

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6

Imports (8)

data.table ggplot2MatrixR.utils rlang Rcpp statgenGWAS stringi

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

rmarkdown knitr tinytest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

statgenMPP

Code & Tests

People & History

People (4)

Maintainer (1)

Bart-Jan van Rossum

Author, Maintainer

Authors (2)

Bart-Jan van Rossum

Author, Maintainer

Martin Boer

Author

Contributors (2)

Johannes Kruisselbrink

Contributor · added in 1.0.5

Wenhao Li

Contributor · added in 1.0.3

Package Timeline

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

1.0.11Latest
2026-05-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.10
2026-03-02 · diff ↗
1.0.9
2025-07-01 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.8
2025-02-05 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.7
2024-02-02 · diff ↗
1.0.6
2023-08-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.5
2022-09-04 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.4
2022-03-07 · diff ↗
1.0.3
2022-02-17 · diff ↗
1.0.2
2021-12-10 · diff ↗
1.0.1
2021-09-14 · diff ↗

Show 4 earlier events

unarchivedReturned to CRAN
2021-09-14
archivedRemoved from CRAN
2021-09-03
check problems were not corrected in time
1.0.0
2021-08-16
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-08-16
Total releases: 12 / 5 yrs
License: GPL
Minimum R: ≥ 3.6
Download size: 2.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("statgenIBD")

Format

van Rossum, B., Boer, M., Kruisselbrink, J., & Li, W. (2026). statgenIBD: Calculation of IBD Probabilities (Version 1.0.11) [Computer software]. https://doi.org/10.32614/CRAN.package.statgenIBD

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 statgenIBD version 1.0.11 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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