statgenMPP

1.0.5

QTL Mapping for Multi Parent Populations

0packages depend

3.5Kdownloads / year

92.0%test coverage

13/13checks pass

Overview

About

Maintained by Bart-Jan van RossumFirst published 2022-03-217 releasesCRAN page ↗GitHub ↗

For Multi Parent Populations (MPP) Identity By Descend (IBD) probabilities are computed using Hidden Markov Models. These probabilities are then used in a mixed model approach for QTL Mapping as described in Li et al. (doi:10.1007/s00122-021-03919-7).

Install

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

install.packages("statgenMPP", 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/statgenMPP")

Development version from Biometris/statgenMPP. 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-statgenmpp

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

# 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-statgenMPP

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

Health

CRAN checks

13OK

Slowest check: 4.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.00

92.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-20
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-19
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 254 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 63%
Documented parameters: 100%
Return-value docs: 100%
References docs: 10%

Downloads

3.5K

CRAN downloads in the past year

Rank #9,039 · ~10/day · ~290/mo

Releases R versions

Daily download trend is not available in this view yet.

16930 days

1.1K90 days

3.5K1 year

Compare downloads with other packages →

Also on166 r2u3 autocran54 c2d4u

Repository

GitHub ↗ biometris/statgenmpp

1Stars

1Forks

1Open issues

0Open PRs

1Releases

292Commits

3Contributors

crangeneticsqtl-mappingr-packagempp

292 commits · Last activity 2026-05-18

Stars over time

2025-05-26 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/biometris/statgenmpp on 2026-08-03.

Continuous integration (2)

GitHub ActionsGitLab CI

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.6statgenGWAS

Imports (9)

data.table foreach ggplot2 gridExtra LMMsolver rlang scales spam statgenIBD

LinkingTo (0)

none

Suggests (3)

rmarkdown knitr tinytest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Bart-Jan van Rossum

Author, Maintainer

Authors (3)

Bart-Jan van Rossum

Author, Maintainer

Martin Boer

Author

Wenhao Li

Author

Contributors (1)

Fred van Eeuwijk

Contributor

Package Timeline

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

1.0.5Latest
2026-05-18 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.4
2025-02-11 · diff ↗
1.0.3
2024-10-29 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.2
2022-12-02 · diff ↗
1.0.1.1
2022-08-24 · diff ↗
1.0.1
2022-08-22 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.0
2022-03-21
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-03-21
Total releases: 7 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.6
Bundled data: 146 KB / 4 files
Download size: 2.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Report a problem with this page →