R Observatory: Metrics for statgenMPP version 1.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

statgenMPP needs sommer (through statgenGWAS), which CRAN will archive unless its check problems are fixed by Nov 14.

statgenMPP

1.0.5Package record

QTL Mapping for Multi Parent Populations

0packages depend

3.8Kdownloads / year

92.0%test coverage

13/13flavors OK

Overview

About

Maintained by Bart-Jan van RossumCRAN page ↗GitHub ↗Website ↗Issues ↗

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).

Changes in 1.0.5

No user visible changes.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)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. 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-statgenMPP

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-statgenMPP

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: 4.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-25
ERROR12 OK, 1 ERROR2026-10-24
OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-04

Show 6 earlier changesHide 6 earlier changes

NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-20
WARNING12 OK, 1 WARNING2026-05-19
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.5

READMEYes · 254 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.5Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 20 (6 internal)includes a package overview page
Examples that run: 63%5 run in a plain check · 3 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 10%

Vignettes (1)

QTL Mapping in Multi-Parent Populations

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #8,162 · ~10/day · ~319/mo

Releases R versions

Daily download trend is not available in this view yet.

33630 days

1.1K90 days

3.8K1 year

Compare downloads with other packages →

Also on109 r2u4 autocran126 c2d4u

How downloads are counted

Repository

biometris/statgenmpp ↗Organization: Biometris

1Stars

1Forks

1Open issues

0Open PRs

1Releases

292Commits

3Commit identities

crangeneticsqtl-mappingr-packagempp

292 commits · Last activity 2026-05-18 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 43
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-05-26 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/biometris/statgenmpp on 2026-10-22.

Continuous integration (3)

GitHub ActionsR CMD check workflowGitLab CI

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-05-18 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing statgenMPP adds 37 packages (18 with compiled code, 55 MB of source tarballs). Heaviest: stringi 11 MB, LMMsolver 7.1 MB, ggplot2 6.0 MB.

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

Dependencies facing archival

CRAN will archive these unless their check problems are fixed by the date shown. This package needs each one to install.

sommer through statgenGWASfix by Nov 14

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Bart-Jan van Rossum

Author, Maintainer since 1.0.0 (2022)

Martin Boer

Author

Wenhao Li

Author

Fred van Eeuwijk

Contributor

Releases (7)

Pick two releases to compare their code metrics.

1.0.5Latest
record
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
record
2025-02-11 · diff ↗
1.0.3
record
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
record
2022-12-02 · diff ↗
1.0.1.1
record
2022-08-24 · diff ↗
1.0.1
record
2022-08-22 · diff ↗ ·
removed 1 export
readRABBIT

added 3 exports
createGDataMPP, kinshipIBD, readRABBITMPP
R
R 4.2.0 released · 2022-04-22
1.0.0
record
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

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("statgenMPP")

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

It points to 10.1093/bioinformatics/btac662.

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 statgenMPP version 1.0.5 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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