R Observatory: Metrics for segtest version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

segtest

2.0.0

Tests for Segregation Distortion in Polyploids

0packages depend

2.1Kdownloads / year

87.7%test coverage

13/13checks pass

Overview

About

Maintained by David GerardFirst published 2024-10-213 releasesCRAN page ↗GitHub ↗

Provides tests for segregation distortion in F1 polyploid populations under different assumptions of meiosis. These tests can account for double reduction, partial preferential pairing, and genotype uncertainty through the use of genotype likelihoods. Parallelization support is provided. Details of these methods are described in Gerard et al. (2025a) doi:10.1007/s00122-025-04816-z and Gerard et al. (2025b) doi:10.1101/2025.06.23.661114. Part of this material is based upon work supported by the National Science Foundation under Grant No. 2132247. The opinions, findings, and conclusions or recommendations expressed are those of the author and do not necessarily reflect the views of the National Science Foundation.

Install

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

install.packages("segtest", 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("dcgerard/segtest")

Development version from dcgerard/segtest. 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-segtest

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-segtest

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-segtest

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

Health

CRAN checks

13OK

Slowest check: 7.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.16

87.7%

Coverage · measured lines

100%

Documentation · exports

9

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
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 · 533 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 94%
Documented parameters: 96%
Return-value docs: 100%
References docs: 23%

Downloads

2.1K

CRAN downloads in the past year

Rank #19,287 · ~6/day · ~171/mo

Releases R versions

Daily download trend is not available in this view yet.

13530 days

57590 days

2.1K1 year

Compare downloads with other packages →

Also on390 r2u15 autocran

Repository

GitHub ↗ dcgerard/segtest

2Stars

0Forks

0Open issues

0Open PRs

0Releases

112Commits

1Contributors

License GPL-3.0 · 112 commits · Last activity 2025-11-15

Stars over time

2025-05-23 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/dcgerard/segtest on 2026-08-09.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (9)

doFuture doRNG foreach future iterators minqa nloptr Rcpp updog

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

knitr polymapR rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

David Gerard

Author, Maintainer

Authors (2)

David Gerard

Author, Maintainer

Mira Thakkar

Author

Contributors (1)

Guilherme da Silva Pereira

Contributor · added in 2.0.0

Funders (1)

NSF DBI 2132247

Funder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.0.0Latest
2025-06-30 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.2
2025-01-16 · diff ↗
1.0.1
2024-10-21
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-10-21
Total releases: 3 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5
Bundled data: 602 KB / 4 files
Download size: 3.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("segtest")

Format

Gerard, D., NSF DBI 2132247, Pereira, G. d. S., & Thakkar, M. (2025). segtest: Tests for Segregation Distortion in Polyploids (Version 2.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.segtest

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 segtest version 2.0.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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