R Observatory: Metrics for segtest version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

segtest

2.0.0Package record

Tests for Segregation Distortion in Polyploids

0packages depend

2.4Kdownloads / year

87.7%test coverage

13/13flavors OK

Overview

About

Maintained by David GerardCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: NSF DBI 2132247

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.

Changes in 2.0.0

seg_lrt(): Tests for segregation distortion for arbitrary (even) ploidy F1 populations.
seg_multi(): Runs seg_lrt() at many loci, with parallelization support from the future package.
gamfreq(): Gamete frequencies under various models of meiosis.
gf_freq(): Genotype frequencies of an F1 population under various models of meiosis.
drbounds(): Two different upper bounds on the double reduction rates.
beta_bounds(): Two different upper bounds on double reduction adjustment for simplex loci.
n_pp_mix(): Number of mixing components in the pairing configuration model for partial preferential pairing.
Added a NEWS.md file to track changes to the package.

From NEWS.md in the release

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. 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-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). 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: 7.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.0

READMEYes · 533 wordsVignettesYes · 3 · dynamicNEWSYes · 67% structured · mentions 2.0.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 39 (1 internal)includes a package overview page
Examples that run: 94%34 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 23%

Vignettes (3)

Introduction to segtest Version 1.0 HTML
Introduction to segtest Version 2.0 HTML
Parallel Testing HTML

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #13,669 · ~7/day · ~204/mo

Releases R versions

Daily download trend is not available in this view yet.

36430 days

84590 days

2.4K1 year

Compare downloads with other packages →

Also on348 r2u2 autocran

How downloads are counted

Repository

dcgerard/segtest ↗Account: dcgerard

2Stars

0Forks

0Open issues

0Open PRs

0Releases

112Commits

1Commit identities

License file reads as GPL-3.0 · 112 commits · Last activity 2025-11-15 · Default branch at 2.0.2, ahead of CRAN 2.0.0 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-23 · 22026-07-07 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/dcgerard/segtest on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Code of conduct

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-11-15

pkgdown site last built 2025-11-15

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 2 practices

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing segtest adds 39 packages (18 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, nloptr 2.1 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (4)

David Gerard

Author, Maintainer since 1.0.1 (2024)

Mira Thakkar

Author

Guilherme da Silva Pereira

Contributor · added in 2.0.0

NSF DBI 2132247

Funder

https://www.nsf.gov/awardsearch/showAward?AWD_ID=2132247

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.0.0Latest
record
2025-06-30 · current release · diff ↗ ·
added 9 exports
beta_bounds, chisq_g, chisq_gl, drbounds, gamfreq, gf_freq, n_pp_mix, seg_lrt, seg_multi
R
R 4.5.0 released · 2025-04-11
1.0.2
record
2025-01-16 · diff ↗
1.0.1
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("segtest")

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

It points to 10.1007/s00122-025-04816-z, 10.1101/2025.06.23.661114.

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 v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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