R Observatory: Metrics for hwep version 2.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hwep

2.0.3

Hardy-Weinberg Equilibrium in Polyploids

1packages depend

3.3Kdownloads / year

76.4%test coverage

8/13checks pass

Overview

About

Maintained by David GerardFirst published 2021-09-286 releasesCRAN page ↗GitHub ↗

Inference concerning equilibrium and random mating in autopolyploids. Methods are available to test for equilibrium and random mating at any even ploidy level (>2) in the presence of double reduction at biallelic loci. For autopolyploid populations in equilibrium, methods are available to estimate the degree of double reduction. We also provide functions to calculate genotype frequencies at equilibrium, or after one or several rounds of random mating, given rates of double reduction. The main function is hwefit(). 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. For details of these methods, see Gerard (2023a) doi:10.1111/biom.13722 and Gerard (2023b) doi:10.1111/1755-0998.13856.

Install

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

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

Development version from dcgerard/hwep. 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-hwep

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-hwep

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-hwep

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

Health

CRAN checks

5NOTE8OK

Failing flavors

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

Slowest check: 11.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.32

76.4%

Coverage · measured lines

100%

Documentation · exports

14

Dependencies · direct

Check history

NOTE2026-07-29
8 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-27
8 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-07-16
11 OK · 2 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

Show 4 earlier snapshots

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 593 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 92%
Documented parameters: 99%
Return-value docs: 81%
References docs: 25%

Downloads

3.3K

CRAN downloads in the past year

Rank #10,092 · ~9/day · ~278/mo

Releases R versions

Daily download trend is not available in this view yet.

24730 days

94990 days

3.3K1 year

Compare downloads with other packages →

Also on414 r2u26 autocran

Repository

GitHub ↗ dcgerard/hwep

4Stars

0Forks

0Open issues

0Open PRs

0Releases

207Commits

2Contributors

License GPL-3.0 · 207 commits · Last activity 2025-07-23

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/dcgerard/hwep on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (14)

bridgesampling doFuture doRNG foreach future iteratorsmethodspracma Rcpp RcppParallel rstan rstantools tensr updog

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.18.0)

Suggests (5)

testthat covr knitr rmarkdown ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

stCEG

Code & Tests

People & History

People (2)

Maintainer (1)

David Gerard

Author, Maintainer

Authors (1)

David Gerard

Author, Maintainer

Funders (1)

NSF DBI 2132247

Funder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.0.3Latest
2025-07-23 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.2
2023-05-16 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.0.1
2023-03-15 · diff ↗
2.0.0
2022-08-16 · diff ↗
0.0.2
2022-05-02 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.0.1
2021-09-28
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-28
Total releases: 6 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.4.0
Download size: 208 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hwep")

Format

Gerard, D., & NSF DBI 2132247. (2025). hwep: Hardy-Weinberg Equilibrium in Polyploids (Version 2.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.hwep

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 hwep version 2.0.3 [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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