R Observatory: Metrics for HardyWeinberg version 1.7.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HardyWeinberg

1.7.9Package record

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

1packages dependsuggested by 3

52.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jan GraffelmanCRAN page ↗Website ↗

Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) doi:10.1038/hdy.2016.20, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots. The functionality of the package is explained in detail in a related JSS paper doi:10.18637/jss.v064.i03.

Install

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

install.packages("HardyWeinberg", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-hardyweinberg

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-HardyWeinberg

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-HardyWeinberg

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: 8.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 4 earlier changesHide 4 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.7.9

READMENoVignettesYes · 2 · dynamicNEWSNoCitation fileYes · cites a publicationWebsiteYes

Cites a JSS article

Help pages: 87includes a package overview page
Examples that run: 99%82 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 62%

Vignettes (2)

How these are measured

Downloads

52.6K

CRAN downloads in the past year

Rank #1,987 · ~144/day · ~4.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.5K30 days

9.3K90 days

52.6K1 year

Compare downloads with other packages →

Also on507 r2u6 autocran6.2K conda_forge344 bioconda142 c2d4u

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing HardyWeinberg adds 62 packages (36 with compiled code, 42 MB of source tarballs). Heaviest: stringi 11 MB, lme4 4.1 MB, glmnet 2.7 MB.

Depends (5)

R >= 1.8.0micennetRsolnp shape

Imports (1)

Rcpp

LinkingTo (1)

Rcpp

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 3

Depends, Imports or LinkingTo, most downloaded first

compareGroups

Suggests, most downloaded first

dartR dartR.base gaawr2

How these are counted

Code & Tests

Datasets

People & History

People (6)

Jan Graffelman

Author, Maintainer since 1.0 (2007)

Christopher Chang

Contributor · added in 1.5.9

William R. Engels

Contributor · added in 1.6.7

Leonardo Ortoleva

Contributor · added in 1.6.7

Xavi Puig

Contributor · added in 1.5.9

Jan Wigginton

Contributor · added in 1.5.9

Releases (30)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.7.9Latest
record
2025-09-10 · current release · diff ↗ ·
added 1 export
HWBalance
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.7.8
record
2024-04-06 · diff ↗
1.7.7
record
2024-03-31 · diff ↗ ·
added 11 exports
afx, he, HWEM, HWLindley.cri, HWStr, HWStrata, is.mono, order.auto, order.x, qqunif, shannon
R
R 4.3.0 released · 2023-04-21
1.7.5
record
2022-05-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.7.4
record
2021-11-26 · diff ↗
1.7.3
record
2021-11-17 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.7.2
record
2021-04-28 · diff ↗ ·
added 1 export
AllelesToTriangular
1.7.1
record
2021-01-04 · diff ↗ ·
added 1 export
HWNetwork
1.7.0
record
2020-12-14 · diff ↗ ·
removed 1 export
HWNetwork
1.6.9
record
2020-12-08 · diff ↗

Show 39 earlier eventsHide 39 earlier events

1.6.8
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2020-09-20 · diff ↗
1.6.7
record
2020-09-20 · diff ↗ ·
added 2 exports
fold, HWNetwork
1.6.6
record
2020-08-13 · diff ↗ ·
added 1 export
HWLindley
R
R 4.0.0 released · 2020-04-24
1.6.3
record
2019-06-29 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.6.2
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2019-04-14 · diff ↗
1.6.1
record
2018-05-30 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.5.9
record
2017-12-16 · diff ↗ ·
added 13 exports
alleles, dgraffelmanweir.bi, dlevene, dlevene.bi, EAFExact, HWAIC, HWLRtest, HWLRAllTests, HWPerm.mult, HWTriExact, n.alleles, strsort, toTriangular
1.5.8
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2017-05-17 · diff ↗ ·
added 1 export
HWPosterior
1.5.7
record
2017-04-22 · diff ↗ ·
added 3 exports
genlabels, HWABO, ThetatoF
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.5.6
record
2016-03-29 · diff ↗ ·
added 6 exports
AFtest, agcounts, HWChisqStats, HWClo, HWExactPrevious, HWExactStats
R
R 3.2.0 released · 2015-04-16
1.5.5
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2015-02-26 · diff ↗ ·
added 1 export
MakeFactor
1.5.4
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2014-08-11 · diff ↗ ·
added 2 exports
HWD, vaf
R
R 3.1.0 released · 2014-04-10
1.5.2
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2013-11-25 · diff ↗ ·
added 1 export
HWPerm
1.5.1
record
2013-11-14 · diff ↗ ·
added 17 exports
fisherz, HWAlltests, HWAlr, HWAlrPlot, HWClr, HWClrPlot, HWf, HWGenotypePlot, HWIlr, HWIlrPlot, HWMissing, HWPower, HWQqplot, ifisherz, mac, MakeCounts, recode
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
1.4.1
record
2012-03-20 · diff ↗ ·
added 5 exports
af, HWChisqMat, HWExactMat, maf, UniqueGenotypeCounts
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
1.4
record
2009-11-23 · diff ↗
R
R 2.10.0 released · 2009-10-26
R
R 2.9.0 released · 2009-04-17
1.3
record
2009-03-27 · diff ↗ ·
added 2 exports
HWCondProbAB, HWExact
R
R 2.8.0 released · 2008-10-20
1.2
record
2008-04-22 · diff ↗ ·
added 1 export
HWData
R
R 2.7.0 released · 2008-04-22
1.1
record
2007-10-03 · diff ↗
R
R 2.6.0 released · 2007-10-03
1.0
record
2007-10-02
R
R 2.5.0 released · 2007-04-24

Package metadata

First published: 2007-10-02
Total releases: 30 / 19 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 1.8.0
Bundled data: 150 KB / 14 files
Download size: 1.2 MB

Appears in task views

Missing Data

Cite

Cite this package

Run in R for the authors' entry:

citation("HardyWeinberg")

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

It points to 10.18637/jss.v064.i03, 10.1159/000108939, 10.1038/hdy.2016.20.

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 HardyWeinberg version 1.7.9 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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