R Observatory: Metrics for genetics version 1.3.8.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

genetics

1.3.8.1.3Package record

Population Genetics

3packages dependsuggested by 1

54.7Kdownloads / year

10.1%test coverage

0/13flavors OK

Overview

About

Maintained by Gregory WarnesCRAN page ↗

Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...

Install

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

install.packages("genetics", 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-genetics

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-genetics

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-genetics

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) LD.Rd:37-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:47-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:66-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:82-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:84-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LD.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:48-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:59-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:78-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:93-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:97-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diseq.Rd:124: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) diseq.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Gregory Warnes <greg@warnes.net>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Gregory",
                      family = "Warnes",
                      role = c("aut", "cre"),
                      email = "greg@warnes.net"),
               person(given = c("with", "contributions", "from", "Gregor"),
                      family = "Gorjanc",
                      role = "aut"),
               person(given = "Friedrich",
                      family = "Leisch",
                      role = "aut"),
               person(given = "Michael",
                      family = "Man.",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.8.1.3

READMENoVignettesNoNEWSYes · 33% structuredCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 20
Examples that run: 94%17 run in a plain check · 1 hold no code
Exported functions with examples: 89%
Documented parameters: 94%
Return-value docs: 89%
Help pages citing references: 35%

How these are measured

Downloads

54.7K

CRAN downloads in the past year

Rank #1,891 · ~150/day · ~4.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.5K30 days

10.3K90 days

54.7K1 year

Compare downloads with other packages →

Also on415 r2u249 autocran2.4K conda_forge101 c2d4u

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing genetics adds 4 packages (2 with compiled code, 1.6 MB of source tarballs). Heaviest: mvtnorm 1.0 MB, gdata 319 KB, gtools 236 KB.

Depends (5)

combinat gdata gtoolsMASSmvtnorm

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

1indirect

Depends 1 · Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

PopGenReport MasterBayes pedtricks

Suggests, most downloaded first

gap

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (4)

Gregory Warnes

with contributions from Gregor Gorjanc

· added in 1.3.0

Friedrich Leisch

Michael Man.

· added in 1.3.0

Maintainer since 0.6.4 (2002)

Releases (26)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.3.8.1.3Latest
record
2021-03-01 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.3.8.1.2
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2019-04-22 · diff ↗
1.3.8.1.1
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2019-02-01 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10

Show 44 earlier eventsHide 44 earlier events

1.3.8.1
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2013-09-03 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.3.8
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2012-12-15 · diff ↗
1.3.7
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2012-08-14 · diff ↗
R
R 2.15.0 released · 2012-03-30
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R 2.14.0 released · 2011-10-31
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R 2.13.0 released · 2011-04-13
1.3.6
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2011-02-02 · diff ↗ ·
added 3 exports
locus<-, gene<-, marker<-
1.3.5
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2011-01-17 · diff ↗
R
R 2.12.0 released · 2010-10-15
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R 2.11.0 released · 2010-04-22
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R 2.10.0 released · 2009-10-26
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R 2.9.0 released · 2009-04-17
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R 2.8.0 released · 2008-10-20
1.3.4
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2008-08-21 · diff ↗
1.3.3
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2008-04-30 · diff ↗
R
R 2.7.0 released · 2008-04-22
1.3.2
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2007-11-21 · diff ↗ ·
added 1 export
genotypeOrder<-
R
R 2.6.0 released · 2007-10-03
1.3.0
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2007-08-09 · diff ↗ ·
removed 1 export
binsearch

added 5 exports
expectedHaplotypes, order, genotypeOrder, groupGenotype, %in%
R
R 2.5.0 released · 2007-04-24
1.2.1
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2006-12-12 · diff ↗
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R 2.4.0 released · 2006-10-03
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R 2.3.0 released · 2006-04-24
1.2.0
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2005-11-09 · diff ↗
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R 2.2.0 released · 2005-10-06
1.1.4
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2005-10-05 · diff ↗ ·
removed 1 export
library.pos
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R 2.1.0 released · 2005-04-18
1.1.3
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2005-03-14 · diff ↗ ·
added 1 export
expectedGenotypes
1.1.2
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2004-12-23 · diff ↗
1.1.1
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2004-11-16 · diff ↗
R
R 2.0.0 released · 2004-10-04
1.1.0
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2004-09-28 · diff ↗ ·
added 52 exports
HWE.chisq, HWE.exact, HWE.test, LD, binsearch, ci.balance, diseq, diseq.ci, genotype, haplotype, is.genotype, is.haplotype, as.genotype, as.haplotype, allele.names, nallele, gregorius, homozygote, heterozygote, carrier, allele, allele.count, library.pos, locus, gene, marker, is.gene, is.locus, is.marker, getlocus and 22 more
1.0.4
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2004-05-27 · diff ↗
R
R 1.9.0 released · 2004-04-12
1.0.3
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2003-12-04 · diff ↗
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R 1.8.0 released · 2003-10-08
1.0.1
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2003-06-06 · diff ↗
1.0.0
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2003-05-30 · diff ↗
0.6.8
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2003-04-23 · diff ↗
R
R 1.7.0 released · 2003-04-16
0.6.6
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2003-02-03 · diff ↗
0.6.4
record
2002-11-13
R
R 1.6.0 released · 2002-10-01

Package metadata

First published: 2002-11-13
Total releases: 26 / 24 yrs
License: GPL
Bundled data: 0.4 KB / 1 file
Download size: 195 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("genetics")

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 genetics version 1.3.8.1.3 [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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