R Observatory: Metrics for adegenet version 2.1.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

adegenet

2.1.11

Exploratory Analysis of Genetic and Genomic Data

34packages depend

195.3Kdownloads / year

28.7%test coverage

8/13checks pass

Overview

About

Maintained by Zhian N. KamvarFirst published 2007-04-1158 releasesCRAN page ↗GitHub ↗

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Install

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

install.packages("adegenet", 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("thibautjombart/adegenet")

Development version from thibautjombart/adegenet. 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-adegenet

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-adegenet

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-adegenet

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: 6.0 min · r-oldrel-windows-x86_64

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

195.3K

CRAN downloads in the past year

Rank #975 · ~535/day · ~16.3K/mo

adegenet Releases R versions

Daily download trend is not available in this view yet.

14.3K30 days

42.7K90 days

195.3K1 year

Compare downloads with other packages →

Also on961 r2u67 autocran11.5K conda_forge238 bioconda85 c2d4u

Repository

GitHub ↗ thibautjombart/adegenet

201Stars

66Forks

67Open issues

1Open PRs

10Releases

947Commits

21Contributors

947 commits · Last activity 2025-02-07 · 0% stars, 30d

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/thibautjombart/adegenet on 2026-08-16.

Continuous integration (3)

GitHub ActionsTravis CIAppVeyor

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (3)

R >= 2.14methodsade4

Imports (14)

utilsstatsgrDevicesMASSigraph ape shiny ggplot2 seqinrparallelbootreshape2 dplyr vegan

LinkingTo (0)

none

Suggests (9)

adespatial pegas hierfstat maps spdep interp splancs poppr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

34direct

10indirect

Code & Tests

People & History

People (22)

Maintainer (1)

Zhian N. Kamvar

Author, Maintainer · added in 2.0.0

Authors (2)

Zhian N. Kamvar

Author, Maintainer · added in 2.0.0

Thibaut Jombart

Author

Contributors (20)

Ismail Ahmed

Contributor · added in 1.3-6

Marie-Pauline Beugin

Contributor · added in 2.1.3

Federico Calboli

Contributor · added in 3.0.1

Lindsay V. Clark

Contributor · added in 2.1.6

Caitlin Collins

Contributor · added in 1.4-0

Anne Cori

Contributor · added in 1.3-6

Max Coulter

Contributor · added in 2.1.11

Alexandre Courtiol

Contributor · added in 2.1.3

Show 12 more contributors

Rebecca DeCamp

Contributor · added in 2.1.2

Pavel Dimens

Contributor · added in 2.1.6

RJ Ewing

Contributor · added in 2.1.0

Brian J. Knaus

Contributor · added in 2.1.0

Ivan Krylov

Contributor · added in 2.1.11

Roman Lustrik

Contributor · added in 2.0.0

Tiago Maié

Contributor · added in 2.1.0

Frédéric Michaud

Contributor · added in 2.1.2

Vladimir Mikryukov

Contributor · added in 2.1.0

Libor Morkovsky

Contributor · added in 2.1.0

Klaus Schliep

Contributor · added in 2.0.0

Peter Solymos

Contributor · added in 2.13.1

Listed in earlier versions (12)

with contributions from Peter Solymos

no longer listed · 1.1-0 to 1.2-3

Francois Balloux