poppr

2.9.8

Genetic Analysis of Populations with Mixed Reproduction

6packages depend

108.9Kdownloads / year

92.8%test coverage

9/13checks pass

Overview

About

Maintained by Zhian N. KamvarFirst published 2013-04-2647 releasesCRAN page ↗GitHub ↗

Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the 'adegenet' package. Originally described in Kamvar, Tabima, and Grünwald (2014) doi:10.7717/peerj.281 with version 2.0 described in Kamvar, Brooks, and Grünwald (2015) doi:10.3389/fgene.2015.00208.

Install

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

install.packages("poppr", 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("grunwaldlab/poppr")

Development version from grunwaldlab/poppr. 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-poppr

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

# 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-poppr

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

Health

CRAN checks

4NOTE9OK

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-gcc
NOTE r-devel-windows-x86_64

Slowest check: 7.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.36

92.8%

Coverage · measured lines

99%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 875 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 99%
Return-value docs: 93%
References docs: 35%

Downloads

108.9K

CRAN downloads in the past year

Rank #1,336 · ~298/day · ~9.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

6.9K30 days

24.9K90 days

108.9K1 year

Compare downloads with other packages →

Also on542 r2u42 autocran7K conda_forge787 bioconda75 c2d4u

Repository

GitHub ↗ grunwaldlab/poppr

72Stars

26Forks

17Open issues

0Open PRs

39Releases

3,259Commits

17Contributors

rmultilocus-genotypesgenetic-distancespopulation-geneticsmultilocus-lineagesgenetic-analysispopulationsminimum-spanning-networks

3,259 commits · Last activity 2025-09-10 · 0% stars, 30d

Stars over time

2025-05-15 · 712026-07-07 · 72

Repository practices

Upstream repositoryBeta

10 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/grunwaldlab/poppr on 2026-07-19.

Continuous integration (3)

GitHub ActionsTravis CIAppVeyor

Reproducibility and dev environment (1)

Makefile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (3)

lintrAirRStudio project

Show all practices

Governance and community (1)

Funding

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (2)

R >= 2.15.1adegenet

Imports (18)

statsgraphicsgrDevicesutilsvegan ggplot2 ape (>= 3.1-1)igraphmethodsade4 pegas polysat dplyr rlangbootshiny magrittr progressr

LinkingTo (0)

none

Suggests (5)

testthat knitr rmarkdown poweRlaw cowplot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

0indirect

cdmetapopR AlleleShift adegenet dartR dartR.base vcfR

Code & Tests

People & History

People (11)

Maintainer (1)

Zhian N. Kamvar

Maintainer, Author

Authors (4)

Zhian N. Kamvar

Maintainer, Author

Jonah C. Brooks

Author

David Folarin

Author · added in 2.9.0

Javier F. Tabima

Author

Contributors (6)

Frédéric D. Chevalier

Contributor

Sydney E. Everhart

Contributor, Data contributor

Brian J. Knaus

Contributor

Stacy A. Krueger-Hadfield

Contributor

Patrick G. Meirmans

Contributor

Erik Sotka

Contributor · added in 2.1.0

Other (1)

Niklaus J. Grünwald

Thesis advisor

Listed in earlier versions (10)

Niklaus J. Grunwald

no longer listed · 3.0.1 to 1.1.2

Javier F.

no longer listed · 1.1.3 to 2.9.8

Niklaus J.

no longer listed · 1.1.3 to 2.9.8

Zhian N.

no longer listed · 1.1.3 to 2.9.8

Jonah C.

no longer listed · 2.0.0 to 2.9.8

Stacy A.

no longer listed · 2.1.0 to 2.9.8

Sydney E.

no longer listed · 2.1.0 to 2.9.8

Brian J.

no longer listed · 2.2.0 to 2.9.8

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.9.8Latest
2025-08-24 · current release · diff ↗
2.9.7
2025-06-19 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.9.6
2024-03-15 · diff ↗
2.9.5
2024-01-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.9.4
2023-03-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.9.3
2021-09-07 · diff ↗
2.9.2
2021-05-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.9.1
2021-03-21 · diff ↗
2.9.0
2021-02-06 · diff ↗
2.8.7
2021-01-06 · diff ↗

Show 45 earlier events

2.8.6
2020-06-02 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.8.5
2020-02-25 · diff ↗
2.8.4
2020-02-12 · diff ↗
2.8.3
2019-06-18 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.8.2
2019-03-11 · diff ↗
2.8.1
2018-08-22 · diff ↗
2.8.0
2018-05-19 · diff ↗
R
R 3.5.0 released · 2018-04-23
2.7.1
2018-03-16 · diff ↗
2.7.0
2018-03-16 · diff ↗
2.6.1
2018-01-15 · diff ↗
2.6.0
2018-01-08 · diff ↗
2.5.0
2017-09-11 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.4.1
2017-04-14 · diff ↗
2.4.0
2017-04-10 · diff ↗
2.3.0
2016-11-23 · diff ↗
2.2.1
2016-08-29 · diff ↗
2.2.0
2016-06-13 · diff ↗
R
R 3.3.0 released · 2016-05-03
2.1.1
2016-03-15 · diff ↗
2.1.0
2015-12-01 · diff ↗
2.0.2
2015-07-18 · diff ↗
2.0.1
2015-07-14 · diff ↗
2.0.0
2015-07-08 · diff ↗
1.1.5
2015-05-13 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.1.4
2015-02-06 · diff ↗
1.1.3
2015-02-03 · diff ↗
1.1.2
2014-07-29 · diff ↗
1.1.1
2014-07-27 · diff ↗
1.1.0
2014-07-24 · diff ↗
R
R 3.1.0 released · 2014-04-10
3.0.3
2014-03-05 · diff ↗
1.0.6
2014-03-05 · diff ↗
1.0.5
2013-12-13 · diff ↗
1.0.4
2013-12-04 · diff ↗
3.0.2
2013-08-21 · diff ↗
1.0.3
2013-08-21 · diff ↗
1.0.1
2013-07-03 · diff ↗
1.0.0
2013-04-26 · diff ↗
3.0.1
2013-04-25
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-04-26
Total releases: 47 / 13 yrs
License: GPL-2 | GPL-3 OSI
Minimum R: ≥ 2.15.1
Bundled data: 32 KB / 7 files
Download size: 2.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

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