dartR.popgen

1.2.2

Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

2packages depend

7.7Kdownloads / year

–test coverage

8/13checks pass

Overview

About

Maintained by Bernd GruberFirst published 2023-11-213 releasesCRAN page ↗

Facilitates the analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. 'dartR.popgen' provides a suit of functions to analyse such data in a population genetics context. It provides several functions to calculate population genetic metrics and to study population structure. Quite a few functions need additional software to be able to run (gl.run.structure(), gl.blast(), gl.LDNe()). You find detailed description in the help pages how to download and link the packages so the function can run the software. 'dartR.popgen' is part of the the 'dartRverse' suit of packages. Gruber et al. (2018) doi:10.1111/1755-0998.12745. Mijangos et al. (2022) doi:10.1111/2041-210X.13918.

Install

R (CRAN)Ubuntu (r2u)

install.packages("dartR.popgen", 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-dartr.popgen

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

Health

CRAN checks

4ERROR1NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc
ERROR r-oldrel-macos-arm64
ERROR r-oldrel-macos-x86_64
ERROR r-release-macos-arm64
ERROR r-release-macos-x86_64

Slowest check: 12.2 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-03-17
10 OK · 0 NOTE · 2 WARNING · 2 ERROR · 0 FAILURE
WARNING2026-03-13
12 OK · 0 NOTE · 2 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 57%
Documented parameters: 100%
Return-value docs: 100%
References docs: 58%

Downloads

7.7K

CRAN downloads in the past year

Rank #3,984 · ~21/day · ~645/mo

Releases R versions

Daily download trend is not available in this view yet.

62130 days

2.2K90 days

7.7K1 year

Compare downloads with other packages →

Also on143 r2u

Repository

GitHub ↗ green-striped-gecko/dartr

36Stars

22Forks

22Open issues

0Open PRs

2Releases

2,357Commits

14Contributors

License GPL-3.0 · 2,357 commits · Last activity 2025-03-27 · +2.9% stars, 30d

Stars over time

2025-03-10 · 332026-07-07 · 36

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/green-striped-gecko/dartr on 2026-08-03.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

40 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.1dartR.base dartR.data

Imports (21)

methodsadegenetutilsMASSdplyr patchwork crayon ggplot2 data.table stringr furrr future ggdendro LEA pillar plyr terra purrr ggpmisc R.utils ape

LinkingTo (0)

none

Suggests (20)

SIBER expm fields gplots gridExtra igraph iterpc label.switching leaflet proxy qvalue raster reshape2 scales snpStats tidyr viridis zoo gsubfn sp

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

1indirect

dartR.sim dartRverse

Code & Tests

People & History

People (11)

Maintainer (1)

Bernd Gruber

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author · added in 1.2.2

Contributors (6)

Eric Archer

Contributor

Oliver Berry

Contributor

Lindsay V. Clark

Contributor

Floriaan Devloo-Delva

Contributor

Ching Ching Lau

Contributor · added in 1.2.2

Peter J. Unmack

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.2Latest
2026-03-16 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
2024-06-28 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.32
2023-11-21
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-11-21
Total releases: 3 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1
Download size: 747 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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