R Observatory: Metrics for dartR.popgen version 1.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dartR.popgen

1.2.2Package record

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

1packages dependsuggested by 1

8.5Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Bernd GruberCRAN page ↗Website ↗Issues ↗

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. 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

Health

CRAN checks

4ERROR9OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-release-macos-arm64, r-release-macos-x86_64

r-oldrel-macos-x86_64, r-release-macos-arm64, r-release-macos-x86_64

Package required but not available: ‘LEA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

r-oldrel-macos-arm64

Package required but not available: ‘LEA’

Package suggested but not available for checking: ‘snpStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 9.2 min · r-oldrel-windows-x86_64

Status changes

ERROR9 OK, 4 ERRORNow
ERROR10 OK, 2 WARNING, 2 ERROR2026-03-17
WARNING12 OK, 2 WARNING2026-03-13
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.2

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 36 (1 internal)
Examples that run: 29%8 run in a plain check (1 of them under a condition) · 1 only when donttest examples are enabled (R CMD check --as-cran) · 19 never run
Exported functions with examples: 80%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 58%

How these are measured

Downloads

8.5K

CRAN downloads in the past year

Rank #4,168 · ~23/day · ~712/mo

Releases R versions

Daily download trend is not available in this view yet.

62530 days

2.1K90 days

8.5K1 year

Compare downloads with other packages →

Also on124 r2u

How downloads are counted

Repository

green-striped-gecko/dartr ↗Account: green-striped-gecko

37Stars

21Forks

22Open issues

0Open PRs

2Releases

2,357Commits

14Commit identities

License file reads as GPL-3.0 · 2,357 commits · Last activity 2025-03-27 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 52
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-13 · 342026-08-26 · 37

How these are measured

PracticesBeta

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

Checks run against github.com/green-striped-gecko/dartr on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Code of conductContributing guide

Docs source (3)

README.Rmd

GitHub Pages site last deployed 2025-03-27 · The repository has a site deploy workflow

Research and citation (1)

codemeta.json

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

40 external dependencies (excludes base and recommended)

Installing dartR.popgen adds 127 packages (71 with compiled code, 130 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 3 more not on CRAN are not measured.

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

1direct

1indirect

Depends 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

dartR.sim

Suggests, most downloaded first

dartRverse

How these are counted

Code & Tests

People & History

People (11)

Bernd Gruber

Author, Maintainer since 0.32 (2023)

Author

Author

Author

Author · added in 1.2.2

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

Releases (3)

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
1.2.2Latest
record
2024-06-27 · current release · diff ↗ ·
added 13 exports
gl.TajimasD, gl.check.panel, gl.find.genes.for.loci, gl.find.loci.in.genes, gl.map.popcluster, gl.map.snmf, gl.plot.popcluster, gl.plot.snmf, gl.read.structure, gl.run.popcluster, gl.run.snmf, gl.select.panel, utils.get.allele.freq
1.0.0
record
2024-06-28 · diff ↗ ·
added 2 exports
gl.run.epos, gl.run.stairway2
R
R 4.4.0 released · 2024-04-24
0.32
record
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: 793 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("dartR.popgen")

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

It points to 10.1111/1755-0998.12745, 10.1111/2041-210x.13918.

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 dartR.popgen version 1.2.2 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →