tidypopgen

0.4.4

Tidy Population Genetics

0packages depend

4.6Kdownloads / year

78.0%test coverage

12/13checks pass

Overview

About

Maintained by Andrea ManicaFirst published 2025-08-276 releasesCRAN page ↗GitHub ↗

We provide a tidy grammar of population genetics, facilitating the manipulation and analysis of data on biallelic single nucleotide polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets by storing genotypes on disk, and performing operations on them in chunks, without ever loading all data in memory. The full functionalities of the package are described in Carter et al. (2025) doi:10.1111/2041-210x.70204.

Install

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

install.packages("tidypopgen", 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("EvolEcolGroup/tidypopgen")

Development version from EvolEcolGroup/tidypopgen. 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-tidypopgen

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-tidypopgen

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 15.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.80

78.0%

Coverage · measured lines

99%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-07-03
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-19
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-17
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 437 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 99%
References docs: 14%

Downloads

4.6K

CRAN downloads in the past year

Rank #7,671 · ~13/day · ~385/mo

Releases R versions

Daily download trend is not available in this view yet.

25530 days

1.3K90 days

4.6K1 year

Compare downloads with other packages →

Also on423 r2u868 conda_forge

Repository

GitHub ↗ evolecolgroup/tidypopgen

15Stars

3Forks

3Open issues

1Open PRs

5Releases

1,152Commits

8Contributors

License GPL-3.0 · 1,152 commits · Last activity 2026-07-30 · +7.1% stars, 30d

Stars over time

2025-06-28 · 102026-07-24 · 15

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/evolecolgroup/tidypopgen on 2026-08-02.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

lintr

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

Dependencies

Declared dependencies

39 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.5.0dplyr tibble

Imports (18)

bigparallelr bigsnpr bigstatsr foreach generics ggplot2methodsMASSpatchwork runner rlang sfstatstidyselect tidyrutilsRcpp vctrs

LinkingTo (4)

Rcpp RcppArmadillo bigstatsr rmio

Suggests (19)

adegenet admixtools broom data.table hierfstat knitr detectRUNS LEA pcadapt RhpcBLASctl rmarkdown rnaturalearth rnaturalearthdata readr reticulate testthat vcfR xgboost spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Andrea Manica

Author, Maintainer, Copyright holder

Authors (3)

Andrea Manica

Author, Maintainer, Copyright holder

Evie Carter

Author

Eirlys Tysall

Author

Contributors (3)

Contributor

Contributor

Contributor

Author, Maintainer, Copyright holder

Package Timeline

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

0.4.4Latest
2026-05-19 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.4.3
2026-01-24 · diff ↗
0.4.2
2026-01-22 · diff ↗
0.4.1
2025-12-20 · diff ↗
0.4.0
2025-10-24 · diff ↗
0.3.2
2025-08-27
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-08-27
Total releases: 6 / 1 yrs
License: GPL (>= 3) OSI
Additional repositories: evolecolgroup.r-universe.dev
Minimum R: ≥ 3.5.0
Bundled data: 0.3 KB / 1 file
Download size: 2.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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