R Observatory: Metrics for tidypopgen version 0.4.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tidypopgen

0.4.4Package record

Tidy Population Genetics

0packages depend

4.6Kdownloads / year

78.0%test coverage

13/13flavors OK

Overview

About

Maintained by Andrea ManicaCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.4.4

fix seed argument of gt_admixture()
implement our own upset plot function to avoid dependency on UpSetR package, which is no longer maintained
fix reading of VCFs when genotype separator symbol is present in the sample information
fix loci_ functions output when calculating across groups for a single loci
fix gt_update_backingfile() to preserve imputation metadata when backing files are updated
add validation in gt_impute_simple() to detect and report SNP dimension mismatches caused by excluded SNPs
add outdir argument in gt_admixture() to store partial outputs for large jobs
fix gt_admixture() output file names when n_runs > 1

From NEWS.md in the release

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. 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

# 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

13OK

CRAN check page ↗

Slowest check: 15.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-17
WARNING12 OK, 1 WARNING2026-10-01
OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-04

Show 9 earlier changesHide 9 earlier changes

WARNING12 OK, 1 WARNING2026-07-03
OK13 OK2026-06-19
WARNING12 OK, 1 WARNING2026-06-17
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-07
OK13 OK2026-05-02
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.4

READMEYes · 437 wordsVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 0.4.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 118 (3 internal)includes a package overview page
Examples that run: 99%113 run in a plain check (27 of them under a condition) · 1 never run
Exported functions with examples: 99%
Documented parameters: 96%
Return-value docs: 99%
Help pages citing references: 14%

Vignettes (5)

tidypopgen HTML
PLINK cheatsheet HTML
Population genetic analysis with tidypopgen HTML
Quality Control HTML
The grammar of population genetics HTML

How these are measured

Downloads

4.6K

CRAN downloads in the past year

Rank #6,252 · ~13/day · ~382/mo

Releases R versions

Daily download trend is not available in this view yet.

49130 days

1.3K90 days

4.6K1 year

Compare downloads with other packages →

Also on408 r2u1.1K conda_forge

How downloads are counted

Repository

evolecolgroup/tidypopgen ↗Organization: EvolEcolGroup

17Stars

3Forks

6Open issues

2Open PRs

5Releases

1,201Commits

8Commit identities

License file reads as GPL-3.0 · 1,201 commits · Last activity 2026-10-18 · +6.3% stars, 30d · Default branch at 0.4.4.9008, ahead of CRAN 0.4.4 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 13
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-09-09 · 122026-10-21 · 17

How these are measured

PracticesBeta

13 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/evolecolgroup/tidypopgen 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)

pkgdown

GitHub Pages site last deployed 2026-10-18 · The repository has a site deploy workflow

pkgdown site last built 2026-05-20

Coverage (1)

Coverage reporting

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (2)

lintrLint workflow

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2026-02-05
Pull request: opened by its own account
Commits: 5 by its own account · at least 1 crediting it in the message
Claude Codefirst seen 2026-05-04
Named in .Rbuildignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 20 crediting it in the message

Models named in its commits

Claude Sonnet 519 commits · Jul to Aug 2026
Claude Opus 5.51 commit · Oct 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

39 external dependencies (excludes base and recommended)

Installing tidypopgen adds 73 packages (45 with compiled code, 81 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, sf 9.3 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Author

Author

Contributor

Author of Hardy-Weinberg Equilibrium algorithm in PLINK 1.90, used in loci_hwe()

Bengtsson Henrik

Contributor

Author of countLines in R.utils, modified for .vcf in count_vcf_variants()

Shaun Purcell

Contributor

Author of Hardy-Weinberg Equilibrium algorithm in PLINK 1.90, used in loci_hwe()

Releases (6)

Pick two releases to compare their code metrics.

0.4.4Latest
record
2026-05-19 · current release · diff ↗ ·
added 1 export
upset_plot
R
R 4.6.0 released · 2026-04-24
0.4.3
record
2026-01-24 · diff ↗
0.4.2
record
2026-01-22 · diff ↗
0.4.1
record
2025-12-20 · diff ↗
0.4.0
record
2025-10-24 · diff ↗ ·
added 1 export
gt_from_genlight
0.3.2
record
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: 2.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("tidypopgen")

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

It points to 10.1111/2041-210x.70204.

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 tidypopgen version 0.4.4 [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.

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