Tidy Population Genetics [R package tidypopgen version 0.4.0]

tidypopgen: Tidy Population Genetics

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:10.1101/2025.06.06.658325>.

Version: 0.4.0

Depends: R (≥ 3.5.0), dplyr, tibble

Imports: bigparallelr, bigsnpr, bigstatsr, foreach, generics, ggplot2, methods, MASS, patchwork, runner, rlang, sf, stats, tidyselect, tidyr, utils, Rcpp, UpSetR, vctrs

LinkingTo: Rcpp, RcppArmadillo (≥ 0.9.600), bigstatsr, rmio

Suggests: adegenet, admixtools, broom, data.table, hierfstat, knitr, detectRUNS, LEA, RhpcBLASctl, rmarkdown, rnaturalearth, rnaturalearthdata, readr, reticulate, testthat (≥ 3.0.0), vcfR, xgboost, spelling

Published: 2025年10月24日

DOI: 10.32614/CRAN.package.tidypopgen

Author: Evie Carter [aut], Eirlys Tysall [aut], Andrea Manica ORCID iD [aut, cre, cph], Chang Christopher [ctb] (Author of Hardy-Weinberg Equilibrium algorithm in PLINK 1.90, used in loci_hwe()), Shaun Purcell [ctb] (Author of Hardy-Weinberg Equilibrium algorithm in PLINK 1.90, used in loci_hwe()), Bengtsson Henrik [ctb] (Author of countLines in R.utils, modified for .vcf in count_vcf_variants())

Maintainer: Andrea Manica <am315 at cam.ac.uk>

BugReports: https://github.com/EvolEcolGroup/tidypopgen/issues

License: GPL (≥ 3)

URL: https://github.com/EvolEcolGroup/tidypopgen, https://evolecolgroup.github.io/tidypopgen/

NeedsCompilation: yes

Additional_repositories: https://evolecolgroup.r-universe.dev/

Language: en-GB

Materials: README, NEWS

CRAN checks: tidypopgen results