R Observatory: Metrics for hierfstat version 0.5-11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hierfstat

0.5-11Package record

Estimation and Tests of Hierarchical F-Statistics

4packages dependsuggested by 4

101.6Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Jerome GoudetCRAN page ↗GitHub ↗Issues ↗

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) https://academic.oup.com/genetics/article/144/4/1933/6017091). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) https://academic.oup.com/genetics/article/206/4/2085/6072590.

Install

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

install.packages("hierfstat", 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("jgx65/hierfstat")

Development version from jgx65/hierfstat. 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-hierfstat

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-hierfstat

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

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

Health

CRAN checks

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) read.VCF.Rd:21: Lost braces
    21 | Reads a \url{https://samtools.github.io/hts-specs/}{Variant Call Format (VCF)} file into a BED object,
       |                                                    ^

CRAN check page ↗

Slowest check: 3.7 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5-11

READMENoVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 76
Examples that run: 79%44 run in a plain check · 12 never run
Exported functions with examples: 76%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 57%

Vignettes (2)

Hierfstat latest features HTML
Importing data in Hierfstat HTML

How these are measured

Downloads

101.6K

CRAN downloads in the past year

Rank #1,051 · ~278/day · ~8.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

5.4K30 days

36.5K90 days

101.6K1 year

Compare downloads with other packages →

Also on451 r2u2.9K conda_forge66 bioconda102 c2d4u

How downloads are counted

Repository

jgx65/hierfstat ↗Account: jgx65

29Stars

16Forks

5Open issues

10Open PRs

0Releases

223Commits

7Commit identities

rhierfstatdevtoolspopulation-geneticspopulation-genomicskinshipquantitative-geneticsgwas

223 commits · Last activity 2024-11-20 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-08 · 252026-09-23 · 29

How these are measured

PracticesBeta

Checks run against github.com/jgx65/hierfstat on 2026-10-22.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing hierfstat adds 67 packages (42 with compiled code, 77 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 2.10

Imports (5)

ade4 adegenet gaston gtoolsmethods

LinkingTo (0)

none

Suggests (5)

ape pegas knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

2indirect

Imports 4

Suggested by 4

Depends, Imports or LinkingTo, most downloaded first

graph4lg dartR.sim GenomeAdmixR wingen

Suggests, most downloaded first

adegenet dartR dartR.base tidypopgen

How these are counted

Code & Tests

Datasets

People & History

People (5)

Jerome Goudet

Author, Maintainer since 0.01-4 (2004)

Thibaut Jombart

Author · added in 0.04-22

Eric Archer

Contributor · added in 0.5-7

Olivier Hardy

Contributor · added in 0.5-7

Zhian N. Kamvar

Contributor · added in 0.5-7

Releases (15)

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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.5-11Latest
record
2022-05-06 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
0.5-10
record
2021-11-17 · diff ↗ ·
added 9 exports
Ho, Hs, TajimaD.dosage, boot.ppbetas, matching, pairwise.betas, pairwise.fst.dosage, pi.dosage, theta.Watt.dosage
R
R 4.1.0 released · 2021-05-18
0.5-7
record
2020-07-20 · diff ↗ ·
removed 6 exports
eucl.dist, eucl.dist.trait, sim.freq, fstat, gstat.randtest, pairwise.fst

added 16 exports
beta.dosage, biall2dos, fis.dosage, fs.dosage, fst.dosage, fstat2dos, grm2kinship, kinship2dist, kinship2grm, kinshipShift, ms2bed, ms2dos, pp.fst, read.VCF, read.ms, sim.genot.metapop.t
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.04-22
record
2015-12-04 · diff ↗ ·
removed 9 exports
betai, cfe.dist, da.dist, print.indpca, plot.indpca, nei.dist, pp.fst, prepdata, print.pp.fst

added 14 exports
betas, genet.dist, pairwise.neifst, pairwise.WCfst, qn2.read.fstat, sim.genot.t, write.bayescan, fstat, gstat.randtest, pairwise.fst, AIc, sexbias.test, genind2hierfstat, write.ped
R
R 3.2.0 released · 2015-04-16

Show 30 earlier eventsHide 30 earlier events

0.04-14
record
2014-09-29 · diff ↗ ·
removed 1 export
pattern:.

added 47 exports
allele.count, allelic.richness, basic.stats, betai, boot.ppfis, boot.ppfst, boot.vc, cfe.dist, da.dist, eucl.dist, eucl.dist.trait, g.stats, g.stats.glob, genot2al, getal, getal.b, ind.count, indpca, print.indpca, plot.indpca, mat2vec, nb.alleles, nei.dist, pcoa, pop.freq, pp.fst, pp.sigma.loc, prepdata, print.pp.fst, read.fstat and 17 more
R
R 3.1.0 released · 2014-04-10
0.04-10
record
2013-04-10 · diff ↗
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
0.04-6
record
2011-11-24 · diff ↗ ·
added 1 export
pattern:.
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
R
R 2.10.0 released · 2009-10-26
R
R 2.9.0 released · 2009-04-17
R
R 2.8.0 released · 2008-10-20
R
R 2.7.0 released · 2008-04-22
R
R 2.6.0 released · 2007-10-03
R
R 2.5.0 released · 2007-04-24
R
R 2.4.0 released · 2006-10-03
0.04-4
record
2006-09-21 · diff ↗
0.04-3
record
2006-07-10 · diff ↗
R
R 2.3.0 released · 2006-04-24
0.04-2
record
2005-12-14 · diff ↗
R
R 2.2.0 released · 2005-10-06
0.04-1
record
2005-06-07 · diff ↗
R
R 2.1.0 released · 2005-04-18
0.03-3
record
2005-03-15 · diff ↗
0.03-1
record
2005-03-03 · diff ↗
0.02-2
record
2005-01-14 · diff ↗
R
R 2.0.0 released · 2004-10-04
0.01-4
record
2004-08-14
R
R 1.9.0 released · 2004-04-12

Package metadata

First published: 2004-08-14
Total releases: 15 / 22 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 17 KB / 7 files
Download size: 193 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hierfstat")

Format

Goudet, J., Archer, E., Hardy, O., Jombart, T., & Kamvar, Z. N. (2022). hierfstat: Estimation and Tests of Hierarchical F-Statistics (Version 0.5-11) [Computer software]. https://doi.org/10.32614/CRAN.package.hierfstat

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 hierfstat version 0.5-11 [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 →