R Observatory: Metrics for poolfstat version 3.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

poolfstat

3.1.0

Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data

0packages depend

6.3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Mathieu GautierFirst published 2018-03-1411 releasesCRAN page ↗

Functions for the computation of F-, f- and D-statistics (e.g., Fst, hierarchical F-statistics, Patterson's F2, F3, F3*, F4 and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in 'TreeMix', 'BayPass' and 'SelEstim' format, see the Package vignette for details).

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("poolfstat", 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-poolfstat

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-poolfstat

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

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-poolfstat

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 5.6 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

15

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 90%
References docs: 0%

Downloads

6.3K

CRAN downloads in the past year

Rank #9,078 · ~17/day · ~523/mo

Releases R versions

Daily download trend is not available in this view yet.

28930 days

1K90 days

6.3K1 year

Compare downloads with other packages →

Also on447 r2u22 autocran2K conda_forge

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0

Imports (15)

Rcppmethodsdata.tableutilsforeach doParallelparallelDiagrammeR apestatsRyacasMatrixRcppProgress progress nnls

LinkingTo (2)

Rcpp RcppProgress

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Mathieu Gautier

Author, Maintainer

Authors (1)

Mathieu Gautier

Author, Maintainer

Listed in earlier versions (2)

Valentin Hivert

no longer listed · 0.0.1 to 1.2.0

Renaud Vitalis

no longer listed · 0.0.1 to 1.2.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
3.1.0Latest
2026-02-23 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
3.0.0
2024-11-23 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.2.0
2023-09-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.2
2023-03-22 · diff ↗
2.1.1
2022-05-02 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.0.0
2021-05-27 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2.0
2020-11-04 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.1
2019-10-22 · diff ↗
1.1.0
2019-06-20 · diff ↗

Show 5 earlier events

R
R 3.6.0 released · 2019-04-26
1.0.0
2018-09-14 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.0.1
2018-03-14
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-14
Total releases: 11 / 8 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.0
Download size: 3.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("poolfstat")

Format

Gautier, M. (2026). poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data (Version 3.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.poolfstat

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 poolfstat version 3.1.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, 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 →