R Observatory: Metrics for pegas version 1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pegas

1.4

Population and Evolutionary Genetics Analysis System

13packages depend

123.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Emmanuel ParadisFirst published 2009-05-1332 releasesCRAN page ↗

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Install

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

install.packages("pegas", 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-pegas

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-pegas

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-pegas

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

Health

CRAN checks

13OK

Slowest check: 4.0 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

4

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: 92%
Return-value docs: 100%
References docs: 53%

Downloads

123.7K

CRAN downloads in the past year

Rank #1,291 · ~339/day · ~10.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

7.2K30 days

24.8K90 days

123.7K1 year

Compare downloads with other packages →

Also on662 r2u18 autocran8.9K conda_forge537 bioconda76 c2d4u

Repository

GitHub ↗ emmanuelparadis/pegas.html

Repository practices

Upstream repositoryBeta

Repository github.com/emmanuelparadis/pegas.html is linked, but repository-practices checks have not run for it yet.

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.2.0ape

Imports (3)

graphicsutilsmethods

LinkingTo (0)

none

Suggests (3)

rgl snpStats adegenet

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

13direct

8indirect

StAMPP HACSim PopGenReport RAINBOWR graph4lg mmod poppr spider wingen adegenet dartR dartR.base hierfstat

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

Emmanuel Paradis

Author, Maintainer, Copyright holder

Authors (7)

Emmanuel Paradis

Author, Maintainer, Copyright holder

Thibaut Jombart

Author, Copyright holder · added in 0.8

Zhian N. Kamvar

Author, Copyright holder · added in 0.11

Brian Knaus

Author, Copyright holder · added in 0.12

Alastair Potts

Author, Copyright holder · added in 0.4

Klaus Schliep

Author, Copyright holder · added in 0.5

David Winter

Author, Copyright holder · added in 0.5-1

Copyright holders (7)

Emmanuel Paradis

Author, Maintainer, Copyright holder

Thibaut Jombart

Author, Copyright holder · added in 0.8

Zhian N. Kamvar

Author, Copyright holder · added in 0.11

Brian Knaus

Author, Copyright holder · added in 0.12

Alastair Potts

Author, Copyright holder · added in 0.4

Klaus Schliep

Author, Copyright holder · added in 0.5

David Winter

Author, Copyright holder · added in 0.5-1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.4Latest
2025-12-08 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.3
2023-12-13 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2
2023-02-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1
2021-12-16 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0-1
2021-05-17 · diff ↗
1.0
2021-04-08 · diff ↗
0.14
2020-09-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.13
2020-03-10 · diff ↗
0.12
2019-10-05 · diff ↗

Show 37 earlier events

R
R 3.6.0 released · 2019-04-26
0.11
2018-07-09 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.10
2017-05-03 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.9
2016-04-16 · diff ↗
0.8-2
2015-09-25 · diff ↗
0.8-1
2015-06-24 · diff ↗
0.8
2015-05-20 · diff ↗
R
R 3.2.0 released · 2015-04-16
0.7
2015-03-05 · diff ↗
0.6
2014-08-21 · diff ↗
R
R 3.1.0 released · 2014-04-10
0.5-1
2014-01-10 · diff ↗
0.5
2013-10-08 · diff ↗
0.4-5
2013-06-06 · diff ↗
R
R 3.0.0 released · 2013-04-03
0.4-4
2013-01-23 · diff ↗
0.4-3
2012-07-31 · diff ↗
0.4-2
2012-05-11 · diff ↗
R
R 2.15.0 released · 2012-03-30
0.4-1
2012-01-19 · diff ↗
R
R 2.14.0 released · 2011-10-31
0.4
2011-07-23 · diff ↗
R
R 2.13.0 released · 2011-04-13
0.3-4
2011-04-01 · diff ↗
0.3-3
2010-11-26 · diff ↗
R
R 2.12.0 released · 2010-10-15
0.3-2
2010-06-10 · diff ↗
0.3-1
2010-05-19 · diff ↗
R
R 2.11.0 released · 2010-04-22
0.3
2009-12-03 · diff ↗
R
R 2.10.0 released · 2009-10-26
0.2
2009-10-07 · diff ↗
0.1
2009-05-13
R
R 2.9.0 released · 2009-04-17

Package metadata

First published: 2009-05-13
Total releases: 32 / 17 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.2.0
Bundled data: 1.9 KB / 1 file
Download size: 380 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pegas")

Format

Paradis, E., Jombart, T., Kamvar, Z. N., Knaus, B., Potts, A., Schliep, K., & Winter, D. (2025). pegas: Population and Evolutionary Genetics Analysis System (Version 1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.pegas

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 pegas version 1.4 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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