R Observatory: Metrics for pegas version 1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pegas

1.4Package record

Population and Evolutionary Genetics Analysis System

9packages dependsuggested by 4

109.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Emmanuel ParadisCRAN page ↗Website ↗

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. 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-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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4

READMENoVignettesYes · 2 · dynamicNEWSYes · 0% structuredCitation fileYes · cites a publicationWebsiteYes

Help pages: 55includes a package overview page
Examples that run: 96%47 run in a plain check · 1 never run · 1 hold no code
Exported functions with examples: 91%
Documented parameters: 92%
Return-value docs: 100%
Help pages citing references: 53%

Vignettes (2)

Plotting Haplotype Networks PDF
Reading Files PDF

How these are measured

Downloads

109.5K

CRAN downloads in the past year

Rank #1,311 · ~300/day · ~9.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

6.4K30 days

22.5K90 days

109.5K1 year

Compare downloads with other packages →

Also on1.1K r2u6 autocran9.4K conda_forge563 bioconda170 c2d4u

How downloads are counted

Repository

emmanuelparadis/pegas.html ↗

Responsiveness

not measured

How these are measured

PracticesBeta

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

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing pegas adds 3 packages (3 with compiled code, 3.4 MB of source tarballs). Heaviest: Rcpp 1.8 MB, ape 1.4 MB, digest 231 KB.

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

9direct

8indirect

Depends 1 · Imports 8

Suggested by 4

Show all 13 packagesHide all 13 packages

Depends, Imports or LinkingTo, most downloaded first

poppr PopGenReport StAMPP mmod graph4lg RAINBOWR spider HACSim wingen

Suggests, most downloaded first

adegenet hierfstat dartR dartR.base

How these are counted

Code & Tests

Datasets

People & History

People (7)

Emmanuel Paradis

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

Releases (32)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.4Latest
record
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
record
2023-12-13 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2
record
2023-02-23 · diff ↗ ·
added 1 export
nullAlleles2NA
R
R 4.2.0 released · 2022-04-22
1.1
record
2021-12-16 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0-1
record
2021-05-17 · diff ↗
1.0
record
2021-04-08 · diff ↗ ·
removed 1 export
dist.snp

added 4 exports
getHaploNetOptions, mutations, setHaploNetOptions, write.vcf
0.14
record
2020-09-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.13
record
2020-03-10 · diff ↗ ·
added 1 export
geoTrans2
0.12
record
2019-10-05 · diff ↗ ·
added 11 exports
allelicrichness, F2, F3, F4, loci2alleles, loci2SnpMatrix, rarefactionplot, rhost, Rst, stairway, theta.tree.hetero

Show 37 earlier eventsHide 37 earlier events

R
R 3.6.0 released · 2019-04-26
0.11
record
2018-07-09 · diff ↗ ·
added 7 exports
dist.asd, dist.snp, getPhi, hap.div, sw, unphase, write.pegas.amova
R
R 3.5.0 released · 2018-04-23
0.10
record
2017-05-03 · diff ↗ ·
added 5 exports
dist.hamming, mjn, msn, plotNetMDS, rmst
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.9
record
2016-04-16 · diff ↗ ·
added 2 exports
LDscan, LDmap
0.8-2
record
2015-09-25 · diff ↗
0.8-1
record
2015-06-24 · diff ↗
0.8
record
2015-05-20 · diff ↗ ·
added 7 exports
alleles2loci, getINFO, rangePOS, selectQUAL, VCFheader, VCFlabels, VCFloci
R
R 3.2.0 released · 2015-04-16
0.7
record
2015-03-05 · diff ↗ ·
added 4 exports
diffHaplo, geod, geoTrans, replot
0.6
record
2014-08-21 · diff ↗ ·
added 7 exports
dist.haplotype.loci, is.phased, is.snp, LD, LD2, proba.genotype, read.vcf
R
R 3.1.0 released · 2014-04-10
0.5-1
record
2014-01-10 · diff ↗
0.5
record
2013-10-08 · diff ↗ ·
added 4 exports
as.igraph.haploNet, as.network.haploNet, haploFreq, theta.msat
0.4-5
record
2013-06-06 · diff ↗ ·
removed 1 export
pattern:^[^\\.]

added 28 exports
amova, as.loci, expand.genotype, Fst, genind2loci, getAlleles, getGenotypes, getPloidy, H, haploNet, haplotype, heterozygosity, hw.test, loci2genind, mst, MMD, nuc.div, R2.test, read.gtx, read.loci, rr.test, site.spectrum, tajima.test, theta.h, theta.k, theta.s, theta.tree, write.loci
R
R 3.0.0 released · 2013-04-03
0.4-4
record
2013-01-23 · diff ↗
0.4-3
record
2012-07-31 · diff ↗
0.4-2
record
2012-05-11 · diff ↗
R
R 2.15.0 released · 2012-03-30
0.4-1
record
2012-01-19 · diff ↗ ·
removed 1 export
pattern:.+

added 1 export
pattern:^[^\\.]
R
R 2.14.0 released · 2011-10-31
0.4
record
2011-07-23 · diff ↗
R
R 2.13.0 released · 2011-04-13
0.3-4
record
2011-04-01 · diff ↗
0.3-3
record
2010-11-26 · diff ↗
R
R 2.12.0 released · 2010-10-15
0.3-2
record
2010-06-10 · diff ↗
0.3-1
record
2010-05-19 · diff ↗
R
R 2.11.0 released · 2010-04-22
0.3
record
2009-12-03 · diff ↗
R
R 2.10.0 released · 2009-10-26
0.2
record
2009-10-07 · diff ↗
0.1
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("pegas")

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

It points to 10.1093/bioinformatics/btp696.

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 v2026-10-23. 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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