R Observatory: Metrics for ape version 5.8-1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ape

5.8-1Package record

Analyses of Phylogenetics and Evolution

300packages dependsuggested by 100

1.5Mdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Emmanuel ParadisCRAN page ↗GitHub ↗Issues ↗

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Install

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

install.packages("ape", 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("emmanuelparadis/ape")

Development version from emmanuelparadis/ape. 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-ape

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-ape

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-ape

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: 7.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 5.8-1

READMEYes · 15 wordsVignettesYes · 3 · dynamicNEWSYes · 0% structuredCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 188 (1 internal)includes a package overview page
Examples that run: 90%131 run in a plain check · 13 never run · 1 hold no code
Exported functions with examples: 80%
Documented parameters: 94%
Return-value docs: 91%
Help pages citing references: 51%

Vignettes (3)

How these are measured

Downloads

1.5M

CRAN downloads in the past year

Rank #307 · ~4K/day · ~123.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

126K30 days

358.9K90 days

1.5M1 year

Compare downloads with other packages →

Also on26.3K r2u187 autocran705.6K conda_forge1.2K c2d4u

How downloads are counted

Repository

emmanuelparadis/ape ↗Account: emmanuelparadis

75Stars

14Forks

7Open issues

0Open PRs

0Releases

284Commits

12Commit identities

License file reads as GPL-2.0 · 284 commits · Last activity 2026-10-20 · +4.2% stars, 30d · Default branch at 5.8-3, ahead of CRAN 5.8-1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 64%
Median days to close, 50 most recently updated closed issues: 10
Median days to close, 50 most recently updated closed PRs: 6

Stars over time

2025-09-21 · 722026-10-15 · 75

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/emmanuelparadis/ape on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing ape adds 2 packages (2 with compiled code, 2.0 MB of source tarballs). Heaviest: Rcpp 1.8 MB, digest 231 KB.

Depends (1)

R >= 3.2.0

Imports (9)

nlmelatticegraphicsmethodsstatsutilsparallelRcpp digest

LinkingTo (1)

Rcpp

Suggests (5)

gee expm igraph phangorn xml2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

300direct

126indirect

Depends 63 · Imports 237

Suggested by 100

Show the 48 most downloaded dependentsHide the 48 most downloaded dependents

Depends, Imports or LinkingTo, most downloaded first

and 252 more dependents and 100 packages that suggest it on CRAN ↗

How these are counted

Code & Tests

Datasets

People & History

People (33)

Emmanuel Paradis

Author, Maintainer, Copyright holder · added in 1.2-7

Simon Blomberg

Author, Copyright holder · added in 3.2

Ben Bolker

Author, Copyright holder · added in 1.2-7

Joseph Brown

Author, Copyright holder · added in 5.0

Santiago Claramunt

Author, Copyright holder · added in 5.4

Julien Claude

Author, Copyright holder · added in 1.2-7

Hoa Sien Cuong

Author, Copyright holder · added in 2.0

Richard Desper

Author, Copyright holder · added in 2.0

Gilles Didier

Author, Copyright holder · added in 3.2

Benoit Durand

Author, Copyright holder · added in 1.10-1

Julien Dutheil

Author, Copyright holder · added in 1.2-7

RJ Ewing

Author, Copyright holder · added in 4.1

Olivier Gascuel

Author, Copyright holder · added in 2.0

Thomas Guillerme

Author, Copyright holder · added in 5.1

Christoph Heibl

Author, Copyright holder · added in 2.0

Anthony Ives

Author, Copyright holder · added in 3.3

Bradley Jones

Author, Copyright holder · added in 4.0

Franz Krah

Author, Copyright holder · added in 5.0

Daniel Lawson

Author, Copyright holder · added in 2.3

Vincent Lefort

Author, Copyright holder · added in 2.0

Pierre Legendre

Author, Copyright holder · added in 2.3

Jim Lemon

Author, Copyright holder · added in 1.8-3

Guillaume Louvel

Author, Copyright holder · added in 5.4

Eric Marcon

Author, Copyright holder · added in 5.2

Federico Marotta

Author, Copyright holder · added in 5.8-1

Rosemary McCloskey

Author, Copyright holder · added in 3.1-3

Johan Nylander

Author, Copyright holder · added in 1.10-1

Rainer Opgen-Rhein

Author, Copyright holder · added in 1.2-7

Andrei-Alin Popescu

Author, Copyright holder · added in 2.8

Manuela Royer-Carenzi

Author, Copyright holder · added in 3.2

Klaus Schliep

Author, Copyright holder · added in 2.6

Korbinian Strimmer

Author, Copyright holder · added in 1.2-7

Damien de Vienne

Author, Copyright holder · added in 2.2

Maintainer since 0.1 (2002)

Listed in earlier versions (8)

Show 8 peopleHide 8 people

Emmanuel Paradis Julien Claude Yvonnick Noel Ben Bolker

no longer listed · 0.1 to 0.2

Emmanuel Paradis Korbibian Strimmer Julien Claude Yvonnick Noel Ben Bolker

no longer listed · 0.2-1

Emmanuel Paradis Korbinian Strimmer Julien Claude Yvonnick Noel Ben Bolker

no longer listed · 1.0

Emmanuel Paradis Korbinian Strimmer Julien Claude Gangolf Jobb Yvonnick Noel Ben Bolker

no longer listed · 1.1 to 1.2-3

Emmanuel Paradis Korbinian Strimmer Julien Claude Gangolf Jobb Rainer Opgen-Rhein Yvonnick Noel Ben Bolker

no longer listed · 1.2-4 to 1.2-5

Emmanuel Paradis Korbinian Strimmer Julien Claude Gangolf Jobb Rainer Opgen-Rhein Julien Dutheil Yvonnick Noel Ben Bolker

no longer listed · 1.2-6

Gangolf Jobb

no longer listed · 1.2-7 to 2.5-1

Yvonnick Noel

no longer listed · 1.2-7 to 3.0-9

Releases (104)

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
5.8-1Latest
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2024-12-16 · current release · diff ↗ ·
added 1 export
write.phyloXML
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R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
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2023-02-16 · diff ↗ ·
added 7 exports
drop.tip.multiPhylo, drop.tip.phylo, efastats, keep.tip.multiPhylo, keep.tip.phylo, letterconf, muscle5
R
R 4.2.0 released · 2022-04-22
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2021-12-21 · diff ↗ ·
added 2 exports
degree, solveAmbiguousBases
R
R 4.1.0 released · 2021-05-18
5.5
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2021-04-25 · diff ↗ ·
added 4 exports
LargeNumber, SHORTwise, rmtopology, rtopology
5.4-1
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2020-08-13 · diff ↗ ·
added 1 export
nexus2DNAbin
5.4
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2020-06-03 · diff ↗ ·
removed 2 exports
neworder_phylo, neworder_pruningwise

added 2 exports
getAnnotationsGenBank, latag2n

Show 123 earlier eventsHide 123 earlier events

R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
5.3
record
2019-03-17 · diff ↗ ·
removed 1 export
pattern:^[^\\.]

added 322 exports
[.DNAbin, AAsubst, abbreviateGenus, ace, add.scale.bar, additive, alex, all.equal.DNAbin, all.equal.phylo, alview, arecompatible, as.AAbin, as.AAbin.character, as.alignment, as.bitsplits, as.bitsplits.prop.part, as.character.AAbin, as.character.DNAbin, as.DNAbin, as.DNAbin.alignment, as.DNAbin.character, as.DNAbin.list, as.evonet, as.evonet.phylo, as.hclust.phylo, as.igraph.evonet, as.igraph.phylo, as.list.AAbin, as.list.DNAbin, as.matching and 292 more
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pattern:.+

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pattern:^[^\\.], .compressTipLabel, .uncompressTipLabel, .PlotPhyloEnv
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R 2.15.0 released · 2012-03-30
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R 2.14.0 released · 2011-10-31
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R 1.6.0 released · 2002-10-01
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2002-08-31
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R 1.5.0 released · 2002-04-29

Package metadata

First published: 2002-08-31
Total releases: 104 / 24 yrs
License: GPL-2 | GPL-3 OSI
Minimum R: ≥ 3.2.0
Bundled data: 125 KB / 16 files
Download size: 1.4 MB

Appears in task views

Analysis of Ecological and Environmental Data Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("ape")

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

It points to 10.1093/bioinformatics/bty633.

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 ape version 5.8-1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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