R Observatory: Metrics for phytools version 2.5-2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phytools

2.5-2Package record

Phylogenetic Tools for Comparative Biology (and Other Things)

47packages dependsuggested by 17

201.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Liam J. RevellCRAN page ↗GitHub ↗

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Install

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

install.packages("phytools", 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("liamrevell/phytools")

Development version from liamrevell/phytools. 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-phytools

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-phytools

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-phytools

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: 8.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-08
ERROR12 OK, 1 ERROR2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.5-2

README· In the repository, left out of the releaseVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 189includes a package overview page
Examples that run: 86%57 run in a plain check · 9 never run
Exported functions with examples: 35%
Documented parameters: 100%
Return-value docs: 96%
Help pages citing references: 99%

How these are measured

Downloads

201.4K

CRAN downloads in the past year

Rank #802 · ~552/day · ~16.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

31.3K30 days

57.9K90 days

201.4K1 year

Compare downloads with other packages →

Also on2.9K r2u7 autocran10.4K conda_forge587 bioconda351 c2d4u

How downloads are counted

Repository

liamrevell/phytools ↗Account: liamrevell

234Stars

58Forks

48Open issues

6Open PRs

1Releases

1,447Commits

3Commit identities

License file reads as GPL-3.0 · 1,447 commits · Last activity 2026-09-15 · +0.4% stars, 30d · Default branch at 2.6-9, ahead of CRAN 2.5-2 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 43
Median days to close, 50 most recently updated closed PRs: 34

Stars over time

2025-10-16 · 2242026-09-21 · 234

How these are measured

PracticesBeta

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

Checks run against github.com/liamrevell/phytools on 2026-10-11.

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing phytools adds 29 packages (16 with compiled code, 17 MB of source tarballs). Heaviest: igraph 4.8 MB, maps 2.2 MB, phangorn 1.9 MB.

Depends (3)

R >= 3.5.0ape maps

Imports (20)

clusterGeneration coda combinat DEoptim doParallel expm foreachgraphicsgrDevicesMASSmethodsmnormtnlmenumDeriv optimParallelparallelphangorn scatterplot3dstatsutils

LinkingTo (0)

none

Suggests (5)

animation geiger plotrix RColorBrewer rgl

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

47direct

26indirect

Depends 8 · Imports 39

Suggested by 17

Show the 48 most downloaded packagesHide the 48 most downloaded packages

Depends, Imports or LinkingTo, most downloaded first

Suggests, most downloaded first

RNeXML

and 16 more packages that suggest it on CRAN ↗

How these are counted

Code & Tests

Datasets

People & History

People (1)

Liam J. Revell

Author, Maintainer since 0.0-8 (2011)

Listed in earlier versions (1)

Revell

no longer listed · 2.4-4 to 2.5-2

Releases (63)

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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
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
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
3.0.3Latest
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2014-03-03 · current release · diff ↗
3.0.2
record
2013-07-16 · diff ↗
3.0.1
record
2013-04-20 · diff ↗

Show 64 earlier eventsHide 64 earlier events

R
R 3.0.0 released · 2013-04-03
3.0.0
record
2013-03-20 · diff ↗
2.15.3
record
2013-02-16 · diff ↗ ·
added 10 exports
add.random, applyBranchLengths, ave.rates, bind.tip, getSisters, orderMappedEdge, plotThresh, roundBranches, splitplotTree, threshState
2.15.2
record
2012-09-29 · diff ↗
2.15.1
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2012-05-01 · diff ↗ ·
added 2 exports
getExtant, getExtinct
R
R 2.15.0 released · 2012-03-30
2.14.2
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2012-02-26 · diff ↗ ·
added 3 exports
findMRCA, getDescendants, paintSubTree
2.14.1
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2011-12-17 · diff ↗ ·
added 3 exports
anc.ML, fitBayes, phenogram
R
R 2.14.0 released · 2011-10-31
2.14.0
record
2011-10-16 · diff ↗ ·
added 49 exports
add.everywhere, allFurcTrees, anc.trend, branching.diffusion, brownie.lite, drop.clade, drop.tip.simmap, estDiversity, evol.rate.mcmc, evol.vcv, exhaustiveMP, expm, fastBM, fitDiversityModel, gammatest, lambda.transform, ls.tree, ltt, make.simmap, map.overlap, minSplit, mrp.supertree, nodeHeights, optim.phylo.ls, paste.tree, phyl.cca, phyl.pairedttest, phyl.pca, phyl.resid, phyl.RMA and 19 more
2.13.2
record
2011-08-18 · diff ↗
2.5-2
record
2025-09-19 · diff ↗ ·
added 7 exports
cladebox, fitcontMk, fitmultiTrend, fitsemiThresh, sim.absorbing, sim.multiTrend, sim.reflective
2.4-4
record
2025-01-08 · diff ↗
2.3-0
record
2024-06-14 · diff ↗ ·
added 6 exports
bounded_bm, fitfnMk, fitmultiBM, fitThresh, plotFanTree.wTraits, plotTree.lollipop
2.1-1
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2024-01-09 · diff ↗ ·
added 2 exports
fitgammaMk, gamma_pruning
2.0-3
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2023-11-09 · diff ↗ ·
removed 1 export
as.princomp.phyl.pca

added 1 export
as.prcomp
1.9-16
record
2023-07-14 · diff ↗ ·
added 7 exports
ancr, ansi_phylo, hide.hidden, midpoint_root, plot.ancr, pscore, simmap
1.5-1
record
2023-02-19 · diff ↗ ·
removed 1 export
drop.tip.multiPhylo

added 7 exports
keep.tip.densityMap, keep.tip.multiSimmap, keep.tip.simmap, rescale, rescale.multiSimmap, rescale.simmap, splinePhylogram
1.2-0
record
2022-09-01 · diff ↗ ·
added 6 exports
fitMk.parallel, ltt.multiPhylo, ltt.multiSimmap, ltt.phylo, ltt.simmap, sigmoidPhylogram
1.0-3
record
2022-04-05 · diff ↗ ·
added 2 exports
as.princomp, as.princomp.phyl.pca
1.0-1
record
2022-01-03 · diff ↗ ·
added 1 export
cotangleplot
0.7-90
record
2021-09-25 · diff ↗ ·
added 1 export
readNexus
0.7-80
record
2021-06-03 · diff ↗ ·
added 1 export
multirateBM
0.7-70
record
2020-09-20 · diff ↗ ·
added 7 exports
drop.tip.multiPhylo, drop.tip.multiSimmap, edge.widthMap, fitHRM, graph.polyMk, keep.tip.contMap, plot.edge.widthMap
0.7-47
record
2020-06-01 · diff ↗ ·
removed 1 export
logLik.gfit

added 5 exports
as.Qmatrix, density.anc.Bayes, plot.anc.Bayes, plot.Qmatrix, print.Qmatrix
0.7-20
record
2020-03-19 · diff ↗ ·
added 7 exports
logLik.gfit, plot.simBMphylo, plot.phylosig, scores, scores.phyl.pca, simBMphylo, tree.grow
0.6-99
record
2019-06-18 · diff ↗ ·
added 7 exports
fitpolyMk, geo.palette, gtt, mccr, phenogram95, phylo.impute, phyloScattergram
0.6-60
record
2018-09-28 · diff ↗ ·
removed 1 export
expm

added 10 exports
ctt, Dtest, fitmultiMk, mcmcMk, plotTree.datamatrix, project.phylomorphospace, sim.ctt, sim.Mk, sim.multiCtt, sim.multiMk
0.6-44
record
2017-11-12 · diff ↗ ·
added 5 exports
fit.bd, fit.yule, lik.bd, posthoc, posthoc.ratebytree
0.6-20
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2017-07-28 · diff ↗ ·
added 7 exports
compare.chronograms, density.multiSimmap, expand.clade, geo.legend, getParent, linklabels, plot.changesMap
0.6-00
record
2017-03-28 · diff ↗ ·
added 12 exports
arc.cladelabels, coef.phyl.RMA, errorbar.contMap, force.ultrametric, get.treepos, getnode, labelnodes, multiOU, pgls.SEy, plot.phyl.RMA, plotTree.errorbars, ratebytree
0.5-64
record
2016-12-05 · diff ↗ ·
added 12 exports
aic.w, allRotations, bd, cospeciation, likSurface.rateshift, modified.Grafen, node.paths, plotTree.barplot, plotTree.boxplot, resolveAllNodes, resolveNode, rotate.multi
0.5-38
record
2016-06-24 · diff ↗ ·
added 13 exports
as.multiPhylo, averageTree, bind.tree.simmap, consensus.edges, ls.consensus, make.transparent, Map.Overlap, mapped.states, matchLabels, minTreeDist, plot.fitMk, plot.fitPagel, plot.gfit
0.5-20
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2016-03-06 · diff ↗ ·
added 5 exports
densityTree, dot.legend, dotTree, phylo.heatmap, rootedge.to.singleton
0.5-10
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2015-12-10 · diff ↗ ·
added 7 exports
compute.mr, edgelabels.cophylo, edgeProbs, fastDist, genus.to.species.tree, nodelabels.cophylo, tiplabels.cophylo
0.5-00
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2015-09-25 · diff ↗ ·
added 7 exports
cophylo, fitMk, markChanges, plot.cophylo, plotTree.splits, splitEdgeColor, tipRotate
0.4-60
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2015-07-10 · diff ↗
0.4-56
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2015-04-29 · diff ↗ ·
added 1 export
collapseTree
0.4-45
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2015-02-05 · diff ↗ ·
added 6 exports
add.arrow, fitPagel, ladderize.simmap, locate.fossil, rep.multiPhylo, rep.phylo
0.4-31
record
2014-08-26 · diff ↗ ·
added 2 exports
drop.tip.contMap, drop.tip.densityMap
0.4-21
record
2014-06-28 · diff ↗ ·
added 3 exports
locate.yeti, plotTree.wBars, setMap
0.4-05
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2014-05-05 · diff ↗ ·
added 6 exports
cladelabels, drop.tip.singleton, fastHeight, nodeheight, paintBranches, roundPhylogram
0.3-93
record
2014-03-03 · diff ↗ ·
removed 1 export
xkcdTree

added 6 exports
add.species.to.genus, biplot.phyl.pca, di2multi.simmap, midpoint.root, rateshift, skewers
0.3-72.1
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2014-03-03 · diff ↗
0.3-72
record
2013-10-25 · diff ↗ ·
added 11 exports
backbone.toPhylo, drop.leaves, genSeq, map.to.singleton, minRotate, multiRF, phylo.toBackbone, phylo.to.map, plot.phylo.to.map, plotTree.singletons, reorder.backbonePhylo
0.3-10
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2013-07-16 · diff ↗ ·
added 1 export
rotateNodes
0.2-90
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2013-06-30 · diff ↗ ·
added 2 exports
add.simmap.legend, collapse.to.star
0.2-80
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2013-05-31 · diff ↗
0.2-70
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2013-05-22 · diff ↗ ·
added 5 exports
extract.clade.simmap, getCladesofSize, mergeMappedStates, plot.contMap, plot.densityMap
0.2-50
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2013-04-20 · diff ↗ ·
added 4 exports
extract.strahlerNumber, ltt95, strahlerNumber, to.matrix
0.2-40
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2013-04-08 · diff ↗ ·
added 3 exports
describe.simmap, getStates, rerootingMethod
0.2-30
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2013-03-20 · diff ↗ ·
added 8 exports
add.color.bar, countSimmap, plotBranchbyTrait, ratebystate, repPhylo, sim.ratebystate, untangle, writeAncestors
0.2-20
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2013-02-17 · diff ↗
0.2-1
record
2012-11-13 · diff ↗ ·
added 9 exports
ancThresh, contMap, densityMap, fastAnc, matchNodes, multi.mantel, threshDIC, writeNexus, xkcdTree
0.2-0
record
2012-09-29 · diff ↗ ·
added 3 exports
bmPlot, likMlambda, threshBayes
0.1-9
record
2012-08-08 · diff ↗ ·
added 8 exports
export.as.xml, fancyTree, fastMRCA, multiC, pgls.Ives, phylomorphospace3d, rescaleSimmap, sim.corrs
0.1-8
record
2012-05-02 · diff ↗
0.1-7
record
2012-02-27 · diff ↗
0.1-6
record
2012-01-11 · diff ↗ ·
added 3 exports
evolvcv.lite, pbtree, sampleFrom
0.1-5
record
2011-12-18 · diff ↗
0.1-2
record
2011-11-27 · diff ↗ ·
added 4 exports
anc.Bayes, brownieREML, make.era.map, vcvPhylo
0.1-0
record
2011-10-17 · diff ↗
0.0-8
record
2011-08-20
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-08-18
Total releases: 63 / 15 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 129 KB / 39 files
Download size: 509 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("phytools")

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

It points to 10.7717/peerj.16505.

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 phytools version 2.5-2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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