R Observatory: Metrics for phangorn version 2.12.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phangorn

2.12.1Package record

Phylogenetic Reconstruction and Analysis

45packages dependsuggested by 18

307.7Kdownloads / year

8.3%test coverage

8/13flavors OK

Overview

About

Maintained by Klaus SchliepCRAN page ↗GitHub ↗Website ↗Issues ↗

Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).

Install

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

install.packages("phangorn", 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("KlausVigo/phangorn")

Development version from KlausVigo/phangorn. 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-phangorn

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-phangorn

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-phangorn

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

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  phangorn/R/bab.R (.Names: 3, .Dim: 2)
  phangorn/R/fitch64.R (.Dim: 1, .Names: 1)
  phangorn/R/phylo.R (.Dim: 2, .Names: 2)
  phangorn/R/splits.R (.Names: 1)
'.Names' should be changed to 'names'.
'.Dim' should be changed to 'dim'.

CRAN check page ↗

Slowest check: 10.5 min · r-devel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-07-16
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.12.1

READMEYes · 223 wordsVignettesYes · 7 · dynamicNEWSYes · 0% structuredCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 76 (4 internal)includes a package overview page
Examples that run: 90%66 run in a plain check · 7 never run
Exported functions with examples: 97%
Documented parameters: 93%
Return-value docs: 97%
Help pages citing references: 51%

Vignettes (7)

How these are measured

Downloads

307.7K

CRAN downloads in the past year

Rank #658 · ~843/day · ~25.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

36K30 days

83.5K90 days

307.7K1 year

Compare downloads with other packages →

Also on5K r2u7 autocran35.9K conda_forge214 bioconda428 c2d4u

How downloads are counted

Repository

klausvigo/phangorn ↗Account: KlausVigo

216Stars

41Forks

29Open issues

0Open PRs

1Releases

2,992Commits

13Commit identities

rphylogenetic-analysisphylogeneticsr-packagerstats

2,992 commits · Last activity 2026-10-21 · 0% stars, 30d · Default branch at 3.0.0.1, ahead of CRAN 2.12.1 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 72%
Median days to close, 50 most recently updated closed issues: 19
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-19 · 2092026-08-15 · 216

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/klausvigo/phangorn on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (2)

Code of conductContributing guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-05-19 · The repository has a site deploy workflow

pkgdown site last built 2026-05-19

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 2 practices

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing phangorn adds 15 packages (11 with compiled code, 11 MB of source tarballs). Heaviest: igraph 4.8 MB, Rcpp 1.8 MB, ape 1.4 MB.

Depends (2)

R >= 4.1.0ape

Imports (13)

digest fastmatch genericsgraphicsgrDevicesigraph (>= 1.0)Matrixmethodsparallelquadprog Rcppstatsutils

LinkingTo (1)

Rcpp

Suggests (13)

apex Biostrings ggseqlogo ggplot2 knitr magick rgl rmarkdown seqinr testthat tinytest vdiffr xtable

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

45direct

68indirect

Depends 3 · Imports 42

Suggested by 18

Show the 48 most downloaded packagesHide the 48 most downloaded packages

Depends, Imports or LinkingTo, most downloaded first

Suggests, most downloaded first

ape TreeTools TreeDist

and 15 more packages that suggest it on CRAN ↗

How these are counted

Code & Tests

Datasets

People & History

People (18)

Klaus Schliep

Author, Maintainer since 0.0-1 (2008)

Iris Bardel-Kahr

Author · added in 2.11.1

Emmanuel Paradis

Author · added in 1.4-1

Alastair Potts

Author · added in 2.0.0

Leonardo de Oliveira Martins

Author · added in 2.1.1

Jeremy Beaulieu

Contributor · added in 2.6.2

Richel Bilderbeek

Contributor · added in 2.5.3

Joseph Brown

Contributor · added in 2.11.1

Santiago Claramunt

Contributor · added in 2.11.1

Mike Gilchrist

Contributor · added in 2.6.2

Keren Halabi

Contributor · added in 2.5.3

Michelle Kendall

Contributor · added in 2.0.4

Brian O'Meara

Contributor · added in 2.6.2

Show 5 more contributorsHide 5 contributors

Long Qu

Contributor · added in 2.6.2

Liam Revell

Contributor · added in 2.6.2

Cyrill Stachniss

Contributor · added in 2.1.1

Tim W. White

Contributor · added in 2.1.1

Kristin Winchell

Contributor · added in 2.5.5

Listed in earlier versions (2)

Joseph

no longer listed · 2.12.1

Santiago

no longer listed · 2.12.1

Releases (70)

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
R
R 3.0.0 released · 2013-04-03
2.15.3Latest
record
2013-01-02 · current release · diff ↗ ·
added 12 exports
dist.p, read.nexus.splits, mrca.phylo, densiTree, superTree, coalSpeciesTree, pml.fit, pml.init, pml.free, edQt, lli, cladePar
2.15.2
record
2012-10-10 · diff ↗

Show 78 earlier eventsHide 78 earlier events

2.15.1
record
2012-04-05 · diff ↗
R
R 2.15.0 released · 2012-03-30
2.14.1
record
2011-12-12 · diff ↗
R
R 2.14.0 released · 2011-10-31
2.13.1
record
2011-06-30 · diff ↗
R
R 2.13.0 released · 2011-04-13
2.13.0
record
2011-03-26 · diff ↗ ·
added 4 exports
as.prop.part, as.networx, allSplits, consensusNet
2.12.2
record
2011-02-14 · diff ↗
2.12.1
record
2024-09-17 · diff ↗ ·
removed 2 exports
hash_phylo, read.aa

added 19 exports
add_mutations, add_support, anc_pars, anc_pml, as.StringSet, as.ancestral, composition_test, dna2aa, gap_as_ambiguous, gap_as_state, has_gap_state, hash, keep_as_tip, latag2n.phyDat, plotSeqLogo, read.nexus.partitions, supgma, write.ancestral, write.pml
R
R 2.12.0 released · 2010-10-15
2.12.0
record
2010-09-15 · diff ↗ ·
added 1 export
write.splits
2.11.1
record
2023-01-23 · diff ↗ ·
added 3 exports
add_boxplot, add_ci, add_edge_length
R
R 2.11.0 released · 2010-04-22
2.11.0
record
2010-04-15 · diff ↗
2.10.1
record
2009-11-27 · diff ↗
2.10.0
record
2022-09-18 · diff ↗ ·
added 4 exports
candidate_tree, hash_phylo, pml_bb, transferBootstrap
2.9.0
record
2022-06-16 · diff ↗ ·
added 6 exports
as.pml, discrete.beta, glance, ratchet.control, removeAmbiguousSites, tidy
2.8.1
record
2021-12-15 · diff ↗
2.8.0
record
2021-11-09 · diff ↗ ·
removed 2 exports
%>%, dist.ml2
R
R 2.10.0 released · 2009-10-26
R
R 2.9.0 released · 2009-04-17
R
R 2.8.0 released · 2008-10-20
2.7.2
record
2008-07-21 · diff ↗
2.7.1
record
2021-07-13 · diff ↗
2.7.0
record
2021-05-03 · diff ↗
2.6.3
record
2021-04-06 · diff ↗
2.6.2
record
2021-03-22 · diff ↗ ·
added 2 exports
dist.ml2, plotRates
2.5.5
record
2019-06-19 · diff ↗ ·
added 3 exports
codonTest, plot_gamma_plus_inv, read.nexus.dist
2.5.3
record
2019-03-23 · diff ↗ ·
removed 4 exports
PNJ, unique.dist, as.networx.splits, c.splits

added 4 exports
%>%, allCompat, c.phyDat, mcc
2.4.0
record
2018-02-16 · diff ↗ ·
added 3 exports
coords, add.tips, map_duplicates
2.3.1
record
2017-11-01 · diff ↗ ·
added 4 exports
unique.dist, mast, allDescendants, threshStateC
2.2.0
record
2017-04-03 · diff ↗ ·
removed 2 exports
countCycles, plot.networx

added 4 exports
write.nexus.dist, multiphyDat2pmlPart, removeTrivialSplits, genlight2phyDat
2.1.1
record
2016-12-04 · diff ↗ ·
added 8 exports
allCircularSplits, sprdist, SPR.dist, distinct.splits, c.splits, dna2codon, codon2dna, as.MultipleAlignment
2.0.4
record
2016-06-21 · diff ↗ ·
added 1 export
wRF.dist
2.0.3
record
2016-05-01 · diff ↗ ·
added 7 exports
read.nexus.networx, write.nexus.networx, KF.dist, path.dist, createLabel, matchSplits, maxCladeCred
2.0.2
record
2016-01-23 · diff ↗
2.0.1
record
2015-12-15 · diff ↗
2.0.0
record
2015-12-10 · diff ↗ ·
added 3 exports
removeUndeterminedSites, phyDat2MultipleAlignment, delta.score
1.99.14
record
2015-07-09 · diff ↗ ·
added 5 exports
phyDat2alignment, AICc, readDist, writeDist, discrete.gamma
1.99-13
record
2015-04-08 · diff ↗ ·
added 3 exports
cbind.phyDat, nnls.phylo, pmlPart2multiPhylo
1.99-12
record
2015-02-14 · diff ↗ ·
added 4 exports
nnls.splits, nnls.networx, neighborNet, addTrivialSplits
1.99-11
record
2014-11-11 · diff ↗
1.99-9
record
2014-10-09 · diff ↗ ·
added 1 export
as.networx.splits
1.99-8
record
2014-10-07 · diff ↗ ·
removed 1 export
as.prop.part

added 6 exports
as.Matrix, addConfidences, countCycles, SOWH.test, plot.networx, presenceAbsence
1.99-7
record
2014-02-02 · diff ↗ ·
added 2 exports
read.nexus.splits, cladePar
1.99-5
record
2014-01-02 · diff ↗ ·
added 5 exports
pml.fit, pml.init, pml.free, edQt, lli
1.99-1
record
2013-08-21 · diff ↗ ·
added 1 export
dist.p
1.7-4
record
2013-04-04 · diff ↗ ·
removed 8 exports
dist.p, read.nexus.splits, pml.fit, pml.init, pml.free, edQt, lli, cladePar
1.7-1
record
2012-10-30 · diff ↗ ·
added 1 export
baseFreq
1.6-5
record
2012-10-10 · diff ↗
1.6-4
record
2012-08-02 · diff ↗
1.6-3
record
2012-07-01 · diff ↗
1.6-0
record
2012-04-05 · diff ↗
1.5-1
record
2011-12-13 · diff ↗
1.5-0
record
2011-12-10 · diff ↗ ·
added 1 export
diversity
1.4-1
record
2011-06-30 · diff ↗ ·
added 3 exports
nnls.tree, bab, random.addition
1.4-0
record
2011-03-27 · diff ↗
1.3-1
record
2011-02-14 · diff ↗
1.3-0
record
2011-01-31 · diff ↗ ·
added 3 exports
acctran, getRoot, plotAnc
1.2-0
record
2010-11-22 · diff ↗ ·
added 3 exports
pratchet, midpoint, pruneTree
1.1-2
record
2010-09-21 · diff ↗
1.1-1
record
2010-09-03 · diff ↗
1.1-0
record
2010-08-28 · diff ↗ ·
added 6 exports
CI, RI, getClans, getSlices, getClips, getDiversity
1.0-2
record
2010-05-16 · diff ↗ ·
added 1 export
pml.control
1.0-1
record
2010-04-15 · diff ↗ ·
added 5 exports
wpgma, compatible, acgt2ry, ancestral.pars, ancestral.pml
1.0-0
record
2010-03-18 · diff ↗ ·
added 3 exports
as.splits, modelTest, lento
0.99-6
record
2010-01-27 · diff ↗ ·
added 1 export
pace
0.99-5
record
2010-01-15 · diff ↗ ·
added 5 exports
plotBS, Ancestors, Descendants, Children, Siblings
0.99-4
record
2009-11-27 · diff ↗ ·
removed 1 export
pmlCluster2
0.99-3
record
2009-10-30 · diff ↗ ·
added 3 exports
pmlCluster2, rNNI, rSPR
0.99-2
record
2009-07-21 · diff ↗ ·
added 8 exports
read.phyDat, write.phyDat, as.phyDat, simSeq, SH.test, bootstrap.pml, bootstrap.phyDat, RF.dist
0.0-5
record
2009-01-22 · diff ↗
0.0-4
record
2008-12-22 · diff ↗ ·
removed 1 export
getEdgeLength

added 2 exports
pmlPen, splitsNetwork
0.0-3
record
2008-10-28 · diff ↗ ·
removed 1 export
phyDat.DNA

added 12 exports
PNJ, nni, allSitePattern, dist.ml, pmlPart, pmlCluster, pmlMix, read.aa, allTrees, designTree, designSplits, getEdgeLength
0.0-2
record
2008-07-20 · diff ↗ ·
added 22 exports
pml, optim.pml, parsimony, optim.parsimony, NJ, UNJ, phyDat, phyDat.DNA, dfactorial, ldfactorial, hadamard, fhm, distanceHadamard, treedist, sankoff, fitch, h2st, h4st, dist.logDet, dist.hamming, upgma, write.nexus.splits
R
R 2.7.0 released · 2008-04-22
0.0-1
record
2008-03-25
R
R 2.6.0 released · 2007-10-03

Package metadata

First published: 2008-03-25
Total releases: 70 / 18 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.1.0
Bundled data: 192 KB / 4 files
Download size: 1.9 MB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phangorn")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 phangorn version 2.12.1 [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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