R Observatory: Metrics for TreeDist version 2.15.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TreeDist

2.15.0Package record

Calculate and Map Distances Between Phylogenetic Trees

4packages dependsuggested by 2

24.8Kdownloads / year

84.5%test coverage

13/13flavors OK

Overview

About

Maintained by Martin R. SmithCRAN page ↗GitHub ↗Website ↗Issues ↗

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) doi:10.1093/bioinformatics/btaa614; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) doi:10.1007/978-3-642-40453-5_13, including the Nye et al. (2006) metric doi:10.1093/bioinformatics/bti720; the Matching Split Distance (Bogdanowicz & Giaro 2012) doi:10.1109/TCBB.2011.48; the Hierarchical Mutual Information (Perotti et al. 2015) doi:10.1103/PhysRevE.92.062825; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance doi:10.1093/molbev/msw124, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) doi:10.1007/3-540-61332-3_168. Includes tools for visualizing mappings of tree space (Smith 2022) doi:10.1093/sysbio/syab100, for identifying islands of trees (Silva and Wilkinson 2021) doi:10.1093/sysbio/syab015, for calculating the median of sets of trees, and for computing the information content of trees and splits.

Changes in 2.15.0

New function NNIMaxStep() computes the largest clustering information distance attainable by a single nearest neighbour interchange on an _n_-leaf tree.
Use grDevices palettes to drop colorspace dependency.

From NEWS.md in the release

Install

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

install.packages("TreeDist", 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("ms609/TreeDist")

Development version from ms609/TreeDist. 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-treedist

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-TreeDist

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-TreeDist

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 OK2026-09-17
NOTE8 OK, 5 NOTE2026-09-08
ERROR8 OK, 4 NOTE, 1 ERROR2026-09-07
NOTE10 OK, 3 NOTE2026-07-16
OK13 OK2026-05-17

Show 4 earlier changesHide 4 earlier changes

ERROR9 OK, 3 NOTE, 2 ERROR2026-04-24
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 2.15.0

README· In the repository, left out of the releaseVignettesYes · 9 · dynamicNEWSYes · 100% structured · mentions 2.15.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 57 (20 internal)includes a package overview page
Examples that run: 100%36 run in a plain check
Exported functions with examples: 72%
Documented parameters: 57%
Return-value docs: 81%
Help pages citing references: 44% with a bibliography file

Vignettes (9)

How these are measured

Downloads

24.8K

CRAN downloads in the past year

Rank #2,786 · ~68/day · ~2.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.4K30 days

5.3K90 days

24.8K1 year

Compare downloads with other packages →

Also on692 r2u9 autocran10.2K conda_forge148 c2d4u

How downloads are counted

Repository

ms609/treedist ↗Account: ms609

40Stars

6Forks

18Open issues

1Open PRs

34Releases

2,652Commits

9Commit identities

rr-packagerstatsphylogenetic-treestree-distancestreesbioinformaticscladistics

2,652 commits · Last activity 2026-10-16 · 0% stars, 30d · Default branch at 2.15.0.9000, ahead of CRAN 2.15.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 85%
Median days to close, 50 most recently updated closed issues: 118
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-28 · 342026-08-18 · 40

How these are measured

PracticesBeta

16 development-tooling and community-health practices detected across 9 families in the upstream repository

Checks run against github.com/ms609/treedist on 2026-10-11.

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 (3)

pkgdown

GitHub Pages site last deployed 2026-09-21 · The repository has a site deploy workflow

pkgdown site last built 2026-09-21

Coverage (2)

Coverage reporting.covrignore

Show all practicesHide 5 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Lint, format, editor (3)

lintrRStudio projectPositron

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-08-21
Seen in the repository: .github/copilot-instructions.md, .github/workflows/copilot-setup-steps.yml
Pull request: opened by its own account
Commits: 7 by its own account · at least 3 crediting it in the message
Claude Codefirst seen 2026-03-12
Seen in the repository: .claude
Named in .Rbuildignore: .claude
Named in .gitignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 18 crediting it in the message
Posit Assistantfirst seen 2026-03-12
Seen in the repository: .positai/plans, .positai/settings.json

Shared conventions any agent may read, so they name no particular tool.

Seen in the repository: AGENTS.md

Models named in its commits

Claude Opus 4.85 commits · Jun 2026
Claude Opus 55 commits · Aug to Sep 2026
Claude Sonnet 4.65 commits · May to Jun 2026
Claude Opus 5.52 commits · Sep to Oct 2026
Claude Haiku 4.51 commit · Jul 2026

1 more model not listed.

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

32 external dependencies (excludes base and recommended)

Installing TreeDist adds 38 packages (24 with compiled code, 31 MB of source tarballs). Heaviest: bslib 5.6 MB, promises 3.1 MB, sass 2.9 MB.

Depends (2)

R >= 4.0stats

Imports (6)

ape cli Rdpack shiny shinyjs TreeTools

LinkingTo (2)

Rcpp TreeTools

Suggests (26)

bookdownclusterggplot2 hypervolume kdensity knitrMASSphangorn plotly PlotTools protoclust Quartet readxl rmarkdown Rcpp rgl Rogue spelling TBRDist testthat Ternary TreeDistData TreeSearch Umatrix vdiffr withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

Imports 4

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

Rogue TreeSearch TBRDist rwty

Suggests, most downloaded first

TreeTools Quartet

How these are counted

Code & Tests

People & History

People (5)

Martin R. Smith

Yi Cao

Contributor, Copyright holder

LAP algorithm

Yong Yang

Contributor, Copyright holder

LAP algorithm

Roy Jonker

prg, Copyright holder

LAP algorithm

Neil Kaye

Copyright holder · added in 2.14.0

Mercator image

Releases (31)

Pick two releases to compare their code metrics.

2.15.0Latest
record
2026-09-11 · current release · diff ↗ ·
added 1 export
NNIMaxStep
2.14.1
record
2026-06-10 · diff ↗
2.14.0
record
2026-05-09 · diff ↗ ·
added 5 exports
MCITree, TransferConsensus, TransferDist, TransferDistSplits, TransferDistance
R
R 4.6.0 released · 2026-04-24
2.12.0
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2026-02-13 · diff ↗ ·
added 1 export
.ThreeDPlotServer
2.11.1
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2025-10-13 · diff ↗
2.11.0
record
2025-09-28 · diff ↗ ·
added 13 exports
AHMI, DisplayMatching, EHMI, HH, HMI, HierarchicalMutualInfo, HierarchicalMutualInformation, PlotMatching, SelfHMI, VisualiseMatching, as.HPart, clone, is.HPart
2.10.1
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2025-08-25 · diff ↗
2.10.0
record
2025-08-22 · diff ↗ ·
added 2 exports
Ntropy, entropy_int
R
R 4.5.0 released · 2025-04-11
2.9.2
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2025-01-11 · diff ↗
2.9.1
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2024-09-07 · diff ↗
2.9.0
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2024-09-03 · diff ↗
2.8.0
record
2024-07-26 · diff ↗ ·
added 2 exports
Islands, ReduceTrees
R
R 4.4.0 released · 2024-04-24
2.7.0
record
2023-10-26 · diff ↗

Show 22 earlier eventsHide 22 earlier events

2.6.3
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2023-08-25 · diff ↗
2.6.2
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2023-06-30 · diff ↗
2.6.1
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2023-05-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.6.0
record
2023-02-20 · diff ↗
2.5.0
record
2022-10-07 · diff ↗ ·
added 11 exports
DistFromMed, DistanceFromMedian, KMeansPP, MeanCentDist, MeanCentroidDist, MeanCentroidDistance, MeanMSTEdge, MeanNN, SumOfRanges, SumOfVariances, SumOfVars
2.4.1
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2022-07-20 · diff ↗ ·
removed 1 export
as.ClusterTable
R
R 4.2.0 released · 2022-04-22
2.4.0
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2022-03-23 · diff ↗ ·
added 2 exports
MSTSegments, StrainCol
2.3.0
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2022-01-04 · diff ↗
2.2.0
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2021-09-13 · diff ↗ ·
added 4 exports
GetParallel, SetParallel, StartParallel, StopParallel
2.1.1
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2021-07-13 · diff ↗
2.1.0
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2021-07-12 · diff ↗ ·
added 9 exports
ConsensusInfo, KCDiameter, Log2TreesConsistentWithTwoSplits, MapTrees, MappingQuality, PathVector, Plot3, SpectralEigens, SplitVector
R
R 4.1.0 released · 2021-05-18
2.0.3
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2021-01-31 · diff ↗
2.0.2
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2021-01-27 · diff ↗
2.0.0
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2021-01-20 · diff ↗ ·
added 4 exports
Project, ProjectionQuality, SpectralClustering, as.ClusterTable
1.2.1
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2020-09-17 · diff ↗
1.2.0
record
2020-08-28 · diff ↗
1.1.1
record
2020-07-10 · diff ↗ ·
removed 1 export
SplitsInBinaryTree

added 1 export
NNIDiameter
1.0.0
record
2020-06-30
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-06-30
Total releases: 31 / 6 yrs
License: GPL (>= 3) OSI
Copyright: Jonker-Volgenant Linear Assignment Problem implementation by Roy Jonker modified by Yong Yang and Yi Cao.
Additional repositories: ms609.github.io
Minimum R: ≥ 4.0
Download size: 2.6 MB

Appears in task views

Optimization and Mathematical Programming Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TreeDist")

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 TreeDist version 2.15.0 [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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