TBRDist

2.0.1

Rearrangement Distances Between Phylogenetic Trees

1packages depend

4.8Kdownloads / year

55.7%test coverage

13/13checks pass

Overview

About

Maintained by Martin R. SmithFirst published 2020-07-016 releasesCRAN page ↗GitHub ↗

Fast calculation of tree rearrangement distances. For unrooted trees: Subtree Prune and Regraft (SPR), Tree Bisection and Reconnection (TBR), and Replug distances, using the algorithms of Whidden and Matsen (2017) doi:10.48550/arXiv.1511.07529. For rooted trees: rooted SPR (rSPR) distance, using the fixed-parameter algorithms of Whidden, Beiko, and Zeh (2013) doi:10.1137/110845045.

Install

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

install.packages("TBRDist", 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/TBRDist")

Development version from ms609/TBRDist. 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-tbrdist

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-TBRDist

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-TBRDist

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.9 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 1.01

55.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-05-17
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-31
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 52%
Return-value docs: 100%
References docs: 33%

Downloads

4.8K

CRAN downloads in the past year

Rank #5,684 · ~13/day · ~397/mo

Releases R versions

Daily download trend is not available in this view yet.

39230 days

1.7K90 days

4.8K1 year

Compare downloads with other packages →

Also on447 r2u30 autocran32 c2d4u

Repository

GitHub ↗ ms609/tbrdist

1Stars

0Forks

4Open issues

0Open PRs

7Releases

169Commits

2Contributors

rphylogeneticsphylogenetic-treesdistance-calculationalgorithmsbioinformatics

License GPL-3.0 · 169 commits · Last activity 2026-07-22 · 0% stars, 30d

Stars over time

2026-03-16 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/ms609/tbrdist on 2026-07-19.

Continuous integration (2)

GitHub ActionsTravis CI

CRAN release process (1)

cran-comments.md

Research and citation (2)

codemeta.jsonZenodo

Coverage (1)

.covrignore

Show all practices

Git structural (2)

.gitattributesSubmodules

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (4)

ape Rdpack TreeDist TreeTools

LinkingTo (3)

BH Rcpp TreeTools

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

TreeDist

Code & Tests

People & History

People (2)

Maintainer (1)

Martin R. Smith

Author, Maintainer, Copyright holder

Authors (1)

Martin R. Smith

Author, Maintainer, Copyright holder

Martin R. Smith

Author, Maintainer, Copyright holder

Chris Whidden

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

2.0.1Latest
2026-07-21 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.0.0
2026-03-30 · diff ↗
1.0.3
2025-11-28 · diff ↗
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
1.0.2
2020-09-17 · diff ↗
1.0.1
2020-07-07 · diff ↗
1.0.0
2020-07-01
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-01
Total releases: 6 / 6 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.6.0
Download size: 52 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

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