R Observatory: Metrics for TBRDist version 2.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TBRDist

2.0.2Package record

Rearrangement Distances Between Phylogenetic Trees

0packages dependsuggested by 1

5.2Kdownloads / year

55.6%test coverage

13/13flavors OK

Overview

About

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

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.

Changes in 2.0.2

Fix segfault in RSPRDist().

From NEWS.md in the release

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. 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-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). 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: 4.0 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-04
ERROR12 OK, 1 ERROR2026-08-29
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-17

Show 5 earlier changesHide 5 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
NOTE13 OK, 1 NOTE2026-04-22
ERROR12 OK, 1 NOTE, 1 ERROR2026-04-18
NOTE13 OK, 1 NOTE2026-03-31
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.2

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 2.0.2Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 6 (4 internal)
Examples that run: 100%2 run in a plain check
Exported functions with examples: 50%
Documented parameters: 52%
Return-value docs: 100%
Help pages citing references: 33% with Rdpack citation macros

Vignettes (1)

Using TBRDist HTML

How these are measured

Downloads

5.2K

CRAN downloads in the past year

Rank #6,708 · ~14/day · ~430/mo

Releases R versions

Daily download trend is not available in this view yet.

44630 days

1.3K90 days

5.2K1 year

Compare downloads with other packages →

Also on446 r2u2 autocran86 c2d4u

How downloads are counted

Repository

ms609/tbrdist ↗Account: ms609

1Stars

0Forks

4Open issues

0Open PRs

8Releases

177Commits

3Commit identities

rphylogeneticsphylogenetic-treesdistance-calculationalgorithmsbioinformatics

License file reads as GPL-3.0 · 177 commits · Last activity 2026-09-24 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2026-03-16 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/ms609/tbrdist on 2026-10-18.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

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 (2)

pkgdown

GitHub Pages site last deployed 2026-09-24

pkgdown site last built 2026-09-24

Coverage (1)

.covrignore

Show all practicesHide 4 practices

CRAN release process (1)

cran-comments.md

Research and citation (2)

codemeta.jsonZenodo

Lint, format, editor (1)

Positron

Git structural (2)

.gitattributesSubmodules

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2026-02-12
Pull request: opened by its own account
Posit Assistantfirst seen 2026-03-08
Seen in the repository: .positai/plans, .positai/settings.json
Claude Codefirst seen 2026-03-10
Seen in the repository: .claude
Named in .Rbuildignore: .claude
Commits: at least 3 crediting it in the message

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 5.52 commits · Sep 2026
Claude Opus 51 commit · Jul 2026

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

10 external dependencies (excludes base and recommended)

Installing TBRDist adds 40 packages (25 with compiled code, 47 MB of source tarballs). Heaviest: BH 14 MB, bslib 5.6 MB, promises 3.1 MB.

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

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

TreeDist

How these are counted

Code & Tests

People & History

People (2)

Martin R. Smith

ms609

Chris Whidden

Copyright holder

rspr, uspr, cwhidden

Releases (7)

Pick two releases to compare their code metrics.

2.0.2Latest
record
2026-09-02 · current release · diff ↗
2.0.1
record
2026-07-21 · diff ↗
R
R 4.6.0 released · 2026-04-24
2.0.0
record
2026-03-30 · diff ↗ ·
added 1 export
RSPRDist
1.0.3
record
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
record
2020-09-17 · diff ↗
1.0.1
record
2020-07-07 · diff ↗
1.0.0
record
2020-07-01
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-01
Total releases: 7 / 6 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.6.0
Download size: 391 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TBRDist")

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 TBRDist version 2.0.2 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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