R Observatory: Metrics for Quartet version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Quartet

1.3.0

Comparison of Phylogenetic Trees Using Quartet and Split Measures

3packages depend

14.4Kdownloads / year

91.7%test coverage

8/13checks pass

Overview

About

Maintained by Martin R. SmithFirst published 2019-01-1612 releasesCRAN page ↗GitHub ↗

Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics, 7, 309-343 doi:10.1016/0196-8858(86)90038-2, and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics, 30, 2079–2080 doi:10.1093/bioinformatics/btu157 for pairs of binary trees.

Install

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

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

Development version from ms609/Quartet. 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-quartet

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-Quartet

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-Quartet

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

Health

CRAN checks

5NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 10.4 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 1.74

91.7%

Coverage · measured lines

100%

Documentation · exports

6

Dependencies · direct

Check history

NOTE2026-07-16
10 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

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

Documentation

READMEYes · 435 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 66%
Return-value docs: 92%
References docs: 46%

Downloads

14.4K

CRAN downloads in the past year

Rank #3,679 · ~39/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

58930 days

2.5K90 days

14.4K1 year

Compare downloads with other packages →

Also on409 r2u21 autocran37 c2d4u

Repository

GitHub ↗ ms609/quartet

18Stars

5Forks

3Open issues

1Open PRs

12Releases

955Commits

9Contributors

phylogeneticsbioinformaticsresearch-toolquartettreecranphylogenetic-treesquartet-distance

955 commits · Last activity 2026-06-19 · +5.9% stars, 30d

Stars over time

2026-07-14 · 172026-08-18 · 18

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/ms609/quartet on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

.covrignore

Git structural (1)

.gitattributes

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-03-18

claude

Most recent: claude on 2026-03-18

Evidence

agents-md: on 2026-03-18 · evidence D
claude: on 2026-03-18 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0TreeTools

Imports (5)

ape PlotTools Rdpack Ternary viridisLite

LinkingTo (1)

Rcpp

Suggests (8)

bookdown knitr phangorn Rcpp rmarkdown testthat usethis vdiffr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

CongreveLamsdell2016 TreeDist TreeSearch

Code & Tests

Datasets

People & History

People (8)

Maintainer (1)

Martin R. Smith

Author, Maintainer, Copyright holder

Authors (1)

Martin R. Smith

Author, Maintainer, Copyright holder

Copyright holders (1)

Martin R. Smith

Author, Maintainer, Copyright holder

Other (7)

ant

ant

ant

ant

Christian N. S. Pedersen

ant

Andreas Sand

ant

Gerth Stølting Brodal

ant

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.3.0Latest
2026-03-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.2.7
2024-10-31 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.6
2024-02-09 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.5
2022-07-08 · diff ↗
1.2.4
2022-05-02 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.2.2
2020-12-09 · diff ↗
1.2.0
2020-10-21 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.0
2020-01-28 · diff ↗
1.0.3
2019-12-30 · diff ↗

Show 7 earlier events

unarchivedReturned to CRAN
2019-12-30
archivedRemoved from CRAN
2019-12-01
installation warnings were not addressed despite reminders
R
R 3.6.0 released · 2019-04-26
1.0.2
2019-03-06 · diff ↗
1.0.1
2019-01-22 · diff ↗
1.0.0
2019-01-16
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-01-16
Total releases: 12 / 7 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 0.8 KB / 1 file
Download size: 694 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Quartet")

Format

Smith, M. R., Fagerberg, R., Holt, M. K., Johansen, J., Mailund, T., Pedersen, C. N. S., Sand, A., & Stølting Brodal, G. (2026). Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures (Version 1.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.Quartet

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 Quartet version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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