R Observatory: Metrics for phyloTop version 2.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phyloTop

2.1.3

Calculating Topological Properties of Phylogenies

1packages depend

5.9Kdownloads / year

37.2%test coverage

13/13checks pass

Overview

About

Maintained by Michelle KendallFirst published 2013-07-309 releasesCRAN page ↗GitHub ↗

Tools for calculating and viewing topological properties of phylogenetic trees.

Install

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

install.packages("phyloTop", 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("MichelleKendall/phyloTop")

Development version from MichelleKendall/phyloTop. 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-phylotop

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-phyloTop

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-phyloTop

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

Health

CRAN checks

13OK

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.06

37.2%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 634 wordsVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

5.9K

CRAN downloads in the past year

Rank #4,435 · ~16/day · ~488/mo

Releases R versions

Daily download trend is not available in this view yet.

24330 days

1.8K90 days

5.9K1 year

Compare downloads with other packages →

Also on111 r2u86 c2d4u

Repository

GitHub ↗ michellekendall/phylotop

1Stars

0Forks

0Open issues

0Open PRs

3Releases

107Commits

5Contributors

107 commits · Last activity 2025-08-28

Stars over time

2016-09-12 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/michellekendall/phylotop on 2026-08-16.

Continuous integration (1)

Travis CI

Docs source (1)

README.Rmd

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.2.2ape

Imports (4)

igraphmethodsNHPoisson phylobase

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

treestats

Code & Tests

People & History

People (3)

Maintainer (1)

Michelle Kendall

Author, Maintainer · added in 2.0.0

Authors (3)

Michelle Kendall

Author, Maintainer · added in 2.0.0

Michael Boyd

Author

Caroline Colijn

Author · added in 1.1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.1.3Latest
2025-08-27 · current release · 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
2.1.2
2023-01-24 · diff ↗
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
2.1.1
2018-02-21 · diff ↗
2.1.0
2017-10-10 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.0.1
2017-04-04 · diff ↗
R
R 3.3.0 released · 2016-05-03

Show 8 earlier events

2.0.0
2016-04-19 · diff ↗
archivedRemoved from CRAN
2015-10-29
check problems were not corrected despite reminders
R
R 3.2.0 released · 2015-04-16
1.1.1
2014-05-14 · diff ↗
1.1
2014-05-11 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.0
2013-07-30
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-07-30
Total releases: 9 / 13 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.2.2
Download size: 50 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("phyloTop")

Format

Kendall, M., Boyd, M., & Colijn, C. (2025). phyloTop: Calculating Topological Properties of Phylogenies (Version 2.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.phyloTop

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 phyloTop version 2.1.3 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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