R Observatory: Metrics for phyloTop version 2.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phyloTop

2.1.3Package record

Calculating Topological Properties of Phylogenies

0packages dependsuggested by 1

4.9Kdownloads / year

37.2%test coverage

13/13flavors OK

Overview

About

Maintained by Michelle KendallCRAN page ↗GitHub ↗Website ↗

Tools for calculating and viewing topological properties of phylogenetic trees.

Changes in 2.1.3

Patch to update the format of cross-references to other packages in Rd files as required by new CRAN standards. Change of maintainer's email address.

From NEWS.md in the release

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. 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-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). 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: 2.2 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.3

READMEYes · 634 wordsVignettesNoNEWSYes · 33% structured · mentions 2.1.3Citation fileNoWebsiteYes · pkgdown

Help pages: 27 (2 internal)
Examples that run: 100%25 run in a plain check
Exported functions with examples: 93%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #9,165 · ~13/day · ~405/mo

Releases R versions

Daily download trend is not available in this view yet.

27430 days

1.1K90 days

4.9K1 year

Compare downloads with other packages →

Also on85 r2u4 autocran139 c2d4u

How downloads are counted

Repository

michellekendall/phylotop ↗Account: MichelleKendall

1Stars

0Forks

0Open issues

0Open PRs

3Releases

107Commits

5Commit identities

107 commits · Last activity 2025-08-26

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 30
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2016-09-12 · 12026-07-07 · 1

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/michellekendall/phylotop on 2026-10-21.

Continuous integration (1)

Travis CI (config file)

Governance and community (1)

Code of conduct

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2025-08-26

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing phyloTop adds 86 packages (50 with compiled code, 75 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

Depends (2)

R >= 3.2.2ape

Imports (4)

igraphmethodsNHPoisson phylobase

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

treestats

How these are counted

Code & Tests

People & History

People (3)

Michelle Kendall

Author, Maintainer since 2.0.0 (2016) · added in 2.0.0

Michael Boyd

Author

Caroline Colijn

Author · added in 1.1

Previously maintained by Michael Boyd (1.0 to 1.1.1).

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.1.3Latest
record
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
record
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
record
2018-02-21 · diff ↗
2.1.0
record
2017-10-10 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.0.1
record
2017-04-04 · diff ↗
R
R 3.3.0 released · 2016-05-03

Show 8 earlier eventsHide 8 earlier events

2.0.0
record
2016-04-19 · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 27 exports
ILnumber, avgLadder, cherries, colless.phylo, configShow, getDepths, getLabGenealogy, ladderShow, ladderSizes, makeEpiRecord, makePhyloTree, maxHeight, nConfig, nodeDepth, nodeDepthFrac, nodeImb, nodeImbFrac, phyloCheck, phyloTop, pitchforks, rtree4, sackin.phylo, splitTop, stairs, subtreeShow, treeImb, widths
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
record
2014-05-14 · diff ↗
1.1
record
2014-05-11 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.0
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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