R Observatory: Metrics for phylogram version 2.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylogram

2.1.0

Dendrograms for Evolutionary Analysis

5packages depend

18.9Kdownloads / year

95.9%test coverage

11/13checks pass

Overview

About

Maintained by Shaun WilkinsonFirst published 2017-06-125 releasesCRAN page ↗GitHub ↗

Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) doi:10.1093/bioinformatics/btg412), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.

Install

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

install.packages("phylogram", 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("ropensci/phylogram")

Development version from ropensci/phylogram. 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-phylogram

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-phylogram

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-phylogram

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 1.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.10

95.9%

Coverage · measured lines

82%

Documentation · exports

3

Dependencies · direct

Check history

NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 299 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 89%
References docs: 50%

Downloads

18.9K

CRAN downloads in the past year

Rank #3,667 · ~52/day · ~1.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

64930 days

2.6K90 days

18.9K1 year

Compare downloads with other packages →

Also on136 r2u20 autocran1.6K conda_forge76 c2d4u

Repository

GitHub ↗ ropensci/phylogram

12Stars

3Forks

3Open issues

0Open PRs

3Releases

86Commits

2Contributors

peer-reviewedrr-packagerstats

86 commits · Last activity 2019-12-09 · 0% stars, 30d

Stars over time

2024-04-18 · 112026-07-07 · 12

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/ropensci/phylogram on 2026-08-09.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

Research and citation (2)

codemeta.jsonJOSS paper

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

apemethodsstats

LinkingTo (0)

none

Suggests (4)

dendextend knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

4indirect

dclust didec insect kmer MoBPS

Code & Tests

People & History

People (2)

Maintainer (1)

Shaun Wilkinson

Author, Maintainer

Authors (2)

Shaun Wilkinson

Author, Maintainer

Simon Davy

Author · added in 2.1.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
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
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
2.1.0Latest
2018-06-25 · current release · diff ↗
R
R 3.5.0 released · 2018-04-23
2.0.1
2018-04-13 · diff ↗
2.0.0
2018-04-10 · diff ↗
1.0.1
2017-06-15 · diff ↗
1.0.0
2017-06-12
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-06-12
Total releases: 5 / 9 yrs
License: GPL-3 OSI
Download size: 636 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("phylogram")

The authors publish a JOSS paper, so they have said how they want this cited. Run citation() and use what it gives you.

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 phylogram version 2.1.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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