R Observatory: Metrics for phylocomr version 0.3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylocomr

0.3.4

Interface to 'Phylocom'

0packages depend

3.7Kdownloads / year

43.3%test coverage

13/13checks pass

Overview

About

Maintained by Luna Luisa Sanchez ReyesFirst published 2018-11-198 releasesCRAN page ↗GitHub ↗

Interface to 'Phylocom' (https://phylodiversity.net/phylocom/), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.

Install

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

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

Development version from ropensci/phylocomr. 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-phylocomr

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-phylocomr

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-phylocomr

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

Health

CRAN checks

13OK

Slowest check: 2.6 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.66

43.3%

Coverage · measured lines

100%

Documentation · exports

2

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

Documentation

READMEYes · 1,122 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 50%
Documented parameters: 100%
Return-value docs: 80%
References docs: 8%

Downloads

3.7K

CRAN downloads in the past year

Rank #12,684 · ~10/day · ~306/mo

Releases R versions

Daily download trend is not available in this view yet.

19830 days

78790 days

3.7K1 year

Compare downloads with other packages →

Also on407 r2u28 autocran81 c2d4u

Repository

GitHub ↗ ropensci/phylocomr

15Stars

7Forks

4Open issues

0Open PRs

7Releases

229Commits

8Contributors

evolutionecologycommunity-ecologyrrstatsr-package

229 commits · Last activity 2023-04-21

Stars over time

2024-10-08 · 152026-07-07 · 15

Repository practices

Upstream repositoryBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/ropensci/phylocomr on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

tibble sys

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown ape

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Luna Luisa Sanchez Reyes

Author, Maintainer · added in 0.3.3

Authors (3)

Luna Luisa Sanchez Reyes

Author, Maintainer · added in 0.3.3

Scott Chamberlain

Author

Jeroen Ooms

Author

Copyright holders (3)

David Ackerly

Copyright holder

Steven Kembel

Copyright holder

Cam Webb

Copyright holder

Package Timeline

8 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
0.3.4Latest
2023-04-22 · current release · diff ↗
unarchivedReturned to CRAN
2023-04-22
R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2023-02-24
issues were not corrected in time
0.3.3
2022-12-05 · 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
0.3.2
2019-12-20 · diff ↗
0.3.0
2019-11-25 · diff ↗
0.2.0
2019-11-13 · diff ↗
0.1.4
2019-07-24 · diff ↗
R
R 3.6.0 released · 2019-04-26

Show 3 earlier events

0.1.2
2018-11-29 · diff ↗
0.1.0
2018-11-19
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-19
Total releases: 8 / 8 yrs
License: BSD_2_clause + file LICENSE OSI
Download size: 831 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phylocomr")

Format

Sanchez Reyes, L. L., Ackerly, D., Chamberlain, S., Kembel, S., Ooms, J., & Webb, C. (2023). phylocomr: Interface to 'Phylocom' (Version 0.3.4) [Computer software]. https://doi.org/10.32614/CRAN.package.phylocomr

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 phylocomr version 0.3.4 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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