R Observatory: Metrics for phylocomr version 0.3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylocomr

0.3.4Package record

Interface to 'Phylocom'

0packages depend

3.5Kdownloads / year

43.3%test coverage

13/13flavors OK

Overview

About

Maintained by Luna Luisa Sanchez ReyesCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.3.4

Maintenance release to:
fix CRAN issues related to compiler warnings [-Warray-parameter=], [-Wstringop-overflow=], and [-Wstringop-truncation]

From NEWS.md in the release

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. 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-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). 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: 2.6 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.4

READMEYes · 1,122 wordsVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 0.3.4Citation fileNoWebsiteYes · pkgdown

Help pages: 12includes a package overview page
Examples that run: 50%5 run in a plain check · 5 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 80%
Help pages citing references: 8%

Vignettes (1)

Introduction to the phylocomr package

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #11,725 · ~10/day · ~294/mo

Releases R versions

Daily download trend is not available in this view yet.

34130 days

93290 days

3.5K1 year

Compare downloads with other packages →

Also on385 r2u6 autocran181 c2d4u

How downloads are counted

Repository

ropensci/phylocomr ↗Organization: ropensci

15Stars

7Forks

4Open issues

0Open PRs

7Releases

229Commits

8Commit identities

evolutionecologycommunity-ecologyrrstatsr-package

229 commits · Last activity 2023-04-21 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 89%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2024-10-08 · 152026-07-07 · 15

How these are measured

PracticesBeta

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

Checks run against github.com/ropensci/phylocomr on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (4)

Code of conduct (inherited from ropensci)Contributing guideIssue templatesPR template

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2017-10-17

Coverage (1)

Coverage reporting

Show all practicesHide 4 practices

Reproducibility and dev environment (1)

Makefile

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing phylocomr adds 11 packages (8 with compiled code, 4.0 MB of source tarballs). Heaviest: vctrs 1.0 MB, rlang 766 KB, cli 629 KB.

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.

How these are counted

Code & Tests

People & History

People (6)

Luna Luisa Sanchez Reyes

Author, Maintainer since 0.3.3 (2022) · added in 0.3.3

Scott Chamberlain

Author

Jeroen Ooms

Author

David Ackerly

Copyright holder

Author of libphylocom (see AUTHORS and COPYRIGHT files for details)

Steven Kembel

Copyright holder

Author of libphylocom (see AUTHORS and COPYRIGHT files for details)

Cam Webb

Copyright holder

Author of libphylocom (see AUTHORS and COPYRIGHT files for details)

Previously maintained by Scott Chamberlain (0.1.0 to 0.3.2).

Releases (8)

Pick two releases to compare their code metrics.

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

Show 3 earlier eventsHide 3 earlier events

0.1.2
record
2018-11-29 · diff ↗
0.1.0
record
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

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 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 phylocomr version 0.3.4 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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