R Observatory: Metrics for phylosem version 1.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylosem

1.1.4Package record

Phylogenetic Structural Equation Model

0packages depend

2.8Kdownloads / year

89.3%test coverage

10/13flavors OK

Overview

About

Maintained by James ThorsonCRAN page ↗GitHub ↗Website ↗Issues ↗

Applies phylogenetic comparative methods (PCM) and phylogenetic trait imputation using structural equation models (SEM), extending methods from Thorson et al. (2023) doi:10.1111/2041-210X.14076. This implementation includes a minimal set of features, to allow users to easily read all of the documentation and source code. PCM using SEM includes phylogenetic linear models and structural equation models as nested submodels, but also allows imputation of missing values. Features and comparison with other packages are described in Thorson and van der Bijl (2023) doi:10.1111/jeb.14234.

Changes in 1.1.4

removing checkDepPackageVersion(dep_pkg="Matrix", this_pkg="TMB") from .onLoad() as requested by K. Kristensen

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("phylosem", 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("James-Thorson-NOAA/phylosem")

Development version from James-Thorson-NOAA/phylosem. 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-phylosem

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

Health

CRAN checks

3NOTE10OK

Check messages

NOTEre-building of vignette outputsr-oldrel-macos-x86_64, r-release-macos-arm64, r-release-macos-x86_64

Note: skipping ‘fisheries.Rmd’ due to unavailable dependencies:
  'phylosignal'

CRAN check page ↗

Slowest check: 14.0 min · r-oldrel-windows-x86_64

Status changes

NOTE10 OK, 3 NOTE2026-06-09
ERROR9 OK, 3 NOTE, 1 ERROR2026-06-07
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.4

READMEYes · 160 wordsVignettesYes · 4 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 1.1.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 19
Examples that run: 100%1 run in a plain check
Exported functions with examples: 10%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 5%

Vignettes (4)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #12,913 · ~8/day · ~232/mo

Releases R versions

Daily download trend is not available in this view yet.

31030 days

86590 days

2.8K1 year

Compare downloads with other packages →

Also on345 r2u

How downloads are counted

Repository

james-thorson-noaa/phylosem ↗Account: James-Thorson-NOAA

1Stars

0Forks

0Open issues

0Open PRs

7Releases

106Commits

2Commit identities

106 commits · Last activity 2026-09-24 · 0% stars, 30d · Discussions: 9 posts

Responsiveness

How these are sampled

PRs merged (all time): 44%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-11-21 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/james-thorson-noaa/phylosem on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-02 · The repository has a site deploy workflow

pkgdown site last built 2026-09-24

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 1 practice

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing phylosem adds 92 packages (55 with compiled code, 77 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB. 1 more not on CRAN is not measured.

Depends (2)

R >= 4.0.0TMB

Imports (5)

sem ape phylobase phylopathmethods

LinkingTo (2)

RcppEigen TMB

Suggests (12)

semPlot TreeTools Rphylopars phylolm fishtree phyr knitr rmarkdown ggplot2 testthat phylosignal adephylo

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

James Thorson

Author, Maintainer since 1.0.0 (2023)

Wouter van der Bijl

Contributor

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
1.1.4Latest
record
2024-04-02 · current release · diff ↗ ·
removed 1 export
checkDepPackageVersion
1.1.3
record
2024-02-01 · diff ↗ ·
removed 2 exports
TMBAIC, fit_tmb

added 1 export
phylosem_control
1.1.2
record
2023-12-20 · diff ↗ ·
added 1 export
checkDepPackageVersion
1.1.1
record
2023-11-26 · diff ↗
1.1.0
record
2023-10-06 · diff ↗
1.0.2
record
2023-09-22 · diff ↗
1.0.1
record
2023-09-19 · diff ↗
1.0.0
record
2023-08-25
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-08-25
Total releases: 8 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 6.6 KB / 1 file
Download size: 313 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("phylosem")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/2041-210x.14076, 10.1111/jeb.14234.

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 phylosem version 1.1.4 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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