R Observatory: Metrics for cauphy version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

cauphy

1.0.3

Trait Evolution on Phylogenies Using the Cauchy Process

0packages depend

2.4Kdownloads / year

92.6%test coverage

13/13checks pass

Overview

About

Maintained by Paul BastideFirst published 2023-09-124 releasesCRAN page ↗GitHub ↗

The Cauchy Process can model pulsed continuous trait evolution on phylogenies. The likelihood is tractable, and is used for parameter inference and ancestral trait reconstruction. See Bastide and Didier (2023) doi:10.1093/sysbio/syad053.

Install

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

install.packages("cauphy", 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("gilles-didier/cauphy")

Development version from gilles-didier/cauphy. 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-cauphy

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-cauphy

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-cauphy

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

Health

CRAN checks

13OK

Slowest check: 5.4 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.64

92.6%

Coverage · measured lines

100%

Documentation · exports

9

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 · 85 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 92%
Return-value docs: 100%
References docs: 17%

Downloads

2.4K

CRAN downloads in the past year

Rank #15,558 · ~7/day · ~202/mo

Releases R versions

Daily download trend is not available in this view yet.

19130 days

69590 days

2.4K1 year

Compare downloads with other packages →

Also on394 r2u33 autocran

Repository

GitHub ↗ gilles-didier/cauphy

1Stars

1Forks

0Open issues

0Open PRs

4Releases

70Commits

2Contributors

License GPL-3.0 · 70 commits · Last activity 2025-05-15

Stars over time

2023-09-01 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/gilles-didier/cauphy on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5ape

Imports (8)

methodsrobustbase phylolm nloptr pracma foreach doParallel HDInterval

LinkingTo (0)

none

Suggests (6)

covr knitr rmarkdown spelling geiger testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Paul Bastide

Author, Maintainer

Authors (2)

Paul Bastide

Author, Maintainer

Gilles Didier

Author, Copyright holder

Copyright holders (1)

Gilles Didier

Author, Copyright holder

Package Timeline

4 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
1.0.3Latest
2024-10-01 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.2
2023-11-29 · diff ↗
1.0.1
2023-09-19 · diff ↗
1.0.0
2023-09-12
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-12
Total releases: 4 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5
Bundled data: 4.3 KB / 1 file
Download size: 357 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("cauphy")

Format

Bastide, P., & Didier, G. (2024). cauphy: Trait Evolution on Phylogenies Using the Cauchy Process (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.cauphy

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 cauphy version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-08-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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