R Observatory: Metrics for cauphy version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

cauphy

1.0.3Package record

Trait Evolution on Phylogenies Using the Cauchy Process

0packages depend

2.6Kdownloads / year

92.6%test coverage

13/13flavors OK

Overview

About

Maintained by Paul BastideCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.0.3

Make 'predict.cauphylm' compatible with 'predict.phylolm' version 2.6.5.
Fix CRAN check results issues with r-devel.

From NEWS.md in the release

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. 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-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). 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: 5.0 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 1.0.3

READMEYes · 85 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.3Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 46 (29 internal)
Examples that run: 100%16 run in a plain check
Exported functions with examples: 100%
Documented parameters: 92%
Return-value docs: 100%
Help pages citing references: 17%

Vignettes (1)

Example Analysis HTML

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #15,851 · ~7/day · ~219/mo

Releases R versions

Daily download trend is not available in this view yet.

26730 days

78690 days

2.6K1 year

Compare downloads with other packages →

Also on357 r2u11 autocran

How downloads are counted

Repository

gilles-didier/cauphy ↗Account: gilles-didier

1Stars

1Forks

0Open issues

0Open PRs

4Releases

70Commits

2Commit identities

License file reads as GPL-3.0 · 70 commits · Last activity 2024-10-01

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 30

Stars over time

2023-09-01 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/gilles-didier/cauphy 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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2024-10-01 · The repository has a site deploy workflow

pkgdown site last built 2024-10-01

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing cauphy adds 17 packages (7 with compiled code, 9.9 MB of source tarballs). Heaviest: robustbase 2.2 MB, nloptr 2.1 MB, Rcpp 1.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Paul Bastide

Author, Maintainer since 1.0.0 (2023)

Gilles Didier

Author, Copyright holder

Releases (4)

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

Cite

Cite this package

Run in R for the authors' entry:

citation("cauphy")

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

It points to 10.1093/sysbio/syad053.

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 v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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