rphylo

0.1.1

Phylogenetic Analysis with Dependent Discrete Models

0packages depend

301downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Vivian G. LiFirst published 2026-06-231 releasesCRAN page ↗

Implementation of dependent discrete models (with reversible jump MCMC) derived from 'BayesTraits' V5.0.3 https://github.com/AndrewPMeade/BayesTraits-Release/tree/Release. Original software copyright Andrew Meade and contributors, distributed under GPL-3. Modifications for this package by Vivian G. Li <liguo.vivian@gmail.com>. The following articles should be referenced when using this package: Pagel, M., A. Meade and D. Barker (2004) "Bayesian estimation of ancestral character states on phylogenies" doi:10.1080/10635150490522232; Pagel, M. (1994) "Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters" doi:10.1098/rspb.1994.0006; Pagel, M. and A. Meade (2006) "Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo" doi:10.1086/503444.

Install

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

install.packages("rphylo", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-rphylo

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-rphylo

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-rphylo

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

Health

CRAN checks

13OK

Slowest check: 2.3 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-24
8 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 234 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 100%
References docs: 0%

Downloads

301

CRAN downloads in the past year

Rank #24,144 · ~1/day · ~25/mo

Releases R versions

Daily download trend is not available in this view yet.

30130 days

30190 days

3011 year

Compare downloads with other packages →

Also on2 r2u6 autocran

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (4)

ape phangorn expmstats

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,269 (82%)Rd 284 (18%)

Code characteristics

Object systems

S31

Cyclomatic complexity: 3.0 median / 64 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

31 3 exported

Complexity

5.1 avg / 64 max

Call network

31 nodes / 29 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
tdata	data.frame	20 × 2	–
tdata2	data.frame	60 × 2	–

People & History

People (3)

Maintainer (1)

Vivian G. Li

Author, Maintainer

Authors (1)

Vivian G. Li

Author, Maintainer

Contributors (2)

Andrew Meade

Contributor

Mark Pagel

Contributor

Package Timeline

1 release. R releases are shown for context.

0.1.1Latest
2026-06-23 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-23
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 506 KB / 4 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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