Package: cauphy 1.0.3

Paul Bastide

cauphy: Trait Evolution on Phylogenies Using the Cauchy Process

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>.

Authors:Gilles Didier [aut, cph], Paul Bastide [aut, cre]

cauphy_1.0.3.tar.gz
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cauphy_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cauphy/json (API)

# Install 'cauphy' in R:

install.packages('cauphy', repos = c('https://gilles-didier.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gilles-didier/cauphy/issues

Pkgdown/docs site:https://gilles-didier.github.io

Datasets:

lizards - Greater Antillean Anolis lizard dataset

On CRAN:

3.70 score 1 stars 6 scripts 225 downloads 10 exports 20 dependencies

Last updated from:5d65b3d1b4. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	178
linux-devel-x86_64	OK	194
source / vignettes	OK	279
linux-release-arm64	OK	170
linux-release-x86_64	OK	185
macos-release-arm64	OK	122
macos-release-x86_64	OK	253
macos-oldrel-arm64	OK	108
macos-oldrel-x86_64	OK	372
windows-devel	OK	162
windows-release	OK	159
windows-oldrel	OK	173
wasm-release	OK	128

Exports:ancestral cauphylm compute_vcov fitCauchy increment logDensityTipsCauchy plot_asr posteriorDensityAncestral posteriorDensityIncrement rTraitCauchy

Dependencies:ape codetools DEoptimR digest doParallel foreach future future.apply globals HDInterval iterators lattice listenv nlme nloptr parallelly phylolm pracma Rcpp robustbase

Example Analysis

Rendered fromlizards.Rmdusingknitr::rmarkdown

Last update: 2023-09-11
Started: 2023-03-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Posterior density of a node	ancestral ancestral.cauphyfit ancestral.cauphylm
Phylogenetic Regression using a Cauchy Process	cauphylm
Compute Approximated Variance Covariance Matrix	compute_vcov
Model fitting for a Cauchy Process	fitCauchy
Highest (Posterior) Density Interval	hdi.ancestralCauchy
Posterior density of an increment	increment increment.cauphyfit increment.cauphylm
Greater Antillean Anolis lizard dataset	lizards
Log Density of a Cauchy Process	logDensityTipsCauchy
Plot Ancestral States Reconstructions	plot_asr
Plot for class 'ancestralCauchy'	plot.ancestralCauchy
Plot for class 'profile.cauphyfit'	plot.profile.cauphyfit
Posterior density of a node	posteriorDensityAncestral
Posterior density of an increment	posteriorDensityIncrement
Generic Methods for S3 class 'cauphyfit'.	AIC.cauphyfit AIC.logLik.cauphyfit coef.cauphyfit confint.cauphyfit logLik.cauphyfit print.cauphyfit vcov.cauphyfit
Generic Methods for S3 class 'cauphylm'.	AIC.cauphylm AIC.logLik.cauphylm coef.cauphylm confint.cauphylm logLik.cauphylm predict.cauphylm print.cauphylm vcov.cauphylm
Method for Profiling 'cauphyfit' Objects	profile.cauphyfit
Cauchy Trait Simulation	rTraitCauchy