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
cauphy_1.0.3.zip(r-4.7)cauphy_1.0.3.zip(r-4.6)cauphy_1.0.3.zip(r-4.5)
cauphy_1.0.3.tgz(r-4.6-x86_64)cauphy_1.0.3.tgz(r-4.6-arm64)cauphy_1.0.3.tgz(r-4.5-x86_64)cauphy_1.0.3.tgz(r-4.5-arm64)
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cauphy_1.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
cauphy/json (API)
NEWS

# 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:

Conda:

3.70 score 1 stars 4 scripts 216 downloads 10 exports 20 dependencies

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

TargetResultTimeFilesSyslog
linux-devel-arm64OK174
linux-devel-x86_64OK200
source / vignettesOK240
linux-release-arm64OK219
linux-release-x86_64OK189
macos-release-arm64OK184
macos-release-x86_64OK379
macos-oldrel-arm64OK212
macos-oldrel-x86_64OK373
windows-develOK188
windows-releaseOK192
windows-oldrelOK147
wasm-releaseOK125

Exports:ancestralcauphylmcompute_vcovfitCauchyincrementlogDensityTipsCauchyplot_asrposteriorDensityAncestralposteriorDensityIncrementrTraitCauchy

Dependencies:apecodetoolsDEoptimRdigestdoParallelforeachfuturefuture.applyglobalsHDIntervaliteratorslatticelistenvnlmenloptrparallellyphylolmpracmaRcpprobustbase

Example Analysis

Paul Bastide

Rendered fromlizards.Rmdusingknitr::rmarkdownon May 18 2026.

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

Readme and manuals

Help Manual

Help pageTopics
Posterior density of a nodeancestral ancestral.cauphyfit ancestral.cauphylm
Phylogenetic Regression using a Cauchy Processcauphylm
Compute Approximated Variance Covariance Matrixcompute_vcov
Model fitting for a Cauchy ProcessfitCauchy
Highest (Posterior) Density Intervalhdi.ancestralCauchy
Posterior density of an incrementincrement increment.cauphyfit increment.cauphylm
Greater Antillean Anolis lizard datasetlizards
Log Density of a Cauchy ProcesslogDensityTipsCauchy
Plot Ancestral States Reconstructionsplot_asr
Plot for class 'ancestralCauchy'plot.ancestralCauchy
Plot for class 'profile.cauphyfit'plot.profile.cauphyfit
Posterior density of a nodeposteriorDensityAncestral
Posterior density of an incrementposteriorDensityIncrement
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' Objectsprofile.cauphyfit
Cauchy Trait SimulationrTraitCauchy