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]

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cauphy.pdf |cauphy.html✨
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 site:https://gilles-didier.github.io

Datasets:
  • lizards - Greater Antillean Anolis lizard dataset

On CRAN:

Conda:

3.70 score 1 stars 4 scripts 251 downloads 10 exports 20 dependencies

Last updated 5 months agofrom:5d65b3d1b4. Checks:11 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 16 2025
R-4.5-win-x86_64OKFeb 16 2025
R-4.5-mac-x86_64OKFeb 16 2025
R-4.5-mac-aarch64OKFeb 16 2025
R-4.5-linux-x86_64OKFeb 16 2025
R-4.4-win-x86_64OKFeb 16 2025
R-4.4-mac-x86_64OKFeb 16 2025
R-4.4-mac-aarch64OKFeb 16 2025
R-4.3-win-x86_64OKFeb 16 2025
R-4.3-mac-x86_64OKFeb 16 2025
R-4.3-mac-aarch64OKFeb 16 2025

Exports:ancestralcauphylmcompute_vcovfitCauchyincrementlogDensityTipsCauchyplot_asrposteriorDensityAncestralposteriorDensityIncrementrTraitCauchy

Dependencies:apecodetoolsDEoptimRdigestdoParallelforeachfuturefuture.applyglobalsHDIntervaliteratorslatticelistenvnlmenloptrparallellyphylolmpracmaRcpprobustbase

Example Analysis

Paul Bastide

Rendered fromlizards.Rmdusingknitr::rmarkdownon Feb 16 2025.

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