Fitting the Cauchy Process

Functions to fit the Cauchy process.

fitCauchy()

Model fitting for a Cauchy Process

print(<cauphyfit>) vcov(<cauphyfit>) logLik(<cauphyfit>) AIC(<logLik.cauphyfit>) AIC(<cauphyfit>) confint(<cauphyfit>) coef(<cauphyfit>)

Generic Methods for S3 class cauphyfit.

profile(<cauphyfit>)

Method for Profiling cauphyfit Objects

plot(<profile.cauphyfit>)

Plot for class profile.cauphyfit

compute_vcov()

Compute Approximated Variance Covariance Matrix

Ancestral Reconstruction

Functions to perform ancestral state and increment reconstruction.

ancestral()

Posterior density of a node

increment()

Posterior density of an increment

hdi(<ancestralCauchy>)

Highest (Posterior) Density Interval

plot(<ancestralCauchy>)

Plot for class ancestralCauchy

plot_asr()

Plot Ancestral States Reconstructions

Simulation

Function to simulate a Cauchy process.

rTraitCauchy()

Cauchy Trait Simulation

Datasets

Example datasets

lizards

Greater Antillean Anolis lizard dataset

Cauchy Phylogenetic Regression

Functions to fit a Cauchy Process phylogenetic regression.

cauphylm()

Phylogenetic Regression using a Cauchy Process

print(<cauphylm>) vcov(<cauphylm>) logLik(<cauphylm>) AIC(<logLik.cauphylm>) AIC(<cauphylm>) predict(<cauphylm>) confint(<cauphylm>) coef(<cauphylm>)

Generic Methods for S3 class cauphylm.

Densities

Functions to compute likelihood and posterior densities.

logDensityTipsCauchy()

Log Density of a Cauchy Process

posteriorDensityAncestral()

Posterior density of a node

posteriorDensityIncrement()

Posterior density of an increment