R: Trait Evolution on Phylogenies Using the Cauchy Process

# Trait Evolution on Phylogenies Using the Cauchy Process

## Documentation for package ‘cauphy’ version 1.0.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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