Trait Evolution on Phylogenies Using the Cauchy Process

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Documentation for package ‘cauphy’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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'.