Trait Evolution on Phylogenies Using the Cauchy Process
Posterior density of a node
Phylogenetic Regression using a Cauchy Process
Check Binary Tree object
Check For Duplicated Entries
Check Matrix Parameter
Compute Approximated Variance Covariance Matrix
NLOPT optimization
Find modes of a distribution
Maximum Likelihood estimator for a Cauchy model
Maximum Likelihood estimator for a Cauchy model
Model fitting for a Cauchy Process
Get bounds
Get bound for a Cauchy process
Get bounds for a Cauchy Lambda
Get parameter names
Get starting values
Get starting values for a Cauchy
Get starting values for a Cauchy Lambda
Highest (Posterior) Density Interval
Posterior density of an increment
Initialization of the dispersion parameter.
Initialization of the lambda parameter.
Initialization of the position parameter.
Log Density of a Cauchy Process
Maximum lambda value
Minus Likelihood function for a Cauchy model
Minus Likelihood function for a Cauchy model
Minus Likelihood function for a Cauchy model
Minus Likelihood function for a Cauchy model
Minus REML function for a Cauchy model
Plot Ancestral States Reconstructions
Plot for class ancestralCauchy
Invisible Plotting
Plot for class profile.cauphyfit
Posterior density of a node
Posterior density of an increment
Print a tree
Method for Profiling cauphyfit Objects
Re root tree at a tip
Cauchy Trait Simulation
Safely get element of a named vector
Simulate using the Cauchy Process
Transform branch lengths
Generic Methods for S3 class cauphyfit.
Generic Methods for S3 class cauphylm.
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>.