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
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Generic Methods for S3 class cauphylm
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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>.