cauphy1.0.3 package

Trait Evolution on Phylogenies Using the Cauchy Process

ancestral

Posterior density of a node

cauphylm

Phylogenetic Regression using a Cauchy Process

check_tree

Check Binary Tree object

checkDuplicates

Check For Duplicated Entries

checkTraitTree

Check Matrix Parameter

compute_vcov

Compute Approximated Variance Covariance Matrix

do_optim

NLOPT optimization

find_modes

Find modes of a distribution

fit_function

Maximum Likelihood estimator for a Cauchy model

fitCauchy.internal

Maximum Likelihood estimator for a Cauchy model

fitCauchy

Model fitting for a Cauchy Process

getBounds

Get bounds

getBoundsCauchy

Get bound for a Cauchy process

getBoundsLambda

Get bounds for a Cauchy Lambda

getParamNames

Get parameter names

getStartingValues

Get starting values

getStartingValuesCauchy

Get starting values for a Cauchy

getStartingValuesLambda

Get starting values for a Cauchy Lambda

hdi.ancestralCauchy

Highest (Posterior) Density Interval

increment

Posterior density of an increment

initDispersionParameter

Initialization of the dispersion parameter.

initLambdaParameter

Initialization of the lambda parameter.

initPositionParameter

Initialization of the position parameter.

logDensityTipsCauchy

Log Density of a Cauchy Process

maxLambda

Maximum lambda value

minusLikelihoodFixedRoot_lm

Minus Likelihood function for a Cauchy model

minusLikelihoodFixedRoot_mu

Minus Likelihood function for a Cauchy model

minusLikelihoodFixedRoot

Minus Likelihood function for a Cauchy model

minusLikelihoodRandomRoot

Minus Likelihood function for a Cauchy model

minusLikelihoodREML

Minus REML function for a Cauchy model

plot_asr

Plot Ancestral States Reconstructions

plot.ancestralCauchy

Plot for class ancestralCauchy

plot.invisible

Invisible Plotting

plot.profile.cauphyfit

Plot for class profile.cauphyfit

posteriorDensityAncestral

Posterior density of a node

posteriorDensityIncrement

Posterior density of an increment

printRTreeTest

Print a tree

profile.cauphyfit

Method for Profiling cauphyfit Objects

reroottip

Re root tree at a tip

rTraitCauchy

Cauchy Trait Simulation

safe_get

Safely get element of a named vector

simulateTipsCauchy

Simulate using the Cauchy Process

transformBranchLengths

Transform branch lengths

vcov.cauphyfit

Generic Methods for S3 class cauphyfit.

vcov.cauphylm

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>.

  • Maintainer: Paul Bastide
  • License: GPL (>= 3)
  • Last published: 2024-10-01