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cauphy

The Cauchy Process to model trait evolution on phylogenies.

Installation

Stable version on the CRAN

The development version can be installed from GitHub using the remotes package:

install.packages("remotes")
remotes::install_github(repo = "gilles-didier/cauphy", ref = "dev")

Documentation

See package documentation (references and vignettes) here: https://gilles-didier.github.io/cauphy/.

(Built with pkgdown).

Reference

Bastide, P. and Didier, G. (2023), The Cauchy Process on Phylogenies: a Tractable Model for Pulsed Evolution. Systematic Biology. doi:10.1093/sysbio/syad053. [bioRxiv].

Pronunciation

Pronounce cauphy like coffee, with a French accent: /ko.fi/.

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Version

Install

install.packages('cauphy')

Monthly Downloads

215

Version

1.0.3

License

GPL (>= 3)

Maintainer

Paul Bastide

Last Published

October 1st, 2024

Functions in cauphy (1.0.3)

initDispersionParameter

Initialization of the dispersion parameter.
fit_function

Maximum Likelihood estimator for a Cauchy model
increment

Posterior density of an increment
minusLikelihoodFixedRoot_mu

Minus Likelihood function for a Cauchy model
hdi.ancestralCauchy

Highest (Posterior) Density Interval
posteriorDensityIncrement

Posterior density of an increment
minusLikelihoodREML

Minus REML function for a Cauchy model
initLambdaParameter

Initialization of the lambda parameter.
logDensityTipsCauchy

Log Density of a Cauchy Process
printRTreeTest

Print a tree
cauphylm

Phylogenetic Regression using a Cauchy Process
print.cauphyfit

Generic Methods for S3 class cauphyfit.
getParamNames

Get parameter names
getStartingValues

Get starting values
getStartingValuesLambda

Get starting values for a Cauchy Lambda
getStartingValuesCauchy

Get starting values for a Cauchy
print.cauphylm

Generic Methods for S3 class cauphylm.
minusLikelihoodFixedRoot

Minus Likelihood function for a Cauchy model
getBounds

Get bounds
profile.cauphyfit

Method for Profiling cauphyfit Objects
rTraitCauchy

Cauchy Trait Simulation
simulateTipsCauchy

Simulate using the Cauchy Process
posteriorDensityAncestral

Posterior density of a node
minusLikelihoodFixedRoot_lm

Minus Likelihood function for a Cauchy model
maxLambda

Maximum lambda value
plot_asr

Plot Ancestral States Reconstructions
transformBranchLengths

Transform branch lengths
plot.profile.cauphyfit

Plot for class profile.cauphyfit
initPositionParameter

Initialization of the position parameter.
plot.invisible

Invisible Plotting
lizards

Greater Antillean Anolis lizard dataset
minusLikelihoodRandomRoot

Minus Likelihood function for a Cauchy model
plot.ancestralCauchy

Plot for class ancestralCauchy
reroottip

Re root tree at a tip
safe_get

Safely get element of a named vector
checkDuplicates

Check For Duplicated Entries
fitCauchy

Model fitting for a Cauchy Process
ancestral

Posterior density of a node
compute_vcov

Compute Approximated Variance Covariance Matrix
checkTraitTree

Check Matrix Parameter
do_optim

NLOPT optimization
check_tree

Check Binary Tree object
fitCauchy.internal

Maximum Likelihood estimator for a Cauchy model
find_modes

Find modes of a distribution
getBoundsCauchy

Get bound for a Cauchy process
getBoundsLambda

Get bounds for a Cauchy Lambda