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bayou (version 2.3.1)

Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Description

Fits and simulates multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using Bayesian reversible-jump methods. See Uyeda and Harmon (2014) .

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Version

Install

install.packages('bayou')

Monthly Downloads

24

Version

2.3.1

License

GPL (>= 2)

Maintainer

Josef Uyeda

Last Published

June 10th, 2025

Functions in bayou (2.3.1)

parmap.W

Calculate the weight matrix of a set of regimes on a phylogeny
plotRegimes

Function to plot the regimes from a simmap tree
load.bayou

Loads a bayou object
plotBranchHeatMap

A function to plot a heatmap of reconstructed parameter values on the branches of the tree
make.powerposteriorFn

Makes a power posterior function in bayou
plotOUtreesim

A function to visualize a multi-optimum OU process evolving on a phylogeny
make.prior

Make a prior function for bayou
print.ssMCMC

S3 method for printing ssMCMC objects
print.refFn

S3 method for printing refFn objects
priorSim

Simulates parameters from bayou models
pull.pars

Utility function for retrieving parameters from an MCMC chain
plotShiftSummaries

A function to plot a list produced by shiftSummaries
dhalfcauchy

Half cauchy distribution taken from the R package LaplacesDemon (Hall, 2012).
dloc

Probability density function for the location of the shift along the branch
makeTransparent

Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)
make.refFn

Make a reference function in bayou
makeBayouModel

This function makes a bayou model object that can be used for customized allometric regression models.
summary.bayouMCMC

S3 method for summarizing bayouMCMC objects
plotBayoupars

Plot parameter list as a simmap tree
plot.ssMCMC

S3 method for plotting ssMCMC objects
model.OU

Bayou Models
phenogram.density

Plot a pheongram with the posterior density for optima values
simmapW

Calculate the weight matrix of a set of regimes on a phylogeny
pars2simmap

Convert a bayou parameter list into a simmap formatted phylogeny
shiftSummaries

A function for summarizing the state of a model after a shift
plot.bayouMCMC

S3 method for plotting bayouMCMC objects
print.bayouFit

S3 method for printing bayouFit objects
set.burnin

Set the burnin proportion for bayouMCMC objects
print.bayouMCMC

S3 method for printing bayouMCMC objects
plotSimmap.mcmc

Plot a phylogenetic tree with posterior probabilities from a bayouMCMC chain (function adapted from phytools' plotSimmap)
regime.plot

Adds visualization of regimes to a plot
print.priorFn

S3 method for printing priorFn objects
OU.lik

Function for calculating likelihood of an OU model in bayou using pruning algorithm or matrix inversion
bayou.checkModel

Function for checking parameter lists, prior and models are consistent and error-free
OUphenogram

Experimental phenogram plotting function for set of model of model parameters
bayou-package

Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
bayou-deprecated

Deprecated functions in package bayou.
OUwie2bayou

Converts OUwie data into bayou format
OU.repar

Calculates the alpha and sigma^2 from a parameter list with supplied phylogenetic half-life and stationary variance
Lposterior

Return a posterior of shift locations
QG.sig2

Calculates the sigma^2 parameter from a QG model
QG.alpha

Calculates the alpha parameter from a QG model
combine.chains

Combine mcmc chains
bayou2OUwie

Converts bayou data into OUwie format
gelman.R

Calculate Gelman's R statistic
dataSim

Simulates data from bayou models
dsb

Probability density functions for bayou
cdpois

Conditional Poisson distribution
bayou.lik

Function for calculating likelihood of an OU model in bayou using the threepoint algorithm
bayou.makeMCMC

Builds a bayouMCMCFn object that can run MCMC and stepping stone analyses.
identifyBranches

Identify shifts on branches of a phylogenetic tree