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bayou (version 2.3.2)

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

10

Version

2.3.2

License

GPL (>= 2)

Maintainer

Josef Uyeda

Last Published

February 13th, 2026

Functions in bayou (2.3.2)

cdpois

Conditional Poisson distribution
bayou2OUwie

Converts bayou data into OUwie format
combine.chains

Combine mcmc chains
makeTransparent

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

Bayou Models
make.prior

Make a prior function for bayou
make.powerposteriorFn

Makes a power posterior function in bayou
phenogram.density

Plot a pheongram with the posterior density for optima values
plot.bayouMCMC

S3 method for plotting bayouMCMC objects
plot.ssMCMC

S3 method for plotting ssMCMC objects
load.bayou

Loads a bayou object
plotBayoupars

Plot parameter list as a simmap tree
dataSim

Simulates data from bayou models
plotOUtreesim

A function to visualize a multi-optimum OU process evolving on a phylogeny
plotBranchHeatMap

A function to plot a heatmap of reconstructed parameter values on the branches of the tree
shiftSummaries

A function for summarizing the state of a model after a shift
identifyBranches

Identify shifts on branches of a phylogenetic tree
priorSim

Simulates parameters from bayou models
pull.pars

Utility function for retrieving parameters from an MCMC chain
print.priorFn

S3 method for printing priorFn objects
print.bayouMCMC

S3 method for printing bayouMCMC objects
pars2simmap

Convert a bayou parameter list into a simmap formatted phylogeny
parmap.W

Calculate the weight matrix of a set of regimes on a phylogeny
print.bayouFit

S3 method for printing bayouFit objects
print.refFn

S3 method for printing refFn objects
plotSimmap.mcmc

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

S3 method for printing ssMCMC objects
simmapW

Calculate the weight matrix of a set of regimes on a phylogeny
summary.bayouMCMC

S3 method for summarizing bayouMCMC objects
makeBayouModel

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

A function to plot a list produced by shiftSummaries
set.burnin

Set the burnin proportion for bayouMCMC objects
make.refFn

Make a reference function in bayou
regime.plot

Adds visualization of regimes to a plot
plotRegimes

Function to plot the regimes from a simmap tree
QG.sig2

Calculates the sigma^2 parameter from a QG model
bayou.checkModel

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

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

Deprecated functions in package bayou.
OUwie2bayou

Converts OUwie data into bayou format
gelman.R

Calculate Gelman's R statistic
QG.alpha

Calculates the alpha parameter from a QG model
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
dsb

Probability density functions for bayou
OU.lik

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

Return a posterior of shift locations
OU.repar

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

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

Experimental phenogram plotting function for set of model of model parameters
bayou.makeMCMC

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