# Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

## Documentation for package ‘bayou’ version 2.3.2

- DESCRIPTION file

## Help Pages

bayou-package | Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
bayou | Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
bayou.checkModel | Function for checking parameter lists, prior and models are consistent and error-free
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.
bayou2OUwie | Converts bayou data into OUwie format
cdpois | Conditional Poisson distribution
combine.chains | Combine mcmc chains
dataSim | Simulates data from bayou models
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
gelman.R | Calculate Gelman's R statistic
identifyBranches | Identify shifts on branches of a phylogenetic tree
load.bayou | Loads a bayou object
Lposterior | Return a posterior of shift locations
make.powerposteriorFn | Makes a power posterior function in bayou
make.prior | Make a prior function for bayou
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.
makeTransparent | Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)
model.OU | Bayou Models
OU.lik | Function for calculating likelihood of an OU model in bayou using pruning algorithm or matrix inversion
OU.repar | Calculates the alpha and sigma^2 from a parameter list with supplied phylogenetic half-life and stationary variance
OUphenogram | Experimental phenogram plotting function for set of model of model parameters
OUwie2bayou | Converts OUwie data into bayou format
parmap.W | Calculate the weight matrix of a set of regimes on a phylogeny
pars2simmap | Convert a bayou parameter list into a simmap formatted phylogeny
phalfcauchy | Half cauchy distribution taken from the R package LaplacesDemon (Hall, 2012).
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
plotBayoupars | Plot parameter list as a simmap tree
plotBranchHeatMap | A function to plot a heatmap of reconstructed parameter values on the branches of the tree
plotOUtreesim | A function to visualize a multi-optimum OU process evolving on a phylogeny
plotRegimes | Function to plot the regimes from a simmap tree
plotShiftSummaries | A function to plot a list produced by 'shiftSummaries'
plotSimmap.mcmc | Plot a phylogenetic tree with posterior probabilities from a bayouMCMC chain (function adapted from phytools' plotSimmap)
print.bayouFit | S3 method for printing bayouFit objects
print.bayouMCMC | S3 method for printing bayouMCMC objects
print.priorFn | S3 method for printing priorFn objects
print.refFn | S3 method for printing refFn objects
print.ssMCMC | S3 method for printing ssMCMC objects
priorSim | Simulates parameters from bayou models
pull.pars | Utility function for retrieving parameters from an MCMC chain
QG.alpha | Calculates the alpha parameter from a QG model
QG.sig2 | Calculates the sigma^2 parameter from a QG model
qhalfcauchy | Half cauchy distribution taken from the R package LaplacesDemon (Hall, 2012).
rdpois | Conditional Poisson distribution
regime.plot | Adds visualization of regimes to a plot
rhalfcauchy | Half cauchy distribution taken from the R package LaplacesDemon (Hall, 2012).
rloc | Probability density function for the location of the shift along the branch
rsb | Probability density functions for bayou
set.burnin | Set the burnin proportion for bayouMCMC objects
shiftSummaries | A function for summarizing the state of a model after a shift
simmapW | Calculate the weight matrix of a set of regimes on a phylogeny
summary.bayouMCMC | S3 method for summarizing bayouMCMC objects