Lposterior              Return a posterior of shift locations
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
QG.alpha                Calculates the alpha parameter from a QG model
QG.sig2                 Calculates the sigma^2 parameter from a QG
                        model
bayou-package           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
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
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
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
regime.plot             Adds visualization of regimes to a plot
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
