Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

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Documentation for package ‘bayou’ version 2.3.1

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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