| bayou2OUwie | Converts bayou data into OUwie format |
| bayou.checkModel | Function for checking parameter lists, prior and models are... |
| bayou-deprecated | Deprecated functions in package bayou. |
| bayou.lik | Function for calculating likelihood of an OU model in bayou... |
| bayou.makeMCMC | Revision of bayou.mcmc that only makes the mcmc loop... |
| bayou-package | Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies |
| cdpois | Conditional Poisson distribution |
| combine.chains | Combine mcmc chains |
| dataSim | Simulates data from bayou models |
| dhalfcauchy | Half cauchy distribution taken from the R package... |
| dloc | Probability density function for the location of the shift... |
| 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 |
| makeBayouModel | This function makes a bayou model object that can be used for... |
| 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 |
| makeTransparent | Make a color transparent (Taken from an answer on... |
| model.OU | Bayou Models |
| OU.lik | Function for calculating likelihood of an OU model in bayou... |
| OUphenogram | Experimental phenogram plotting function for set of model of... |
| OU.repar | Calculates the alpha and sigma^2 from a parameter list with... |
| OUwie2bayou | Converts OUwie data into bayou format |
| parmap.W | Calculate the weight matrix of a set of regimes on a... |
| pars2simmap | Convert a bayou parameter list into a simmap formatted... |
| phenogram.density | Plot a pheongram with the posterior density for optima values |
| plot.bayouMCMC | S3 method for plotting bayouMCMC objects |
| plotBayoupars | Plot parameter list as a simmap tree |
| plotBranchHeatMap | A function to plot a heatmap of reconstructed parameter... |
| plotOUtreesim | A function to visualize a multi-optimum OU process evolving... |
| 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... |
| plot.ssMCMC | S3 method for plotting ssMCMC objects |
| 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 |
| 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 |
| simmap.W | Calculate the weight matrix of a set of regimes on a... |
| steppingstone | Stepping stone estimation of the marginal likelihood for a... |
| summary.bayouMCMC | S3 method for summarizing bayouMCMC objects |
