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| bayou-package | bayou-package |
| bayou | bayou-package |
| bayou.lik | Function for calculating likelihood of an OU model in bayou using the threepoint algorithm |
| bayou.mcmc | Bayesian sampling of multi-optima OU models |
| 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 |
| makeTransparent | Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe) |
| 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 |
| overparameterize.startingPoint | Generate an overparameterized starting point for the MCMC |
| 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 |
| plotRegimes | Function to plot the regimes from a simmap tree |
| 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.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 |
| simmap.W | Calculate the weight matrix of a set of regimes on a phylogeny |
| steppingstone | Stepping stone estimation of the marginal likelihood for a bayou model |
| summary.bayouMCMC | S3 method for summarizing bayouMCMC objects |