anoles                  Data and phylogenetic tree for Anolis lizards
centrarchidae           Data and phylogenetic tree for Centrarchidae
                        fishes
checkConvergence        Performs convergence tests
computeESS              Compute the ESS for the MCMC samples
continueMCMC            Continue unfinished MCMC chain or add more
                        generations
estimateTimeMCMC        Time estimate to complete a MCMC chain
extractCorrelation      Extract the posterior distribution of
                        evolutionary correlation
fastSimmap              Fast implementation of stochastic mapping.
getStartPointFromPosterior
                        Extract sample from MCMC to use as starting
                        point for another MCMC
likelihoodFunction      Likelihood function for the multivariate
                        Brownian motion model
logAnalyzer             Make analysis of the log file of the MCMC chain
makePrior               Generate prior distributions for the
                        multivariate Brownian motion model
mergePosterior          Merge posterior distributions
mergeSimmap             Merge two or more regimes of a 'simmap' tree
plotPrior               Plot the prior distribution used in the MCMC
                        analysis
plotRatematrix          Plot the distribution of evolutionary rate
                        matrices
plotRootValue           Plot posterior distribution of root values for
                        the traits
print.ratematrix_multi_chain
                        Print method for the "ratematrix_multi_chain"
                        class.
print.ratematrix_multi_mcmc
                        Print method for the "ratematrix_multi_mcmc"
                        class.
print.ratematrix_prior_function
                        Print method for the
                        "ratematrix_prior_function" class.
print.ratematrix_prior_sample
                        Print method for the "ratematrix_prior_sample"
                        class.
print.ratematrix_single_chain
                        Print method for the "ratematrix_single_chain"
                        class.
print.ratematrix_single_mcmc
                        Print method for the "ratematrix_single_mcmc"
                        class.
ratematrix              ratematrix.
ratematrixJointMCMC     Estimate the evolutionary rate matrix together
                        with the regimes using Markov-chain Monte Carlo
ratematrixMCMC          Estimate the evolutionary rate matrix using
                        Markov-chain Monte Carlo
readMCMC                Read the MCMC output files
readMCMC_Mk             Read output files of MCMC for the predictor
                        regimes.
samplePrior             Take samples from the prior distribution
simRatematrix           Simulates multivariate trait evolution using a
                        Brownian motion model
testRatematrix          Test for difference between evolutionary rate
                        matrix estimates
