# Bayesian Estimation of the Evolutionary Rate Matrix

## Documentation for package ‘ratematrix’ version 1.2.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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