Bayesian Estimation of the Evolutionary Rate Matrix

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Documentation for package ‘ratematrix’ version 1.2.4

• 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