Man pages for Caetanods/ratematrix
Bayesian estimation of the evolutionary rate matrix

checkConvergencePerforms convergence tests
continueMCMCContinue unfinished MCMC chain or add more generations
estimateTimeMCMCTime estimate to complete a MCMC chain
likelihoodFunctionLikelihood function for the multivariate Brownian motion...
logAnalyzerMake analysis of the log file of the MCMC chain
makePriorGenerate prior distributions for the multivariate Brownian...
makeStartSample a starting point for the MCMC.
mergePosteriorMerge posterior distributions
mergeSimmapMerge two or more regimes of a 'simmap' tree
mvLogLikMultivariate Brownian motion log likelihood
plotPriorPlot the prior distribution used in the MCMC analysis
plotRatematrixPlot distribution of evolutionary rate matrices
plotRootValuePlot the posterior distribution of the root values for the...
print.ratematrix_multi_chainPrint method for the "ratematrix_multi_chain" class.
print.ratematrix_multi_mcmcPrint method for the "ratematrix_multi_mcmc" class.
print.ratematrix_prior_functionPrint method for the "ratematrix_prior_function" class.
print.ratematrix_prior_samplePrint method for the "ratematrix_prior_sample" class.
print.ratematrix_single_chainPrint method for the "ratematrix_single_chain" class.
print.ratematrix_single_mcmcPrint method for the "ratematrix_single_mcmc" class.
ratematrixMCMCEstimate the evolutionary rate matrix using Markov-chain...
readMCMCRead the output files from the MCMC
samplePriorTake samples from the prior distribution
simRatematrixSimulates multivariate trait evolution using a Brownian...
testRatematrixTest for difference between evolutionary rate matrix...
Caetanods/ratematrix documentation built on Aug. 26, 2017, 4:09 p.m.