Man pages for Caetanods/ratematrix
Bayesian Estimation of the Evolutionary Rate Matrix

anolesData and phylogenetic tree for Anolis lizards
centrarchidaeData and phylogenetic tree for Centrarchidae fishes
checkConvergencePerforms convergence tests
computeESSCompute the ESS for the MCMC samples
continueMCMCContinue unfinished MCMC chain or add more generations
estimateTimeMCMCTime estimate to complete a MCMC chain
extractCorrelationExtract the posterior distribution of evolutionary...
fastSimmapFast implementation of stochastic mapping.
likelihoodFunctionLikelihood function for the multivariate Brownian motion...
logAnalyzerMake analysis of the log file of the MCMC chain
makePriorGenerate prior distributions for the multivariate Brownian...
mergePosteriorMerge posterior distributions
mergeSimmapMerge two or more regimes of a 'simmap' tree
plotPriorPlot the prior distribution used in the MCMC analysis
plotRatematrixPlot the distribution of evolutionary rate matrices
plotRootValuePlot posterior distribution of root values for the traits
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.
ratematrixratematrix.
ratematrixJointMCMCEstimate the evolutionary rate matrix together with the...
ratematrixMCMCEstimate the evolutionary rate matrix using Markov-chain...
readMCMCRead the MCMC output files
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 Oct. 31, 2018, 5:42 a.m.