Man pages for Caetanods/ratematrix
Bayesian Estimation of the Evolutionary Rate Matrix
| 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... |
| fastSimmap | Fast implementation of stochastic mapping. |
| getStartPointFromPosterior | Extract sample from MCMC to use as starting point for another... |
| likelihoodFunction | Likelihood function for the multivariate Brownian motion... |
| logAnalyzer | Make analysis of the log file of the MCMC chain |
| makePrior | Generate prior distributions for the multivariate Brownian... |
| 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... |
| ratematrixMCMC | Estimate the evolutionary rate matrix using Markov-chain... |
| 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... |
| testRatematrix | Test for difference between evolutionary rate matrix... |
