Bayesian Estimation of the Evolutionary Rate Matrix
Performs convergence tests
Compute the ESS for the MCMC samples
Continue unfinished MCMC chain or add more generations
Time estimate to complete a MCMC chain
Extract the posterior distribution of evolutionary correlation
Fast implementation of stochastic mapping.
Extract sample from MCMC to use as starting point for another MCMC
Likelihood function for the multivariate Brownian motion model
Make analysis of the log file of the MCMC chain
Generate prior distributions for the multivariate Brownian motion mode...
Merge posterior distributions
Merge two or more regimes of a 'simmap' tree
Plot the prior distribution used in the MCMC analysis
Plot the distribution of evolutionary rate matrices
Plot posterior distribution of root values for the traits
Print method for the "ratematrix_multi_chain" class.
Print method for the "ratematrix_multi_mcmc" class.
Print method for the "ratematrix_prior_function" class.
Print method for the "ratematrix_prior_sample" class.
Print method for the "ratematrix_single_chain" class.
Print method for the "ratematrix_single_mcmc" class.
ratematrix.
Estimate the evolutionary rate matrix together with the regimes using ...
Estimate the evolutionary rate matrix using Markov-chain Monte Carlo
Read output files of MCMC for the predictor regimes.
Read the MCMC output files
Take samples from the prior distribution
Simulates multivariate trait evolution using a Brownian motion model
Test for difference between evolutionary rate matrix estimates
The Evolutionary Rate Matrix is a variance-covariance matrix which describes both the rates of trait evolution and the evolutionary correlation among multiple traits. This package has functions to estimate these parameters using Bayesian MCMC. It is possible to test if the pattern of evolutionary correlations among traits has changed between predictive regimes painted along the branches of the phylogenetic tree. Regimes can be created a priori or estimated as part of the MCMC under a joint estimation approach. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.