Running a MCMC | Input data format | Setting up the joint MCMC estimation | Choosing parameters for the MCMC analyses | Checking for convergence | Computing summary statistics from the posterior distribution | Extract the correlation from the model | Using overlap tests | Extracting the posterior samples of rate matrices

General comments | Structure of the starting point list | Order of the regimes in the start point object | Worked example

Priors on the root value | Uniform prior on the root | Informative prior on the root | Priors on the evolutionary rate matrix | Uniformative priors on the evolutionary correlation | Using informative prior distributions on the structure of evolutionary correlation among traits | Final considerations

Probabilistic PCA using do3PCA | Non-phylogenetic PCA | 3PCA: probabilistic phylogenetic PCA | PIC-PCA: Probabilistic PCA of independent contrasts