threshBayes(tree, X, types=NULL, ngen=1000, control=list())"phylo".X should be species names.ncol(X) containing the data types for each column of X, for instance c("discrete","continuous").sample, the sampling interval for the MCMC; propvar, a vector containing (in this order) proposal variances for the two rates (if the type is "discrete" this will be ignored), the two ancestral states, and the correlation; propliab, a single proposal variance for the liabilities; pr.mean, a vector for the mean of the prior probability distributions for each parameter, in the same order as propvar; pr.liab, currently ignored; pr.var, a vector with variances for the prior densities for each parameter, in the same order as pr.mean - note that for the rates we use an exponential distribution so the first two means are currently ignored; and pr.vliab currently ignored.par a matrix containing the posterior sample for the model parameters (evolutionary rates, ancestral states, and correlation); liab a matrix containing the posterior sample of the liabilities. For continuous characters, the liabilities are treated as known and so the posterior samples are just the observed values.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
Revell, L. J. (2014) Ancestral character estimation under the threshold model from quantitative genetics. Evolution, bold68, 743-759.
anc.Bayes, bmPlot, evol.rate.mcmc