anc.Bayes {phytools}R Documentation

Bayesian ancestral character estimation


This function uses Bayesian MCMC to sample from the posterior distribution for the states at internal nodes in the tree.


anc.Bayes(tree, x, ngen=10000, control=list())



an object of class "phylo".


a vector of tip values for species; names(x) should be the species names.


a integer indicating the number of generations for the MCMC.


a list of control parameters containing the following elements: sig2: starting value for σ^2 (BM rate); a: starting for the state at the root node; y: starting values for the states at all internal nodes excluding the root (should be labeled with node numbers); pr.mean: means for the prior distributions in the following order - sig2, a, y, note that the prior probability distribution is exponential for sig2 and normal for a and y; pr.var: variances on the prior distributions, same order as pr.mean (but the variance is not used for sig2); prop: variances on the normal proposal distributions in the same order as pr.mean; sample: sample frequency from the MCMC.


A matrix with number of rows ngen/sample+1 containing the posterior sample and likelihoods. Matrix columns are labeled either sig2 or by the node number of the internal node.


Liam Revell


Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

See Also

ace, anc.ML, anc.trend, evol.rate.mcmc, fastAnc


x<-fastBM(tree,sig2=2) # simulate using fastBM
X<-anc.Bayes(tree,x,ngen=10000) # sample ancestral states
estimates<-colMeans(X[21:nrow(X),]) # get estimates, excluding burnin

[Package phytools version 0.4-60 Index]