phytools (version 0.2-50)

anc.Bayes: Bayesian ancestral character estimation

Description

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

Usage

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

Arguments

tree

an object of class "phylo".

x

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

ngen

a integer indicating the number of generations for the MCMC.

control

a list of control parameters containing the following elements: sig2: starting value for $\sigma^2$ (BM rate); a: starting for the state at the root node; y: starting values for the states at all internal nodes exclu

Value

• 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.

See Also

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

Examples

tree<-rtree(50)
	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