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

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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 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.

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.

Author(s)

Liam Revell liam.revell@umb.edu

References

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

Examples

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tree<-pbtree(n=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

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