R: Bayesian ancestral character estimation

anc.Bayes {phytools}

R Documentation

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 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.

Examples

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

[Package phytools version 0.4-60 Index]