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.

`ace`, `anc.ML`, `anc.trend`, `evol.rate.mcmc`, `fastAnc`
```tree<-pbtree(n=50)