phytools (version 0.2-1)

ancThresh: Ancestral character estimation under the threshold model using Bayesian MCMC

Description

This function uses Bayesian MCMC to estimate ancestral states and thresholds for a discrete character under the threshold model from quantitative genetics (Felsenstein 2012).

Usage

ancThresh(tree, x, ngen=1000, sequence=NULL, method="mcmc", control=list())

Arguments

tree

phylogenetic tree.

x

named vector containing discrete character states.

ngen

number of generations to run the MCMC.

sequence

assumed ordering of the discrete character state. If not supplied then numerical/alphabetical order is assumed!

method

only method currently available is "mcmc".

control

list containing the following elements: sample, the sampling interval; propliabvariance of the proposal distribution for liabilities; propthresh variance on the proposal distribution for the thresholds; pr.anc<

Value

• This function returns as list with four elements:
• ace
  posterior probabilities for each character state at each internal node.
• mcmc
  full posterior sample for the states.
• par
  full posterior sample for the thresholds and likelihood.
• liab
  full posterior sample of the liabilities at internal and tip nodes.

See Also

anc.Bayes, threshBayes