make.simmap: Simulate stochastic character map on a phylogenetic tree

Description

This function fits a continuous-time reversible Markov model for the evolution of x (using ace) and then simulates stochastic character histories using that model and the tip states on the tree.

Usage

make.simmap(tree,x,model="SYM",nsim=1)

Arguments

tree

a phylogenetic tree as an object of class "phylo".

a vector containing the tip states for a discretely valued character.

model

a character string containing the model - options as in ace.

nsim

number of simulations.

Value

a modified phylogenetic tree of class "phylo" (or a modified "multiPhylo" object, for nsim > 1) with the following additional elements:
mapsa list of named vectors containing the times spent in each state on each branch, in the order in which they occur.
mapped.edgea matrix containing the total time spent in each state along each edge of the tree.

Details

Samples trees from the conditional posterior distribution - conditioning on the maximum likelihood transition matrix given our model.

References

Paradis, E., J. Claude, and K. Strimmer. 2004. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289--290. Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Systematic Biology, 52, 131-138. Bollback, J. P. 2006. Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.