This function computes the relative frequencies of character state changes along edges from a sample of stochastically mapped character histories. This function assumes that all trees in the sample differ only in their mapped histories & not at all in topology or branch lengths. Note that it only asks whether the starting and ending states of the edge differ in a particular way, and thus ignores multiple-hits along a single edge.
an object of class
The object that is returned is a matrix with the state changes & the relative frequency of each state change. Rows are in the order of the matrix
edge for any of the mapped trees.
Liam Revell email@example.com
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.