Reading SIMMAPv1.0 trees from file.

Input

tree<-read.simmap(file="",text,format="phylip")

"tree" is a phylogenetic tree or trees in modified "phylo" or "multiPhylo" format;
"file" is a string corresponding to a text file (or path to text file);
"text" is an optional text string with the tree;
"format" is the tree input format, can be "phylip" or "nexus".

Output

read.simmap() outputs an R "phylo" or "multiPhylo" object with:

"$maps" a list of named vectors containing the times spent in each state on each branch, in the order in which they occur; "$mapped.edge" a matrix containing the total time spent in each state along each edge of the tree.

Citation

Function written by Liam J. Revell 2011. Uses limited code from "read.nexus" written by Paradis et al. (2004) as part of the "ape" package.