This function computes the fraction of a stochastic character mapping that is shared between two differently mapped trees. In map.overlap it will compute a single quantity giving the overall similarity of the maps, consequently this measure only makes sense of some or all of the states are shared between the two mapped tress. In Map.Overlap what is computed instead is a matrix in which the rows correspond to the states observed in tree1 and the columns give the states for tree2, with the numerical values of the matrix showing the total overlap between each pair of mapped states on the two trees.
map.overlap(tree1, tree2, tol=1e-6, ...)
Map.Overlap(tree1, tree2, tol=1e-06, standardize=TRUE, ...)A numerical value on the interval (0, 1), for map.overlap; or a matrix whose elements should sum to 1.0 (Map.Overlap).
an object of class "simmap".
an object of class "simmap".
an optional tolerance value.
for Map.Overlap, a logical value indicating whether or not to standardize overlap by dividing by the summed branch length of the tree.
optional arguments, such as check.equal, a logical value indicating whether or not to check if tree1 and tree2 match in underlying topology and branch lengths (they should). This value is TRUE by default, but can be set to FALSE if tree1 and tree2 are known to be equal to speed up calculation.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
make.simmap, read.simmap