phytools: map.overlap – R documentation

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map.overlap

Proportional overlap between two mapped character histories on a tree

Description

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.

Usage

map.overlap(tree1, tree2, tol=1e-6, ...)
Map.Overlap(tree1, tree2, tol=1e-06, standardize=TRUE, ...)

Arguments

`tree1`	an object of class `"simmap"`.
`tree2`	an object of class `"simmap"`.
`tol`	an optional tolerance value.
`standardize`	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.

Value

A numerical value on the interval (0, 1), for map.overlap; or a matrix whose elements should sum to 1.0 (Map.Overlap).

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.