\name{map.overlap}
\alias{map.overlap}
\alias{Map.Overlap}
\title{Proportional overlap between two mapped character histories on a tree}
\usage{
map.overlap(tree1, tree2, tol=1e-6, ...)
Map.Overlap(tree1, tree2, tol=1e-06, standardize=TRUE, ...)
}
\arguments{
	\item{tree1}{an object of class \code{"simmap"}.}
	\item{tree2}{an object of class \code{"simmap"}.}
	\item{tol}{an optional tolerance value.}
	\item{standardize}{for \code{Map.Overlap}, a logical value indicating whether or not to standardize overlap by dividing by the summed branch length of the tree.}
	\item{...}{optional arguments, such as \code{check.equal}, a logical value indicating whether or not to check if \code{tree1} and \code{tree2} match in underlying topology and branch lengths (they should). This value is \code{TRUE} by default, but can be set to \code{FALSE} if \code{tree1} and \code{tree2} are known to be equal to speed up calculation.}
}
\description{
	This function computes the fraction of a stochastic character mapping that is shared between two differently mapped trees. In \code{map.overlap} it will compute a single quantitying 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 \code{Map.Overlap} is computed in which the rows are states observed in \code{tree1} and columns give the states for \code{tree2}.
}
\value{
	A numerical value on the interval 0-1, for \code{map.overlap}; or a matrix (\code{Map.Overlap}).
}
\references{
	Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). \emph{Methods Ecol. Evol.}, \bold{3}, 217-223.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
	\code{\link{make.simmap}}, \code{\link{read.simmap}}
}
\keyword{phylogenetics}
\keyword{comparative method}