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\name{markChanges}
\alias{markChanges}
\title{Add marked changes to a plotted tree with mapped discrete character}
\usage{
markChanges(tree, colors=NULL, cex=1, lwd=2, plot=TRUE)
}
\arguments{
\item{tree}{an object of class \code{"simmap"}.}
\item{colors}{a named vector of colors used to plot the stochastically mapped character on the tree.}
\item{cex}{expansion factor for line height.}
\item{lwd}{line width.}
\item{plot}{logical value indicating whether the changes should be plotted or not.}
}
\description{
This function adds the reconstructed changes to a plotted tree with a stochastically mapped discrete character.
}
\value{
This function returns (invisibly) a matrix containing the x & y coordinates of the marked changes.
}
\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{plotSimmap}}
}
\keyword{phylogenetics}
\keyword{plotting}
|
