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\name{write.simmap}
\alias{write.simmap}
\title{Write a stochastic character mapped tree to file}
\usage{
write.simmap(tree, file=NULL, append=FALSE, map.order=NULL, quiet=FALSE,
format="phylip", version=1.0)
}
\arguments{
\item{tree}{an object of class \code{"simmap"} or \code{"multiSimmap"}.}
\item{file}{an optional filename.}
\item{append}{a logical value indicating whether to append to file.}
\item{map.order}{a optional value specifying whether to write the map in left-to-right or right-to-left order. Acceptable values are "left-to-right" or "right-to-left" or some abbreviation of either. If not provided, \code{write.simmap} will use \code{attr(tree,"map.order")} if available.}
\item{quiet}{logical value indicating whether or not to print a warning message when \code{map.order} is neither specified by a function argument or as an attribute of \code{tree}.}
\item{format}{file format for output.}
\item{version}{version of SIMMAP. Note that the options are \code{1.0} and \code{1.5}. \code{version=1.5} is generally recommended because in this format the tree can also be parsed by typical tree readers, but absent its mapped trait.}
}
\description{
Writes one or multiple stochastic character mapped trees to file in several formats (following Bollback, 2006).
}
\value{
A file.
}
\references{
Bollback, J. P. (2006) Stochastic character mapping of discrete traits on phylogenies. \emph{BMC Bioinformatics}, \bold{7}, 88.
Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback (2003) Stochastic mapping of morphological characters. \emph{Systematic Biology}, \bold{52}, 131-138.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). \emph{PeerJ}, \bold{12}, e16505.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
\code{\link{make.simmap}}, \code{\link{read.simmap}}, \code{\link{plotSimmap}}
}
\keyword{phylogenetics}
\keyword{comparative method}
\keyword{input/output}
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