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\name{phylomorphospace3d}
\alias{phylomorphospace3d}
\title{Creates tree-dimensional phylomorphospace plot}
\usage{
phylomorphospace3d(tree, X, A=NULL, label=TRUE, control=list(),
method=c("dynamic","static"), ...)
}
\arguments{
\item{tree}{a phylogenetic tree in \code{"phylo"} format.}
\item{X}{an \code{n} x 3 matrix of tip values for two characters in \code{n} species.}
\item{A}{an optional \code{m} x 3 matrix (for \code{m} nodes) of values for two taits at internal nodes in the tree - if not supplied, these values will be estimated using \code{\link{anc.ML}}.}
\item{label}{logical value indicating whether to print tip labels next to terminal nodes in the plot (presently doesn't do anything, but labels can be dropped using \code{control}).}
\item{control}{a list containing the following optional control parameters: \code{spin}: a logical value indicating whether to animate the plot when created; \code{axes}: a logical indicating whether to plot the axes; \code{box}: a logical value indicating whether to plot in box; \code{simple.axes}: logical value indicating whether to replace \code{box} and \code{axes} with simpler axes; \code{lwd}: line widths; \code{ftype}: font type ("off" turns off labels altogether); \code{col.edge} a vector of colors of length \code{nrow(tree$edge)}.}
\item{method}{a string either \code{"dynamic"} for a dynamic (animated) plot created using \code{rgl}; or \code{"static"} for a flat 3D plot created using \code{scatterplot3d} and base graphics. The latter has the advantage of being very easy to export in standard format.}
\item{...}{optional arguments to be passed to \code{scatterplot3d}. Most options not available. \code{angle} is an important option that does work here.}
}
\description{
This function creates a phylomorphospace plot for three characters using the 3D visualization package, 'rgl'.
}
\value{
This function creates a three dimensional phylomorphospace plot. The function returns a function from \code{spin3d} (for \code{method="dynamic"}); or a series of functions from \code{\link{scatterplot3d}} (for \code{method="static"}).
}
\references{
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). \emph{Methods Ecol. Evol.}, \bold{3}, 217-223.
Sidlauskas, B. (2008) Continuous and arrested morphological diversification in sister clades of characiform fishes: A phylomorphospace approach. \emph{Evolution}, \bold{62}, 3135-3156.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\examples{
tree<-pbtree(n=26,tip.label=LETTERS)
X<-fastBM(tree,nsim=3)
\dontrun{
phylomorphospace3d(tree,X,control=list(spin=FALSE))
}
phylomorphospace3d(tree,X,method="static")
}
\seealso{
\code{\link{fancyTree}}, \code{\link{phenogram}}, \code{\link{phylomorphospace}}
}
\keyword{phylogenetics}
\keyword{comparative method}
\keyword{plotting}
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