removing evolve.phylo + bug fix in as.phylo.hclust

[ape.git] / man / plot.ancestral.Rd

diff --git a/man/plot.ancestral.Rd b/man/plot.ancestral.Rd
deleted file mode 100644 (file)
index 4279432..0000000
--- a/man/plot.ancestral.Rd
+++ /dev/null
@@ -1,43 +0,0 @@
-\name{plot.ancestral}
-\alias{plot.ancestral}
-\title{Plot Ancestral Character Values on a Tree}
-\description{
-  Plot a phylogenetic tree with edge colors picked according to the
-  corresponding node ancestral character value.
-}
-\usage{
-\method{plot}{ancestral}(x, which = names(x$node.character), n.col = 10,
-col.fun = function(n) rainbow(n, start = 0.4, end = 0),
-plot.node.values = FALSE,
-ask = prod(par("mfcol")) < length(which) && dev.interactive(),
-...)
-}
-\arguments{
-  \item{x}{An object of class 'ancestral'.}
-  \item{which}{Which characters to plot. Can be a vecotr of names, or a
-    vector of indices.}
-  \item{n.col}{The number of colors to use in the gradient.}
-  \item{col.fun}{the color function to use.}
-  \item{plot.node.values}{Should character values used as node labels?}
-  \item{ask}{Ask before each plot?}
-  \item{\dots}{Further parameters to pass to the plot.phylo function.}
-}
-\details{
-  This function produces one plot by selected ancestral character. It
-  uses the plot.phylo function with particular arguments to display edge
-  colors according to ancestral character values.
-}
-\author{Julien Dutheil \email{Julien.Dutheil@univ-montp2.fr}}
-\seealso{
-  \code{\link{plot.phylo}}, \code{\link{evolve.phylo}}
-}
-\examples{
-data(bird.orders)
-x <- rep(0, 4)
-names(x) <- c("A", "B", "C", "D")
-anc <- evolve.phylo(bird.orders, x, 1)
-plot(anc, edge.width = 3, plot.node.values = TRUE)
-par(mfrow = c(2, 2), mar = c(5.5, 0, 0, 0))
-plot(anc, edge.width = 3, type = "r")
-}
-\keyword{hplot}