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

[ape.git] / man / evolve.phylo.Rd

diff --git a/man/evolve.phylo.Rd b/man/evolve.phylo.Rd
deleted file mode 100644 (file)
index b277039..0000000
--- a/man/evolve.phylo.Rd
+++ /dev/null
@@ -1,48 +0,0 @@
-\name{evolve.phylo}
-\alias{evolve.phylo}
-\title{Ancestral Character Simulation}
-\description{
-  Simulate the (independent) evolution of one or several continuous
-  characters along a given phylogenetic tree under a homogeneous
-  Brownian model.
-}
-\usage{
-evolve.phylo(phy, value, var)
-}
-\arguments{
-  \item{phy}{an object of class 'phylo' with branch lengths.}
-  \item{value}{ancestral states, one by character. The (optional) names
-    of this vector will be used as character names.}
-  \item{var}{the variance of each character.}
-}
-\details{
-  Let x be a continuous character.
-  If it evolves according to a Brownian model, its value at time t follows a normal law with mean x0 and variance t*sigma\_x,
-  where x0 is the value of the character at time 0, and sigma\_x is the 'inner' variance of the character.
-  The evolution of a continuous character is performed by letting the character evolve on each branch, from its ancestral root state.
-  The final state of a branch is the ancestral states of the daughter branches, and so on.
-}
-\value{
-  An object of class 'ancestral', inheriting from the 'phylo' class. The
-  following components are added:
-
-  \item{node.character}{a data.frame with node ids as rownames and one
-    column by character, containing all the inner node values for each
-    character.}
-  \item{tip.character}{a data.frame with tip ids as rownames and one
-    column by character, containing all the tip values for each
-    character.}
-}
-\author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr}}
-\seealso{
-  \code{\link{plot.ancestral}}, \code{\link{ace}}
-}
-\examples{
-data(bird.orders)
-x <- rep(0, 5)
-names(x) <- c("A", "B", "C", "D", "E")
-anc1 <- evolve.phylo(bird.orders, x, 1)
-anc2 <- evolve.phylo(bird.orders, x, 1)
-cor(anc1$tip.character, anc2$tip.character)
-}
-\keyword{models}