NEW FEATURES
o Four new functions have been written by Damien de Vienne for the
- graphical exploration of large trees (plot.cophylo, subtrees,
+ graphical exploration of large trees (cophyloplot, subtrees,
subtreeplot), and to return the graphical coordinates of tree
(without plotting).
o The new function corPagel() implements the Pagel's "lambda"
correlation structure.
+ o chronopl() has been improved and gains several options: see its
+ help page for details.
+
BUG FIXES
o seg.sites() failed with a list.
-OTHER CHANGES
-
- o chronopl() has been improved and gains several options: see its
- help page for details.
-
-
CHANGES IN APE VERSION 2.1-3
Package: ape
Version: 2.2
-Date: 2008-04-24
+Date: 2008-05-02
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
-## rtree.R (2008-01-13)
+## rtree.R (2008-05-06)
## Generates Random Trees
if (is.null(tip.label)) paste("t", sample(n), sep = "")
else sample(tip.label)
if (is.function(br)) phy$edge.length <- br(nbr, ...)
- phy$Nnode <- if (rooted) n - 1 else n - 2
+ phy$Nnode <- n - 2 + rooted
class(phy) <- "phylo"
phy
}
-## subtreeplot.R (2008-04-14)
+## subtreeplot.R (2008-04-30)
## Zoom on a Portion of a Phylogeny by Successive Clicks
N.tip<-Ntip(x)
N.node<-Nnode(x)
- coor<-plot.phylo.coor(x)
+ coor<-plotPhyloCoor(x)
tips<-x$tip.label
nodes<-x$node.label
if (is.null(x$node.label)) nodes<-(N.tip+1):(N.tip+N.node)
\alias{floating.pie.asp}
\alias{checkLabel}
\alias{getMRCA}
-\alias{plot.cophylo2}
-\alias{plot.phylo.coor}
+\alias{plotCophylo2}
+\alias{plotPhyloCoor}
\title{Internal Ape Functions}
\description{
Internal ape functions.
\code{\link{plot.phylo}}, \code{\link{drop.tip}}, \code{\link{subtrees}}
}
\examples{
+\dontrun{
#example 1: simple
tree1<-rtree(50) #random tree with 50 leaves
tree2<-subtreeplot(tree1, wait=TRUE) # on exit, tree2 will be a subtree of tree1.
tree1<-rtree(60)
tree2<-subtreeplot(subtreeplot(subtreeplot(tree1))) #allows three succssive zooms.
}
+}
\keyword{hplot}