From 9531f5a42f8783c6da5092de9e5481265da0a528 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Tue, 6 May 2008 13:40:20 +0000
Subject: [PATCH] cosmetic modif on rtree() + last (?) changes to Damien's
 functions

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@29 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 Changes             | 11 ++++-------
 DESCRIPTION         |  2 +-
 R/rtree.R           |  4 ++--
 R/subtreeplot.R     |  4 ++--
 man/ape-internal.Rd |  4 ++--
 man/subtreeplot.Rd  |  2 ++
 6 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/Changes b/Changes
index da98ec1..9633e88 100644
--- a/Changes
+++ b/Changes
@@ -4,13 +4,16 @@
 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
 
@@ -31,12 +34,6 @@ 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
 
diff --git a/DESCRIPTION b/DESCRIPTION
index 5ded9a5..abf1906 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 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,
diff --git a/R/rtree.R b/R/rtree.R
index cba5d4e..1c2052c 100644
--- a/R/rtree.R
+++ b/R/rtree.R
@@ -1,4 +1,4 @@
-## rtree.R (2008-01-13)
+## rtree.R (2008-05-06)
 
 ##   Generates Random Trees
 
@@ -95,7 +95,7 @@ rtree <- function(n, rooted = TRUE, tip.label = NULL, br = runif, ...)
       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
 }
diff --git a/R/subtreeplot.R b/R/subtreeplot.R
index 4e6f81f..b733e90 100644
--- a/R/subtreeplot.R
+++ b/R/subtreeplot.R
@@ -1,4 +1,4 @@
-## subtreeplot.R (2008-04-14)
+## subtreeplot.R (2008-04-30)
 
 ##  Zoom on a Portion of a Phylogeny by Successive Clicks
 
@@ -23,7 +23,7 @@ subtreeplot<-function(x, wait=FALSE, ...) {
         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)
diff --git a/man/ape-internal.Rd b/man/ape-internal.Rd
index 441d39f..464d304 100644
--- a/man/ape-internal.Rd
+++ b/man/ape-internal.Rd
@@ -44,8 +44,8 @@
 \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.
diff --git a/man/subtreeplot.Rd b/man/subtreeplot.Rd
index 62c621b..f72ab8f 100644
--- a/man/subtreeplot.Rd
+++ b/man/subtreeplot.Rd
@@ -28,6 +28,7 @@ subtreeplot(x, wait=FALSE, ...)
   \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.
@@ -36,4 +37,5 @@ 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}
-- 
2.39.5