From 3d25bf9304a2ec03022275950e4ccc720fc70675 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Mon, 4 Jan 2010 18:37:09 +0000
Subject: [PATCH] various changes...

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@102 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 R/plot.phylo.R         | 8 ++++----
 inst/CITATION          | 2 +-
 man/compar.cheverud.Rd | 2 --
 man/makeNodeLabel.Rd   | 4 +++-
 man/vcv.phylo.Rd       | 1 -
 5 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/R/plot.phylo.R b/R/plot.phylo.R
index 3328472..e02ba30 100644
--- a/R/plot.phylo.R
+++ b/R/plot.phylo.R
@@ -1,8 +1,8 @@
-## plot.phylo.R (2009-11-10)
+## plot.phylo.R (2010-01-04)
 
 ##   Plot Phylogenies
 
-## Copyright 2002-2009 Emmanuel Paradis
+## Copyright 2002-2010 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -62,12 +62,12 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
 
     phyloORclado <- type %in% c("phylogram", "cladogram")
     horizontal <- direction %in% c("rightwards", "leftwards")
+    xe <- x$edge # to save
     if (phyloORclado) {
         ## we first compute the y-coordinates of the tips.
         phyOrder <- attr(x, "order")
         ## make sure the tree is in cladewise order:
         if (is.null(phyOrder) || phyOrder != "cladewise") {
-            xe <- x$edge
             x <- reorder(x) # fix from Klaus Schliep (2007-06-16)
             if (!identical(x$edge, xe)) {
                 ## modified from Li-San Wang's fix (2007-01-23):
@@ -386,7 +386,7 @@ plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
               label.offset = label.offset, x.lim = x.lim, y.lim = y.lim,
               direction = direction, tip.color = tip.color,
               Ntip = Ntip, Nnode = Nnode)
-    assign("last_plot.phylo", c(L, list(edge = x$edge, xx = xx, yy = yy)),
+    assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
            envir = .PlotPhyloEnv)
     invisible(L)
 }
diff --git a/inst/CITATION b/inst/CITATION
index 09f3ae9..9c7ef12 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -7,7 +7,7 @@ citEntry(entry="Article",
   	year = "2004",
 	volume = "20",
 	pages = "289-290",
-	         
+
         textVersion = "Paradis E., Claude J. & Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.")
 
 citFooter("As ape is evolving quickly, you may want to cite also its version number (found with 'library(help = ape)').")
\ No newline at end of file
diff --git a/man/compar.cheverud.Rd b/man/compar.cheverud.Rd
index 4a6f86d..d7729d0 100644
--- a/man/compar.cheverud.Rd
+++ b/man/compar.cheverud.Rd
@@ -52,11 +52,9 @@ compar.cheverud(y, W, tolerance = 1e-06, gold.tol = 1e-04)
 \seealso{\code{\link{compar.lynch}}}
 \examples{
 ### Example from Harvey and Pagel's book:
-\dontrun{
 y<-c(10,8,3,4)
 W <- matrix(c(1,1/6,1/6,1/6,1/6,1,1/2,1/2,1/6,1/2,1,1,1/6,1/2,1,1), 4)
 compar.cheverud(y,W)
-}
 ### Example from Rohlf's 2001 article:
 W<- matrix(c(
   0,1,1,2,0,0,0,0,
diff --git a/man/makeNodeLabel.Rd b/man/makeNodeLabel.Rd
index 6fda0e6..e7e920a 100644
--- a/man/makeNodeLabel.Rd
+++ b/man/makeNodeLabel.Rd
@@ -45,7 +45,9 @@ makeNodeLabel(phy, method = "number", prefix = "Node", nodeList = list(), ...)
   specified node labels (so that if the other nodes have already labels
   they are not modified) while the two others change all labels.
 }
-
+\value{
+  an object of class \code{"phylo"}.
+}
 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
 \seealso{
   \code{\link{makeLabel}}, \code{\link[base]{grep}}
diff --git a/man/vcv.phylo.Rd b/man/vcv.phylo.Rd
index 7af6975..98def31 100644
--- a/man/vcv.phylo.Rd
+++ b/man/vcv.phylo.Rd
@@ -50,7 +50,6 @@ tr <- rtree(5)
 vcv(tr)
 vcv(corBrownian(1, tr))
 vcv(corPagel(1, tr))
-vcv(corPagel(0, tr))
 }
 \keyword{manip}
 \keyword{multivariate}
-- 
2.39.2