From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Wed, 2 Mar 2011 06:47:44 +0000 (+0000)
Subject: fixes in bind.tree()
X-Git-Url: https://git.donarmstrong.com/?p=ape.git;a=commitdiff_plain;h=2061f73318413f7a23db30be1deb8d42ab12f64c

fixes in bind.tree()


git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@148 6e262413-ae40-0410-9e79-b911bd7a66b7
---

diff --git a/ChangeLog b/ChangeLog
index c88556f..e163a85 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -15,7 +15,12 @@ BUG FIXES
     o prop.part() failed in some situations with unrooted trees.
 
     o read.nexus() shuffled node labels when a TRANSLATE block was
-      present
+      present.
+
+    o varCompPhylip() did not work if 'exec' was specified.
+
+    o bind.tree() shuffled node labels when position > 0 and 'where'
+      was not the root.
 
 
 OTHER CHANGES
diff --git a/DESCRIPTION b/DESCRIPTION
index 7a2aa94..e364002 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.6-4
-Date: 2011-02-28
+Date: 2011-03-02
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Klaus Schliep, Korbinian Strimmer, Damien de Vienne
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
diff --git a/R/bind.tree.R b/R/bind.tree.R
index b862b37..58d7cab 100644
--- a/R/bind.tree.R
+++ b/R/bind.tree.R
@@ -1,8 +1,8 @@
-## bind.tree.R (2010-05-25)
+## bind.tree.R (2011-03-02)
 
 ##    Bind Trees
 
-## Copyright 2003-2010 Emmanuel Paradis
+## Copyright 2003-2011 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -77,7 +77,7 @@ bind.tree <- function(x, y, where = "root", position = 0, interactive = FALSE)
         }
     }
 
-    ## the special of substituting two tips:
+    ## the special case of substituting two tips:
     if (case == 2 && ny == 1 && !position) {
         x$tip.label[x$edge[i, 2]] <- y$tip.label
         if (wbl)
@@ -88,14 +88,14 @@ bind.tree <- function(x, y, where = "root", position = 0, interactive = FALSE)
     x <- reorder(x)
     y <- reorder(y)
 
-### because in all situations internal nodes need to be renumbered,
-### they are changed to negatives first, and nodes that eventually
-### will be added will be numbered sequentially
+### because in all situations internal nodes need to be
+### renumbered, they are changed to negatives first, and
+### nodes eventually added will be numbered sequentially
 
     nodes <- x$edge > nx
     x$edge[nodes] <- -(x$edge[nodes] - nx) # -1, ..., -mx
     nodes <- y$edge > ny
-    y$edge[nodes] <- -(y$edge[nodes] - ny + mx) #  -(mx+1), ..., -(mx+my)
+    y$edge[nodes] <- -(y$edge[nodes] - ny + mx) # -(mx+1), ..., -(mx+my)
     ROOT <- -1L # may change later
     next.node <- -(mx + my) - 1L
 
@@ -198,19 +198,18 @@ bind.tree <- function(x, y, where = "root", position = 0, interactive = FALSE)
     ## update the node labels before renumbering (this adds NA for
     ## the added nodes, and drops the label for those deleted)
     if (!is.null(x$node.label))
-        x$node.label <- x$node.label[-unique(x$edge[, 1])]
+        x$node.label <- x$node.label[sort(-unique(x$edge[, 1]))]
 
     ## renumber nodes:
     newNb <- integer(x$Nnode)
     newNb[-ROOT] <- n + 1L
     sndcol <- x$edge[, 2] < 0
     ## executed from right to left, so newNb is modified before x$edge:
-    x$edge[sndcol, 2] <- newNb[-x$edge[sndcol, 2]] <-
-        (n + 2):(n + x$Nnode)
+    x$edge[sndcol, 2] <- newNb[-x$edge[sndcol, 2]] <- n + 2:x$Nnode
     x$edge[, 1] <- newNb[-x$edge[, 1]]
 
     if (!is.null(x$node.label))
-        x$node.label <- x$node.label[newNb[newNb == 0] - n]
+        x$node.label <- x$node.label[order(newNb[newNb > 0])]
 
     x
 }
diff --git a/R/pic.R b/R/pic.R
index 122b60d..816a09b 100644
--- a/R/pic.R
+++ b/R/pic.R
@@ -1,8 +1,8 @@
-## pic.R (2010-11-15)
+## pic.R (2011-03-01)
 
 ##   Phylogenetically Independent Contrasts
 
-## Copyright 2002-2010 Emmanuel Paradis
+## Copyright 2002-2011 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -174,7 +174,7 @@ varCompPhylip <- function(x, phy, exec = NULL)
     odir <- setwd(pfx)
     on.exit(setwd(odir))
     if (file.exists("outfile")) unlink("outfile")
-    system("phylip contrast", intern = TRUE, input = c("W", "A", "Y"))
+    system(exec, intern = TRUE, input = c("W", "A", "Y"))
     varA <- scan("outfile", skip = 7, nlines = p, quiet = TRUE)
     varE <- scan("outfile", skip = 11 + p, nlines = p, quiet = TRUE)
     if (p > 1) {