From 5c40f536fadaa42ad1683969cfe249c4fabba87a Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Thu, 19 Jun 2008 10:24:37 +0000
Subject: [PATCH] bug fix in collapsed.singles()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@36 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 Changes              |  7 +++++--
 DESCRIPTION          |  2 +-
 R/collapse.singles.R | 15 ++++++++++++++-
 Thanks               |  4 ++--
 4 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/Changes b/Changes
index 3d1da07..df065d4 100644
--- a/Changes
+++ b/Changes
@@ -9,11 +9,14 @@ NEW FEATURES
 
 BUG FIXES
 
-    o root() failed with resolve.root = TRUE when the root was already
-      the specified root.
+    o root() failed with 'resolve.root = TRUE' when the root was
+      already the specified root.
 
     o Several bugs were fixed in mlphylo().
 
+    o collapsed.singles() did not propagate the 'Nnode' and
+      'node.labels' elements (thanks to Elizabeth Purdom for the fix.
+
 
 OTHER CHANGES
 
diff --git a/DESCRIPTION b/DESCRIPTION
index 985cdf0..71e4a76 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.2-1
-Date: 2008-06-18
+Date: 2008-06-19
 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/collapse.singles.R b/R/collapse.singles.R
index cfbf4c8..ad3cd98 100644
--- a/R/collapse.singles.R
+++ b/R/collapse.singles.R
@@ -1,4 +1,4 @@
-## collapse.singles.R (2006-07-15)
+## collapse.singles.R (2008-06-19)
 
 ##    Collapse "Single" Nodes
 
@@ -11,6 +11,11 @@ collapse.singles <- function(tree)
 {
     elen <- tree$edge.length
     xmat <- tree$edge
+    ## added by Elizabeth Purdom (2008-06-19):
+    node.lab<-tree$node.label
+    nnode<-tree$Nnode
+    ntip<-length(tree$tip.label)
+    ## end
     singles <- NA
     while (length(singles) > 0) {
         ## changed by EP to make it slightly more efficient:
@@ -30,10 +35,18 @@ collapse.singles <- function(tree)
             xmat[xmat > i] <- xmat[xmat > i] - 1 ## adjust indices
             ## END
             elen[prev.node] <- elen[prev.node] + elen[next.node]
+            ## added by Elizabeth Purdom (2008-06-19):
+            if(!is.null(node.lab)) node.lab<-node.lab[-c(i-ntip)]
+            nnode<-nnode-1
+            ## end
             elen <- elen[-next.node]
         }
     }
     tree$edge <- xmat
     tree$edge.length <- elen
+    ## added by Elizabeth Purdom (2008-06-19):
+    tree$node.label<-node.lab
+    tree$Nnode<-nnode
+    ## end
     tree
 }
diff --git a/Thanks b/Thanks
index 8b19985..0bac636 100644
--- a/Thanks
+++ b/Thanks
@@ -5,8 +5,8 @@ Many users gave important feed-back with their encouragements,
 comments, or bug reports: thanks to all of you!
 
 Significant bug fixes were provided by James Bullard, Éric Durand,
-Olivier François, Bret Larget, Klaus Schliep, Li-San Wang, and
-Yan Wong. Contact me if I forgot someone.
+Olivier François, Bret Larget, Elizabeth Purdom, Klaus Schliep,
+Li-San Wang, and Yan Wong. Contact me if I forgot someone.
 
 Kurt Hornik, of the R Core Team, helped in several occasions to
 fix some problems and bugs.
-- 
2.39.2