some updates for ape 3.0-7

[ape.git] / R / collapse.singles.R

diff --git a/R/collapse.singles.R b/R/collapse.singles.R
index bbde0a17e003ce464a68dab76afa7d4aa412b416..e4d2bfe410516dcc0da6cd586cd6c65f40b6e8a6 100644 (file)
--- a/R/collapse.singles.R
+++ b/R/collapse.singles.R
@@ -1,14 +1,15 @@
-## collapse.singles.R (2010-07-23)
+## collapse.singles.R (2013-01-16)
 
 ##    Collapse "Single" Nodes
 
-## Copyright 2006 Ben Bolker
+## Copyright 2006 Ben Bolker, 2013 Klaus Schliep
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
 collapse.singles <- function(tree)
 {
+    tree <- reorder(tree) # added by Klaus
     elen <- tree$edge.length
     xmat <- tree$edge
     ## added by Elizabeth Purdom (2008-06-19):
@@ -16,32 +17,26 @@ collapse.singles <- function(tree)
     nnode <- tree$Nnode
     ntip <- length(tree$tip.label)
     ## end
-    singles <- NA
-    while (length(singles) > 0) {
-        ## changed by EP to make it slightly more efficient:
-        ## tx <- table(xmat[xmat < 0])
-        ## singles <- as.numeric(names(tx)[tx < 3])
-        tx <- tabulate(xmat[, 1])
-        singles <- which(tx == 1)
-        ## END
-        if (length(singles) > 0) {
-            i <- singles[1]
-            prev.node <- which(xmat[, 2] == i)
-            next.node <- which(xmat[, 1] == i)
-            xmat[prev.node, 2] <- xmat[next.node, 2]
-            xmat <- xmat[xmat[, 1] != i, ] # drop
-            ## changed by EP for the new coding of "phylo" (2006-10-05):
-            ## xmat[xmat < i] <- xmat[xmat < i] + 1 ## adjust indices
-            xmat[xmat > i] <- xmat[xmat > i] - 1L ## adjust indices # changed '1' by '1L' (2010-07-23)
-            ## 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 - 1L
-            ## end
-            elen <- elen[-next.node]
+    ## Added by Klaus (2013-01-16):
+    tx <- tabulate(xmat[, 1])
+    singles <- which(tx == 1)
+    if (length(singles) > 0) {
+        prev.nodes <- match(singles, xmat[,2])
+        next.nodes <- match(singles, xmat[,1])
+        for(j in length(singles):1) {
+            i <- singles[j]
+            xmat[prev.nodes[j], 2] <- xmat[next.nodes[j], 2]
+            elen[prev.nodes[j]] <- elen[prev.nodes[j]] + elen[next.nodes[j]]
         }
+        xmat <- xmat[-next.nodes,]
+        elen <- elen[-next.nodes]
+        if (!is.null(node.lab)) node.lab <- node.lab[-c(singles - ntip)]
+        nnode = nnode - as.integer(length(singles))
+        tmp = integer(max(xmat))
+        tmp[sort(unique(as.vector(xmat)))] = as.integer(c(1:(ntip+nnode)))
+        xmat[] = tmp[xmat]
     }
+    # End
     tree$edge <- xmat
     tree$edge.length <- elen
     ## added by Elizabeth Purdom (2008-06-19):