more corrections for ape 3.0-7

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

diff --git a/R/collapse.singles.R b/R/collapse.singles.R
index e4d2bfe410516dcc0da6cd586cd6c65f40b6e8a6..bbde0a17e003ce464a68dab76afa7d4aa412b416 100644 (file)
--- a/R/collapse.singles.R
+++ b/R/collapse.singles.R
@@ -1,15 +1,14 @@
-## collapse.singles.R (2013-01-16)
+## collapse.singles.R (2010-07-23)
 
 ##    Collapse "Single" Nodes
 
-## Copyright 2006 Ben Bolker, 2013 Klaus Schliep
+## Copyright 2006 Ben Bolker
 
 ## 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):
@@ -17,26 +16,32 @@ collapse.singles <- function(tree)
     nnode <- tree$Nnode
     ntip <- length(tree$tip.label)
     ## end
-    ## 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]]
+    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]
         }
-        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):