[Phylobase-commits] r210 - branches/pdcgsoc/R

[noreply at r-forge.r-project.org]

Author: pdc
Date: 2008-07-21 09:26:56 +0200 (Mon, 21 Jul 2008)
New Revision: 210

Modified:
   branches/pdcgsoc/R/phylo4.R
Log:
bug fixes -- nice to have working code

Modified: branches/pdcgsoc/R/phylo4.R
===================================================================
--- branches/pdcgsoc/R/phylo4.R	2008-07-21 06:55:41 UTC (rev 209)
+++ branches/pdcgsoc/R/phylo4.R	2008-07-21 07:26:56 UTC (rev 210)
@@ -90,17 +90,17 @@
         nord <- NULL
         for(i in nextr) {
             if(i <= tips) {next()}
-            nord <- c(nord, myorder(edge, tips, root = i))
+            nord <- c(nord, reorder.prune(edge, tips, root = i))
         }
         c(nord, which(index))
     }
     if(type == 'pruningwise') {
-        index <- reorder.prune(phy at edge, length(phy at tip.label))
+        index <- reorder.prune(object at edge, length(object at tip.label))
     }
-    phy at edge        <- phy at edge[index, ]
-    phy at edge.label  <- phy at edge.label[index]
-    phy at edge.length <- phy at edge.length[index]
-    phy
+    object at edge        <- object at edge[index, ]
+    object at edge.label  <- object at edge.label[index]
+    object at edge.length <- object at edge.length[index]
+    object
 },
     useAsDefault = function(object, type = 'pruningwise') {
         reorder.prune <- function(edge, tips, root = tips + 1) {
@@ -114,17 +114,17 @@
             nord <- NULL
             for(i in nextr) {
                 if(i <= tips) {next()}
-                nord <- c(nord, myorder(edge, tips, root = i))
+                nord <- c(nord, reorder.prune(edge, tips, root = i))
             }
             c(nord, which(index))
         }
         if(type == 'pruningwise') {
-            index <- reorder.prune(phy at edge, length(phy at tip.label))
+            index <- reorder.prune(object at edge, length(object at tip.label))
         }
-        phy at edge        <- phy at edge[index, ]
-        phy at edge.label  <- phy at edge.label[index]
-        phy at edge.length <- phy at edge.length[index]
-        phy
+        object at edge        <- object at edge[index, ]
+        object at edge.label  <- object at edge.label[index]
+        object at edge.length <- object at edge.length[index]
+        object
 })