[Phylobase-commits] r676 - pkg/R

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

Author: regetz
Date: 2009-09-29 18:07:54 +0200 (Tue, 29 Sep 2009)
New Revision: 676

Modified:
   pkg/R/methods-phylo4.R
Log:
changed edgeLength and edgeLabels to return vector with named elements
for every edge even when some/all values are missing; fixes bug #668.


Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2009-09-29 05:57:47 UTC (rev 675)
+++ pkg/R/methods-phylo4.R	2009-09-29 16:07:54 UTC (rev 676)
@@ -191,11 +191,13 @@
  function(x, node) {
     ## [JR: below, using match for ordering rather than direct character
     ## indexing b/c the latter is slow for vectors of a certain size]
-    elen <- x at edge.length[match(edgeId(x, "all"), names(x at edge.length))]
     if (!missing(node)) {
-        n <- getNode(x, node)
-        elen <- elen[match(n, x at edge[,2])]
+        id <- getEdge(x, node)
+    } else {
+        id <- edgeId(x, "all")
     }
+    elen <- x at edge.length[match(id, names(x at edge.length))]
+    names(elen) <- id
     return(elen)
 })
 
@@ -344,7 +346,10 @@
   function(x) {
     ## [JR: below, using match for ordering rather than direct character
     ## indexing b/c the latter is slow for vectors of a certain size]
-    x at edge.label[match(edgeId(x, "all"), names(x at edge.label))]
+    id <- edgeId(x, "all")
+    lbl <- x at edge.label[match(id, names(x at edge.label))]
+    names(lbl) <- id
+    return(lbl)
 })
 
 setReplaceMethod("edgeLabels", signature(x="phylo4", value="character"),