[Phylobase-commits] r377 - pkg/R

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

Author: bbolker
Date: 2008-12-20 22:40:36 +0100 (Sat, 20 Dec 2008)
New Revision: 377

Modified:
   pkg/R/setAs-Methods.R
Log:
  tweaked for roundtrip phylo to phylo4 consistency



Modified: pkg/R/setAs-Methods.R
===================================================================
--- pkg/R/setAs-Methods.R	2008-12-20 21:10:41 UTC (rev 376)
+++ pkg/R/setAs-Methods.R	2008-12-20 21:40:36 UTC (rev 377)
@@ -50,10 +50,13 @@
   if (inherits(from,"phylo4d"))
     warning("losing data while coercing phylo4d to phylo")
   brlen <- from at edge.length
-  if (isRooted(from)) brlen <- brlen[nodeId(from,"all")!=rootNode(from)]
-  edgemat <- na.omit(from at edge)
-  y <- list(edge = na.omit(from at edge), edge.length = brlen,
-            Nnode = from at Nnode, tip.label = from at tip.label,
+  rootpos <- which(nodeId(from,"all")==rootNode(from))
+  if (isRooted(from)) brlen <- brlen[-rootpos]
+  edgemat <- unname(from at edge[-rootpos,])
+  y <- list(edge = edgemat,
+            Nnode = from at Nnode,
+            tip.label = from at tip.label,
+            edge.length = brlen,
             node.label = from at node.label)
   class(y) <- "phylo"
   if (length(y$edge.length) == 0)