[Phylobase-commits] r155 - pkg/R

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

Author: pdc
Date: 2008-03-08 02:16:11 +0100 (Sat, 08 Mar 2008)
New Revision: 155

Modified:
   pkg/R/phylo4.R
   pkg/R/subset.R
Log:
Move extract.tree() to the subset file, open to other suggestions

Modified: pkg/R/phylo4.R
===================================================================
--- pkg/R/phylo4.R	2008-03-08 01:13:31 UTC (rev 154)
+++ pkg/R/phylo4.R	2008-03-08 01:16:11 UTC (rev 155)
@@ -111,12 +111,4 @@
     paste(base,numstr,sep="")
 }
 
-## convert from phylo to phylo4
-## coerce phylo4d to phylo4 -- on purpose, so no warning
-extract.tree <- function(from) {
-    phylo4(edge=from at edge,
-           edge.length=from at edge.length,
-           Nnode=from at Nnode,
-           tip.label=from at tip.label)
-}
 

Modified: pkg/R/subset.R
===================================================================
--- pkg/R/subset.R	2008-03-08 01:13:31 UTC (rev 154)
+++ pkg/R/subset.R	2008-03-08 01:16:11 UTC (rev 155)
@@ -1,10 +1,7 @@
 ################
 ## subset phylo4
 ################
-##
 
-## 
-
 setGeneric("subset")
 setMethod("subset", "phylo4",
           function(x,tips.include=NULL,tips.exclude=NULL,
@@ -94,3 +91,10 @@
               return(res)
           })
 
+
+## coerce phylo4d to phylo4 -- on purpose, so no warning
+
+extract.tree <- function(from) {
+    phylo4(edge = from at edge, edge.length = from at edge.length, 
+        Nnode = from at Nnode, tip.label = from at tip.label)
+}