[Phylobase-commits] r342 - pkg/R

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

Author: skembel
Date: 2008-12-19 21:36:12 +0100 (Fri, 19 Dec 2008)
New Revision: 342

Modified:
   pkg/R/prune.R
   pkg/R/setAs-Methods.R
Log:
Second half of root.node purge

Modified: pkg/R/prune.R
===================================================================
--- pkg/R/prune.R	2008-12-19 20:32:29 UTC (rev 341)
+++ pkg/R/prune.R	2008-12-19 20:36:12 UTC (rev 342)
@@ -59,9 +59,9 @@
 
 ## setMethod("prune","ANY",
 ##           function(phy, tip, trim.internal = TRUE, subtree = FALSE,
-##                    root.edge = 0,...) {
+##                    ,...) {
 ##             if (class(phy)=="phylo") {
-##               ape::prune(phy, tip, trim.internal, subtree, root.edge)
+##               ape::prune(phy, tip, trim.internal, subtree)
 ##               } else stop("no prune method available for",
 ##                     deparse(substitute(phy)),
 ##                     "(class",class(phy),")")

Modified: pkg/R/setAs-Methods.R
===================================================================
--- pkg/R/setAs-Methods.R	2008-12-19 20:32:29 UTC (rev 341)
+++ pkg/R/setAs-Methods.R	2008-12-19 20:36:12 UTC (rev 342)
@@ -134,7 +134,7 @@
     tl <- labels(x)
     label <- c(nl, tl)
     node.type <- nodeType(x)[node]
-    return(data.frame(label, node, ancestor, branch.length,
+    return(data.frame(FIXMElabel=label, node, ancestor, branch.length,
         node.type,stringsAsFactors=FALSE))
 })