[Phylobase-commits] r530 - in pkg: . R

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

Author: bbolker
Date: 2009-08-20 17:57:02 +0200 (Thu, 20 Aug 2009)
New Revision: 530

Modified:
   pkg/NAMESPACE
   pkg/R/methods-phylo4.R
Log:
added match.arg(), renamed back to orderIndex (not exported)



Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2009-08-20 15:37:05 UTC (rev 529)
+++ pkg/NAMESPACE	2009-08-20 15:57:02 UTC (rev 530)
@@ -83,7 +83,7 @@
 #export(internEdges, terminEdges, isPoly)
 
 ## presumably these should remain hidden
-#export(.createLabels, .createEdge, .phylo4Data, .orderIndex, .genlab,
+#export(.createLabels, .createEdge, .phylo4Data, orderIndex, .genlab,
 #    .chnumsort, .phylo4ToDataFrame, .bubLegendGrob)
 
 ## recently removed:

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2009-08-20 15:37:05 UTC (rev 529)
+++ pkg/R/methods-phylo4.R	2009-08-20 15:57:02 UTC (rev 530)
@@ -44,7 +44,7 @@
 ###  6.7. summary()
 
 ### 7. Ordering
-###  7.1. .orderIndex()
+###  7.1. orderIndex()
 ###  7.2. reorder()
 
 
@@ -470,10 +470,11 @@
 ### Ordering
 #########################################################
 
-.orderIndex <- function(phy, order = c('preorder', 'postorder')) {
+orderIndex <- function(phy, order = c('preorder', 'postorder')) {
     ## get an root node free edge matrix
     ## R scoping allows us to call this variable in
     ## the postOrder() func defined above
+    order <- match.arg(order)
     edge <- phy at edge[!is.na(phy at edge[, 1]), ]
     ## Sort edges -- ensures that starting order of edge matrix doesn't
     ## affect the order of reordered trees
@@ -516,7 +517,7 @@
     function(x, order = c('preorder', 'postorder')) {
     ## call orderIndex and use that index to order edges, labels and lengths
     order   <- match.arg(order)
-    index   <- .orderIndex(x, order)
+    index   <- orderIndex(x, order)
     x at order <- order
     x at edge  <- x at edge[index, ]
     if(hasEdgeLabels(x)) { x at edge.label  <- x at edge.label[index] }