[Phylobase-commits] r526 - in pkg: R man

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

Author: pdc
Date: 2009-08-20 05:08:10 +0200 (Thu, 20 Aug 2009)
New Revision: 526

Modified:
   pkg/R/methods-phylo4.R
   pkg/man/reorder-methods.Rd
Log:
don't export .orderIndex, use reorder(phy, order) instead

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2009-08-20 03:07:38 UTC (rev 525)
+++ pkg/R/methods-phylo4.R	2009-08-20 03:08:10 UTC (rev 526)
@@ -44,7 +44,7 @@
 ###  6.7. summary()
 
 ### 7. Ordering
-###  7.1. orderIndex()
+###  7.1. .orderIndex()
 ###  7.2. reorder()
 
 
@@ -470,7 +470,7 @@
 ### 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
@@ -516,7 +516,7 @@
     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] }

Modified: pkg/man/reorder-methods.Rd
===================================================================
--- pkg/man/reorder-methods.Rd	2009-08-20 03:07:38 UTC (rev 525)
+++ pkg/man/reorder-methods.Rd	2009-08-20 03:08:10 UTC (rev 526)
@@ -4,7 +4,7 @@
 \alias{reorder,phylo-method}
 \alias{reorder,phylo4-method}
 \alias{reorder,phylo4d-method}
-\alias{orderIndex}
+\alias{.orderIndex}
 \title{reordering trees within phylobase objects}
 \description{
  Methods for reordering trees into various traversal orders
@@ -20,7 +20,7 @@
 \usage{
 \S4method{reorder}{phylo}(x, order = "cladewise")
 \S4method{reorder}{phylo4}(x, order = c("preorder", "postorder"))
-orderIndex(phy, order = c('preorder','postorder'))
+.orderIndex(phy, order = c('preorder','postorder'))
 }
 
 \arguments{