[Phylobase-commits] r679 - in pkg: R man

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

Author: pdc
Date: 2009-09-29 22:30:46 +0200 (Tue, 29 Sep 2009)
New Revision: 679

Modified:
   pkg/R/methods-phylo4.R
   pkg/R/phylo4.R
   pkg/man/phylo4-accessors.Rd
Log:
Remove unused order argument from edges. Fixes bug #603.  Allowing reorder of the the edges through the accessor, in addition to being unimplemented, doesn't add significant benefit over reordering the tree, then accessing the edges.

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2009-09-29 19:20:42 UTC (rev 678)
+++ pkg/R/methods-phylo4.R	2009-09-29 20:30:46 UTC (rev 679)
@@ -150,7 +150,7 @@
 
 # return edge matrix in its current order
 setMethod("edges", signature(x="phylo4"),
- function(x, order, drop.root=FALSE, ...) {
+ function(x, drop.root=FALSE, ...) {
      e <- x at edge
      if (drop.root) e <- e[e[, 1] != 0, ]
      e

Modified: pkg/R/phylo4.R
===================================================================
--- pkg/R/phylo4.R	2009-09-29 19:20:42 UTC (rev 678)
+++ pkg/R/phylo4.R	2009-09-29 20:30:46 UTC (rev 679)
@@ -27,7 +27,7 @@
 })
 
 ## edges
-setGeneric("edges", function(x, order, ...) {
+setGeneric("edges", function(x, ...) {
     standardGeneric("edges")
 })
 

Modified: pkg/man/phylo4-accessors.Rd
===================================================================
--- pkg/man/phylo4-accessors.Rd	2009-09-29 19:20:42 UTC (rev 678)
+++ pkg/man/phylo4-accessors.Rd	2009-09-29 20:30:46 UTC (rev 679)
@@ -78,7 +78,7 @@
 % https://stat.ethz.ch/pipermail/r-devel/2008-May/049653.html
 \S4method{nNodes}{phylo4}(x)
 \S4method{nTips}{phylo4}(x)
-\S4method{edges}{phylo4}(x, order, drop.root=FALSE, \dots)
+\S4method{edges}{phylo4}(x, drop.root=FALSE, \dots)
 \S4method{nEdges}{phylo4}(x)
 \S4method{edgeOrder}{phylo4}(x, \dots)
 \S4method{hasEdgeLength}{phylo4}(x)
@@ -96,7 +96,6 @@
   \item{node}{which edge lengths to extract (indexed by descendant
     node)} 
   \item{value}{a vector of edge lengths or a node number}
-  \item{order}{(not yet implemented)}
   \item{use.names}{Should the names of \code{value} be used to match
   edge lengths provided? }
   \item{drop.root}{logical: drop root row from edge matrix?}