[Phylobase-commits] r222 - branches/pdcgsoc/R

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

Author: pdc
Date: 2008-08-02 10:40:26 +0200 (Sat, 02 Aug 2008)
New Revision: 222

Added:
   branches/pdcgsoc/R/methods-oldclasses.R
Modified:
   branches/pdcgsoc/R/methods-phylo4.R
   branches/pdcgsoc/R/methods-phylo4d.R
   branches/pdcgsoc/R/phylo4.R
Log:
change reorder to conform to stats generic
add a reorder method for oldclass phylo so that ape commands aren't broken

Added: branches/pdcgsoc/R/methods-oldclasses.R
===================================================================
--- branches/pdcgsoc/R/methods-oldclasses.R	                        (rev 0)
+++ branches/pdcgsoc/R/methods-oldclasses.R	2008-08-02 08:40:26 UTC (rev 222)
@@ -0,0 +1,4 @@
+setMethod("reorder", signature(x = "phylo"), function(x, order = 'cladewise') {
+    x <- reorder.phylo(x,  order)
+    x
+})

Modified: branches/pdcgsoc/R/methods-phylo4.R
===================================================================
--- branches/pdcgsoc/R/methods-phylo4.R	2008-08-02 05:33:15 UTC (rev 221)
+++ branches/pdcgsoc/R/methods-phylo4.R	2008-08-02 08:40:26 UTC (rev 222)
@@ -295,7 +295,7 @@
     object
 })
 
-setMethod("reorder", signature(object = 'phylo4'), function(object, type = 'pruningwise') {
+setMethod("reorder", signature(x = 'phylo4'), function(x, order = 'cladewise') {
     reorder.prune <- function(edge, tips, root = tips + 1) {
         ## if(is.null(root)) {
         ##     root <- tips + 1
@@ -314,7 +314,6 @@
     if(type == 'pruningwise') {
         index <- reorder.prune(object at edge, length(object at tip.label))
     }
-    print('test')
     object at edge        <- object at edge[index, ]
     object at edge.label  <- object at edge.label[index]
     object at edge.length <- object at edge.length[index]

Modified: branches/pdcgsoc/R/methods-phylo4d.R
===================================================================
--- branches/pdcgsoc/R/methods-phylo4d.R	2008-08-02 05:33:15 UTC (rev 221)
+++ branches/pdcgsoc/R/methods-phylo4d.R	2008-08-02 08:40:26 UTC (rev 222)
@@ -157,7 +157,7 @@
     return(rev(temp))
 })
 
-setMethod("reorder", signature(object = 'phylo4d'), function(object, type = 'pruningwise') {
+setMethod("reorder", signature(x = 'phylo4d'), function(x, order = 'cladewise') {
     reorder.prune <- function(edge, tips, root = tips + 1) {
         ## if(is.null(root)) {
         ##     root <- tips + 1

Modified: branches/pdcgsoc/R/phylo4.R
===================================================================
--- branches/pdcgsoc/R/phylo4.R	2008-08-02 05:33:15 UTC (rev 221)
+++ branches/pdcgsoc/R/phylo4.R	2008-08-02 08:40:26 UTC (rev 222)
@@ -82,7 +82,7 @@
 
 setGeneric("na.omit")
 
-setGeneric("reorder", def = function(object, type = 'pruningwise') {
+setGeneric("reorder", def = function(x, order = 'cladewise') {
     standardGeneric("reorder")}, package = 'phylobase', useAsDefault = FALSE)