[Phylobase-commits] r133 - in pkg: . R

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

Author: skembel
Date: 2008-03-02 23:15:38 +0100 (Sun, 02 Mar 2008)
New Revision: 133

Modified:
   pkg/R/phylo4.R
   pkg/TODO
Log:
Modified labels method to optionally return tips, int. nodes or all labels

Modified: pkg/R/phylo4.R
===================================================================
--- pkg/R/phylo4.R	2008-02-29 19:37:39 UTC (rev 132)
+++ pkg/R/phylo4.R	2008-03-02 22:15:38 UTC (rev 133)
@@ -158,6 +158,12 @@
     object at tip.label
 })
 
+setMethod("labels","phylo4", function(object,which=c("tip","node","allnode"),...) {
+    which <- match.arg(which)
+    switch(which,tip=object at tip.label,node=object at node.label,
+           allnode=c(object at tip.label,object at node.label))
+})
+
 setGeneric("labels<-",
            function(object,...,value) {
                standardGeneric("labels<-")
@@ -168,7 +174,6 @@
     object
 })
 
-
 setGeneric("NodeLabels", function(x) {
     standardGeneric("NodeLabels")
 })

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-02-29 19:37:39 UTC (rev 132)
+++ pkg/TODO	2008-03-02 22:15:38 UTC (rev 133)
@@ -16,6 +16,7 @@
 ## Data classes
 ### Tree model:
 * assigning edge and node labels -- is there/should there be an option to turn this off?  assign empty ("") labels? how about assigning the node number if there are no user-supplied labels?(mb)
+* basic checks when assigning labels (do number of labels and number of nodes/tips match?)
 * should default node labels start at N(nTips+1), to match internal node numbers?
 * should coercing phylo4d to phylo4 give a warning message about losing data?   Should phylo4d to phylo4?  Yes(mb)
 * order: All phylo4 edge matrices are internally stored as "cladewise"/Newick traversal order.  Extend edges accessor method with optional argument that allows edges to be extracted in a different order (possibly with an attribute as in ape); need to steal 'reorder' from ape, extend for phylo4d keeping track of traits also see ape::ladderize