[Phylobase-commits] r610 - in pkg: . R

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

Author: francois
Date: 2009-08-31 23:54:27 +0200 (Mon, 31 Aug 2009)
New Revision: 610

Modified:
   pkg/NAMESPACE
   pkg/R/methods-phylo4.R
   pkg/R/methods-phylo4d.R
   pkg/R/phylo4.R
Log:
reorganization of phylo4.R in preparation of renaming of variables, removed from NAMESPACE rootNode (no methods associated) and commented out na.omit which is not functional

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2009-08-31 01:20:54 UTC (rev 609)
+++ pkg/NAMESPACE	2009-08-31 21:54:27 UTC (rev 610)
@@ -6,7 +6,7 @@
 
 import(methods)
 importFrom(graphics, plot)
-importFrom(stats, na.omit, reorder)
+importFrom(stats, reorder)
 importFrom(utils, head, tail)
 
 #----------------------------------------------------------------------
@@ -16,7 +16,7 @@
 #----------------------------------------------------------------------
 
 # utility methods
-exportMethods("[", "[<-", "[[", "[[<-", print, head, tail, na.omit,
+exportMethods("[", "[<-", "[[", "[[<-", print, head, tail,
     reorder, subset, plot, summary)
 
 # tree constructor methods
@@ -31,7 +31,7 @@
 
 # root methods
 exportMethods(isRooted, rootNode, "rootNode<-")
-export(rootEdge)  # no methods defined yet?
+#export(rootEdge)  # no methods defined yet?
 
 # node methods
 exportMethods(nodeId, nodeType)

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2009-08-31 01:20:54 UTC (rev 609)
+++ pkg/R/methods-phylo4.R	2009-08-31 21:54:27 UTC (rev 610)
@@ -52,10 +52,6 @@
 ### Tip accessors
 #########################################################
 
-setGeneric("nTips", function(x,...) {
-    standardGeneric("nTips")
-})
-
 setMethod("nTips", "phylo4", function(x, ...) {
     E <- edges(x)
     if(nrow(E) == 0)

Modified: pkg/R/methods-phylo4d.R
===================================================================
--- pkg/R/methods-phylo4d.R	2009-08-31 01:20:54 UTC (rev 609)
+++ pkg/R/methods-phylo4d.R	2009-08-31 21:54:27 UTC (rev 610)
@@ -243,8 +243,8 @@
 
 ## FIXME: doesn't deal with missing node data
 ##   (don't even know how that should be done in this case)
-setMethod("na.omit", "phylo4d", function(object, ...) {
-    tipdata <- tdata(object, "tip")
-    na.index <- which(!complete.cases(tipdata))
-    prune(object, tip = na.index)
-})
+## setMethod("na.omit", "phylo4d", function(object, ...) {
+##    tipdata <- tdata(object, "tip")
+##    na.index <- which(!complete.cases(tipdata))
+##    prune(object, tip = na.index)
+##})

Modified: pkg/R/phylo4.R
===================================================================
--- pkg/R/phylo4.R	2009-08-31 01:20:54 UTC (rev 609)
+++ pkg/R/phylo4.R	2009-08-31 21:54:27 UTC (rev 610)
@@ -1,131 +1,172 @@
-setGeneric("nNodes", function(x) {
-    standardGeneric("nNodes")
-})
+## Same order as in methods-phylo4.R
 
-setGeneric("nEdges", function(x) {
-    standardGeneric("nEdges")
+## nTips
+setGeneric("nTips", function(x,...) {
+    standardGeneric("nTips")
 })
 
-setGeneric("edges", function(x, order, ...) {
-    standardGeneric("edges")
+## nNodes
+setGeneric("nNodes", function(x) {
+    standardGeneric("nNodes")
 })
 
-setGeneric("rootEdge", function(x, order, ...) {
-    standardGeneric("rootEdge")
-})
-
+## nodeType
 setGeneric("nodeType", function(phy) {
     standardGeneric("nodeType")
 })
 
-setGeneric("isRooted", function(x) {
-    standardGeneric("isRooted")
+## nodeId
+setGeneric("nodeId", function(x, type=c("internal", "tip", "all")) {
+    standardGeneric("nodeId")
 })
 
-setGeneric("rootNode", function(x) {
-    standardGeneric("rootNode")
+## nEdges
+setGeneric("nEdges", function(x) {
+    standardGeneric("nEdges")
 })
 
-setGeneric("rootNode<-", function(x, value) {
-    standardGeneric("rootNode<-")
+## edges
+setGeneric("edges", function(x, order, ...) {
+    standardGeneric("edges")
 })
 
+## edgeOrder
+setGeneric("edgeOrder", function(x, ...) {
+  standardGeneric("edgeOrder")
+})
+
+## hasEdgeLength
 setGeneric("hasEdgeLength", function(x) {
     standardGeneric("hasEdgeLength")
 })
 
+## edgeLength
 setGeneric("edgeLength", function(x, ...) {
     standardGeneric("edgeLength")
 })
 
+## edgeLength<-
 setGeneric("edgeLength<-", function(x, ..., value) {
     standardGeneric("edgeLength<-")
 })
 
+## sumEdgeLength
 setGeneric("sumEdgeLength", function(phy, node) {
     standardGeneric("sumEdgeLength")
 })
 
-setGeneric("hasNodeLabels", function(x) {
-    standardGeneric("hasNodeLabels")
+## isRooted
+setGeneric("isRooted", function(x) {
+    standardGeneric("isRooted")
 })
 
-setGeneric("hasEdgeLabels", function(x) {
-    standardGeneric("hasEdgeLabels")
+## rootNode
+setGeneric("rootNode", function(x) {
+    standardGeneric("rootNode")
 })
 
-setGeneric("edgeOrder", function(x, ...) {
-  standardGeneric("edgeOrder")
+## rootNode<-
+setGeneric("rootNode<-", function(x, value) {
+    standardGeneric("rootNode<-")
 })
 
+## labels
 setGeneric("labels")
 
+## labels<-
 setGeneric("labels<-",
            function(object, type, use.names, ..., value) {
                standardGeneric("labels<-")
            })
 
+## hasNodeLabels
+setGeneric("hasNodeLabels", function(x) {
+    standardGeneric("hasNodeLabels")
+})
+
+## nodeLabels
 setGeneric("nodeLabels", function(object) {
     standardGeneric("nodeLabels")
 })
 
+## nodeLabels<-
 setGeneric("nodeLabels<-",
            function(object, ..., value) {
                standardGeneric("nodeLabels<-")
            })
 
+## tipLabels
 setGeneric("tipLabels", function(object) {
     standardGeneric("tipLabels")
 })
 
+## tipLabels<-
 setGeneric("tipLabels<-",
    function(object, ..., value) {
        standardGeneric("tipLabels<-")
    })
 
-setGeneric("nodeId", function(x, type=c("internal", "tip", "all")) {
-    standardGeneric("nodeId")
+## hasEdgeLabels
+setGeneric("hasEdgeLabels", function(x) {
+    standardGeneric("hasEdgeLabels")
 })
 
+## edgeLabels
 setGeneric("edgeLabels", function(x) {
     standardGeneric("edgeLabels")
 })
 
+## edgeLabels<-
 setGeneric("edgeLabels<-",
            function(object, ..., value) {
                standardGeneric("edgeLabels<-")
            })
 
+## print
 setGeneric("print")
 
+## head
 setGeneric("head")
 
+## tail
 setGeneric("tail")
 
+### ----------- phylo4d methods -----------
+
+## tdata
 setGeneric("tdata", function(x, ...) {
     standardGeneric("tdata")
 })
 
+## tdata<-
 setGeneric("tdata<-", function(x, ..., value) {
     standardGeneric("tdata<-")
 })
 
+## addData
 setGeneric("addData", function(x, ...) {
     standardGeneric("addData")
 })
 
+## hasTipData
+setGeneric("hasTipData", function(x) {
+    standardGeneric("hasTipData")
+})
+
+## hasNodeData
 setGeneric("hasNodeData", function(x) {
     standardGeneric("hasNodeData")
 })
 
-setGeneric("hasTipData", function(x) {
-    standardGeneric("hasTipData")
-})
+##
+##setGeneric("na.omit")
 
-setGeneric("na.omit")
-
 setGeneric("reorder")
 
+##setGeneric("rootEdge", function(x, order, ...) {
+##    standardGeneric("rootEdge")
+##})
+
 ###################
 ## Function .genlab
 ###################