[Phylobase-commits] r622 - in pkg: . R man

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

Author: regetz
Date: 2009-09-08 18:15:07 +0200 (Tue, 08 Sep 2009)
New Revision: 622

Modified:
   pkg/NAMESPACE
   pkg/R/methods-phylo4.R
   pkg/R/phylo4.R
   pkg/man/treewalk.Rd
Log:
added new edgeId method and exported via NAMESPACE; no documentation yet


Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2009-09-04 21:54:25 UTC (rev 621)
+++ pkg/NAMESPACE	2009-09-08 16:15:07 UTC (rev 622)
@@ -25,7 +25,7 @@
 exportMethods(nTips, nNodes, nEdges)
 
 # edge methods
-exportMethods(edges, hasEdgeLength, edgeLength, "edgeLength<-",
+exportMethods(edges, edgeId, hasEdgeLength, edgeLength, "edgeLength<-",
     sumEdgeLength, edgeOrder)
 
 # root methods

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2009-09-04 21:54:25 UTC (rev 621)
+++ pkg/R/methods-phylo4.R	2009-09-08 16:15:07 UTC (rev 622)
@@ -137,6 +137,25 @@
     x at order
 })
 
+# return edge IDs (or a subset thereof) in edge matrix order
+setMethod("edgeId", "phylo4", function(x, type=c("all", "tip",
+    "internal", "root")) {
+    type <- match.arg(type)
+    edge <- edges(x)
+    if (type=="tip") {
+        isTip <- !(edge[, 2] %in% edge[, 1])
+        edge <- edge[isTip, , drop=FALSE]
+    } else if (type=="internal") {
+        isInt <- (edge[, 2] %in% edge[, 1])
+        edge <- edge[isInt, , drop=FALSE]
+    } else if (type=="root") {
+        isRoot <- is.na(edge[, 1])
+        edge <- edge[isRoot, , drop=FALSE]
+    } # else just use complete edge matrix if type is "all"
+    id <- paste(edge[, 1], edge[, 2], sep="-")
+    return(id)
+})
+
 setMethod("hasEdgeLength","phylo4", function(x) {
     !all(is.na(x at edge.length))
 })

Modified: pkg/R/phylo4.R
===================================================================
--- pkg/R/phylo4.R	2009-09-04 21:54:25 UTC (rev 621)
+++ pkg/R/phylo4.R	2009-09-08 16:15:07 UTC (rev 622)
@@ -35,6 +35,12 @@
   standardGeneric("edgeOrder")
 })
 
+## edgeId
+setGeneric("edgeId", function(x, type=c("all", "tip", "internal",
+    "root")) {
+    standardGeneric("edgeId")
+})
+
 ## hasEdgeLength
 setGeneric("hasEdgeLength", function(x) {
     standardGeneric("hasEdgeLength")

Modified: pkg/man/treewalk.Rd
===================================================================
--- pkg/man/treewalk.Rd	2009-09-04 21:54:25 UTC (rev 621)
+++ pkg/man/treewalk.Rd	2009-09-08 16:15:07 UTC (rev 622)
@@ -12,6 +12,8 @@
 \alias{sumEdgeLength,phylo4-method}
 \alias{nodeId}
 \alias{nodeId,phylo4-method}
+\alias{edgeId}
+\alias{edgeId,phylo4-method}
 \title{tree traversal and utility functions}
 \description{
   Functions for describing relationships among