[Phylobase-commits] r295 - in pkg: R man

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

Author: jombart
Date: 2008-11-21 15:24:12 +0100 (Fri, 21 Nov 2008)
New Revision: 295

Modified:
   pkg/R/treewalk.R
   pkg/man/treewalk.Rd
Log:
Added a getedges function. It identifies the number of an edge given the number / label of its terminal node. 


Modified: pkg/R/treewalk.R
===================================================================
--- pkg/R/treewalk.R	2008-11-21 10:28:41 UTC (rev 294)
+++ pkg/R/treewalk.R	2008-11-21 14:24:12 UTC (rev 295)
@@ -139,7 +139,7 @@
 # shortestPath
 ###############
 shortestPath <- function(phy, node1, node2){
-    if(!require(phylobase)) stop("phylobase package is not installed")
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
 
     ## conversion from phylo, phylo4 and phylo4d
     x <- as(phy, "phylo4")
@@ -170,3 +170,30 @@
 
     return(res)
 } # end shortestPath
+
+
+
+
+
+###########
+# getedges
+###########
+getedges <- function(phy, node){
+
+    ## conversion from phylo, phylo4 and phylo4d
+    x <- as(phy, "phylo4")
+
+    ## come checks
+    if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+    node <- getnodes(x, node)
+    if(any(is.na(node))) stop("wrong node specified")
+    root <- rootNode(x)
+    node[node==root] <- NA
+
+    ## main computations
+    E <- x at edge
+    res <- match(node, E[,2])
+    names(res) <- names(node)
+
+    return(res)
+} # end getedges

Modified: pkg/man/treewalk.Rd
===================================================================
--- pkg/man/treewalk.Rd	2008-11-21 10:28:41 UTC (rev 294)
+++ pkg/man/treewalk.Rd	2008-11-21 14:24:12 UTC (rev 295)
@@ -6,6 +6,7 @@
 \alias{siblings}
 \alias{MRCA}
 \alias{getnodes}
+\alias{getedges}
 \alias{shortestPath}
 \title{tree traversal and utility functions}
 \description{
@@ -42,6 +43,9 @@
   \code{getnodes} takes character strings corresponding to tip or
   node labels, or node numbers; it returns a named
   vector of node numbers.
+  \code{getedges} takes character strings naming terminal
+  node of edges, or the corresponding node numbers; it returns a named
+  vector of edge numbers.
   \code{ancestors} and \code{descendants}
   return named vectors of the ancestors and descendants of
   a node; \code{ancestor} is a synonym for
@@ -74,7 +78,12 @@
   ancestors(geospiza,"N11")
   MRCA(geospiza,"conirostris","difficilis","fuliginosa")
   MRCA(geospiza,"olivacea","conirostris")
+  ## shortest path between 2 nodes
   shortestPath(geospiza, "fortis","fuliginosa")
   shortestPath(geospiza, "N02","N05")
+  ## identifying an edge fron its terminal node
+  getedges(geospiza,c("olivacea","N02","fortis"))
+  getnodes(geospiza, c("olivacea","N02","fortis"))
+  geospiza$edge[c(26,1,11),]
 }
 \keyword{misc}