[Adephylo-commits] r15 - pkg/R

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

Author: jombart
Date: 2008-11-21 11:29:20 +0100 (Fri, 21 Nov 2008)
New Revision: 15

Modified:
   pkg/R/partition.R
Log:
Commented out shortestPath -> moved to phylobase package. This is definitely part of treewalk stuff.


Modified: pkg/R/partition.R
===================================================================
--- pkg/R/partition.R	2008-11-20 19:55:17 UTC (rev 14)
+++ pkg/R/partition.R	2008-11-21 10:29:20 UTC (rev 15)
@@ -96,33 +96,38 @@
 ###############
 # shortestPath
 ###############
-shortestPath <- function(x, node1, node2){
-    if(!require(phylobase)) stop("phylobase package is not installed")
+## shortestPath <- function(x, node1, node2){
+##     if(!require(phylobase)) stop("phylobase package is not installed")
 
-    ## conversion from phylo, phylo4 and phylo4d
-    x <- as(x, "phylo4")
+##     ## conversion from phylo, phylo4 and phylo4d
+##     x <- as(x, "phylo4")
 
-    ## check phylo4 object
-    if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+##     ## come checks
+##     if (is.character(checkval <- check_phylo4(x))) stop(checkval)
+##     t1 <- getnodes(x, node1)
+##     t2 <- getnodes(x, node2)
+##     if(any(is.na(c(t1,t2)))) stop("wrong node specified")
+##     if(t1==t2) return(NULL)
 
-    ## main computations
-    t1 <- getnodes(x, node1)
-    t2 <- getnodes(x, node2)
+##     ## main computations
+##     comAnc <- MRCA(x, t1, t2) # common ancestor
+##     desComAnc <- descendants(x, comAnc, which="all")
+##     ancT1 <- ancestors(x, t1, which="all")
+##     path1 <- intersect(desComAnc, ancT1) # path: common anc -> t1
 
-    comAnc <- MRCA(x, t1, t2) # common ancestor
-    desComAnc <- descendants(x, comAnc, which="all")
-    ancT1 <- ancestors(x, t1, which="all")
-    path1 <- intersect(desComAnc, ancT1) # path: common anc -> t1
+##     ancT2 <- ancestors(x, t2, which="all")
+##     path2 <- intersect(desComAnc, ancT2) # path: common anc -> t2
 
-    ancT2 <- ancestors(x, t2, which="all")
-    path2 <- intersect(desComAnc, ancT2) # path: common anc -> t2
+##     res <- union(path1, path2) # union of the path
+##     ## add the common ancestor if it differs from t1 or t2
+##     if(!comAnc %in% c(t1,t2)){
+##         res <- c(comAnc,res)
+##     }
 
-    res <- union(path1, path2) # union of the path
-    res <- c(comAnc,res) # add the common ancestor
-    res <- getnodes(x, res)
+##     res <- getnodes(x, res)
 
-    return(res)
-} # end shortestPath
+##     return(res)
+## } # end shortestPath