[Adephylo-commits] r10 - pkg/R

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

Author: jombart
Date: 2008-11-20 19:39:10 +0100 (Thu, 20 Nov 2008)
New Revision: 10

Modified:
   pkg/R/partition.R
Log:
Added a distRoot function.


Modified: pkg/R/partition.R
===================================================================
--- pkg/R/partition.R	2008-11-20 18:25:52 UTC (rev 9)
+++ pkg/R/partition.R	2008-11-20 18:39:10 UTC (rev 10)
@@ -119,7 +119,7 @@
     res <- getnodes(res)
 
     return(res)
-}
+} # end path2tips
 
 
 
@@ -130,14 +130,24 @@
 ###########
 distRoot <- function(x, tip){
     if(!require(phylobase)) stop("phylobase package is not installed")
-    
+
     ## conversion from phylo, phylo4 and phylo4d
     x <- as(x, "phylo4")
-    
+
     ## check phylo4 object
     if (is.character(checkval <- check_phylo4(x))) stop(checkval)
-    
+
     ## main computations
-  tip <- getnodes(tip)
-    
-}
+    tip <- getnodes(x, tip)
+    root <- getnodes(x, nTips(x)+1)
+    ancTip <- ancestors(x, tip, which="all")
+
+    pathNodes <- setdiff(ancTip, root) # only internal nodes, without root
+    pathNodes <- c(tip, pathNodes)
+
+    pathNodes <- getnodes(x, pathNodes)
+
+    res <- sumEdgeLength(x, pathNodes)
+
+    return(res)
+} # end distRoot