[Phylobase-commits] r291 - pkg/R

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

Author: francois
Date: 2008-11-20 23:36:38 +0100 (Thu, 20 Nov 2008)
New Revision: 291

Modified:
   pkg/R/treewalk.R
Log:
added new option for 'ancestors' which fixes bug in MRCA

Modified: pkg/R/treewalk.R
===================================================================
--- pkg/R/treewalk.R	2008-11-20 17:47:17 UTC (rev 290)
+++ pkg/R/treewalk.R	2008-11-20 22:36:38 UTC (rev 291)
@@ -81,11 +81,11 @@
 }
 
 ## get ancestors (all nodes)
-ancestors <- function (phy, node, which=c("all","parent"))
+ancestors <- function (phy, node, which=c("all","parent","ALL"))
 {
     which <- match.arg(which)
     if (which=="parent") return(ancestor(phy,node))
-    node <- getnodes(phy,node)
+    oNode <- node <- getnodes(phy,node)
     if (is.na(node)) stop("node ",node," not found in tree")
     res <- numeric(0)
     n <- nTips(phy)
@@ -95,6 +95,7 @@
         node <- anc
         if (anc==n+1) break
     }
+    if(which == "ALL") res <- c(oNode, res)
     return(getnodes(phy,res))
 }
 
@@ -112,7 +113,7 @@
         uniqueNodes[[1]]
     }
     else {
-        ancests <- lapply(nodes,ancestors,phy=phy)
-        getnodes(phy,max(Reduce(intersect,ancests)))
+        ancests <- lapply(nodes, ancestors, phy=phy, which="ALL")
+        getnodes(phy, max(Reduce(intersect, ancests)))
     }
 }