[Adephylo-commits] r40 - in pkg: R man

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

Author: jombart
Date: 2008-11-26 16:12:14 +0100 (Wed, 26 Nov 2008)
New Revision: 40

Modified:
   pkg/R/utils.R
   pkg/man/miscUtils.Rd
Log:
Bugfix to .tipToRoot: added an argument to return the root.


Modified: pkg/R/utils.R
===================================================================
--- pkg/R/utils.R	2008-11-26 14:58:26 UTC (rev 39)
+++ pkg/R/utils.R	2008-11-26 15:12:14 UTC (rev 40)
@@ -18,7 +18,7 @@
 ## root: to root node; could be computed inside the function,
 ## but will often be computed outside, once and for all.
 ##
-.tipToRoot <- function(x, tip, root){
+.tipToRoot <- function(x, tip, root, include.root=FALSE){
     E <- x$edge
     path <- NULL
     curNode <- tip
@@ -27,7 +27,9 @@
         path <- c(path, curNode)
     } # end while
 
-    path <- getnodes(x, path[-length(path)]) # exclude the root
+    if(!include.root) {
+        path <- getnodes(x, path[-length(path)]) # exclude the root
+    }
     return(path)
 } # end tipToRoot
 
@@ -109,7 +111,7 @@
 
 
     ## main computations
-    allPathToRoot <- lapply(allTips, function(i) .tipToRoot(x, i, root))
+    allPathToRoot <- lapply(allTips, function(i) .tipToRoot(x, i, root, include.root=TRUE))
     names(allPathToRoot) <- allTips
 
     allPath1 <- allPathToRoot[as.character(t1)]

Modified: pkg/man/miscUtils.Rd
===================================================================
--- pkg/man/miscUtils.Rd	2008-11-26 14:58:26 UTC (rev 39)
+++ pkg/man/miscUtils.Rd	2008-11-26 15:12:14 UTC (rev 40)
@@ -13,12 +13,16 @@
 
 }
 \usage{
-.tipToRoot(x, tip, root)
+.tipToRoot(x, tip, root, include.root=FALSE)
 }
 \arguments{
   \item{x}{A valid tree of  class \linkS4class{phylo4}.}
   \item{tip}{An integer identifying a tip by its numbers.}
-  \item{root}{An integer identifying the root of the tree by its numbers.}
+  \item{root}{An integer identifying the root of the tree by its
+    numbers.}
+  \item{include.root}{a logical stating whether the root must be
+    included as a node of the path from tip to root (TRUE), or not
+    (FALSE, default).}
 }
 \value{
   \code{.tipToRoot}: a vector of named integers identifying nodes.\cr