[Adephylo-commits] r41 - in pkg: R man

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

Author: jombart
Date: 2008-11-26 16:25:31 +0100 (Wed, 26 Nov 2008)
New Revision: 41

Modified:
   pkg/R/utils.R
   pkg/man/listTips.Rd
   pkg/man/treePart.Rd
Log:
Various fixes. Package still broken:
> if(require(ape) & require(phylobase)){
+ ## make a tree
+ x <- as(rtree(20),"phylo4")
+ plot(x,show.node=TRUE)
+ ## get shortest path between tip 1 and all other tips.
+ sp.tips(x, "t1", "t2")
+ sp.tips(x, 1, 2:20, TRUE)
+ }
Loading required package: ape
Loading required package: phylobase
Error in .setupMethodsTables(fdef) : 
  trying to get slot "group" from an object of a basic class ("NULL") with no slots
Calls: plot ... plot -> as -> .getMethodsTable -> .setupMethodsTables
Execution halted



Modified: pkg/R/utils.R
===================================================================
--- pkg/R/utils.R	2008-11-26 15:12:14 UTC (rev 40)
+++ pkg/R/utils.R	2008-11-26 15:25:31 UTC (rev 41)
@@ -28,9 +28,10 @@
     } # end while
 
     if(!include.root) {
-        path <- getnodes(x, path[-length(path)]) # exclude the root
+        path <- path[-length(path)] # exclude the root
     }
-    return(path)
+
+    return(getnodes(x, path))
 } # end tipToRoot
 
 

Modified: pkg/man/listTips.Rd
===================================================================
--- pkg/man/listTips.Rd	2008-11-26 15:12:14 UTC (rev 40)
+++ pkg/man/listTips.Rd	2008-11-26 15:25:31 UTC (rev 41)
@@ -17,7 +17,7 @@
   A list whose components are vectors of named tips for a given node.
 }
 \author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
-\seealso{\code{\link{listNodes}} which lists the direct descendants for
+\seealso{\code{\link{listDD}} which lists the direct descendants for
   each node. \cr
   
   \code{\link{treePart}} which defines partitions of tips

Modified: pkg/man/treePart.Rd
===================================================================
--- pkg/man/treePart.Rd	2008-11-26 15:12:14 UTC (rev 40)
+++ pkg/man/treePart.Rd	2008-11-26 15:25:31 UTC (rev 41)
@@ -19,7 +19,7 @@
   tip (rows).
 }
 \author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
-\seealso{\code{\link{listNodes}} which is called by \code{treePart}.
+\seealso{\code{\link{listDD}} which is called by \code{treePart}.
 }
 \examples{
 if(require(ape) & require(phylobase)){