[Adephylo-commits] r89 - pkg/man

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

Author: jombart
Date: 2008-12-12 19:32:37 +0100 (Fri, 12 Dec 2008)
New Revision: 89

Modified:
   pkg/man/treePart.Rd
Log:
Added an example comparing results of $Bscores and treePart in treePart doc.


Modified: pkg/man/treePart.Rd
===================================================================
--- pkg/man/treePart.Rd	2008-12-12 18:24:42 UTC (rev 88)
+++ pkg/man/treePart.Rd	2008-12-12 18:32:37 UTC (rev 89)
@@ -47,5 +47,18 @@
 temp <- phylo4d(x, partition)
 s.phylo4d(temp, cent=FALSE, scale=FALSE)
 }
+
+if(require(ade4)){
+## former orthobasis in ade4
+data(ungulates)
+ung.Bscores <- newick2phylog(ungulates$tre)$Bscores
+
+## version using treePart
+ung <- read.tree(text=ungulates$tre)
+ung.orthobas <- treePart(ung, res="orthobasis")
+
+## comparison of the first 3 vectors
+cbind(ung.Bscores[,1], ung.orthobas[,1],ung.Bscores[,2], ung.orthobas[,2], ung.Bscores[,3], ung.orthobas[,3])
 }
+}
 \keyword{manip}