[Picante-commits] r92 - branches/gsoc/R

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

Author: mrhelmus
Date: 2008-06-10 04:56:35 +0200 (Tue, 10 Jun 2008)
New Revision: 92

Modified:
   branches/gsoc/R/phylodiversity.R
Log:
Fixed Bug: Changed pruneMissing to prune.sample

Modified: branches/gsoc/R/phylodiversity.R
===================================================================
--- branches/gsoc/R/phylodiversity.R	2008-06-09 07:32:26 UTC (rev 91)
+++ branches/gsoc/R/phylodiversity.R	2008-06-10 02:56:35 UTC (rev 92)
@@ -131,7 +131,7 @@
 
   if(is(tree)[1]=="phylo")
   {
-    tree<-pruneMissing(samp[1,],tree)$tree
+    tree<-prune.sample(samp,tree)
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
@@ -257,7 +257,7 @@
 
   if(is(tree)[1]=="phylo")
   {
-    tree<-pruneMissing(samp[1,],tree)$tree
+    tree<-prune.sample(samp,tree) 
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
@@ -322,7 +322,7 @@
 
   if(is(tree)[1]=="phylo")
   {
-    tree<-pruneMissing(samp[1,],tree)$tree
+    tree<-prune.sample(samp,tree)
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
@@ -384,7 +384,7 @@
   }  
   if(is(tree)[1]=="phylo")
   {
-    tree<-pruneMissing(samp[1,],tree)$tree
+    tree<-prune.sample(samp,tree)
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny