[Picante-commits] r90 - branches/gsoc/R

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

Author: mrhelmus
Date: 2008-06-09 09:26:23 +0200 (Mon, 09 Jun 2008)
New Revision: 90

Modified:
   branches/gsoc/R/phylodiversity.R
Log:
Fixed Bug: in PSE,PSC,PSV and sppPSV. Prunes the tree to the species found in the sample. Now the tree or the Cmatrix can have more species than the sample.

Modified: branches/gsoc/R/phylodiversity.R
===================================================================
--- branches/gsoc/R/phylodiversity.R	2008-06-05 06:13:53 UTC (rev 89)
+++ branches/gsoc/R/phylodiversity.R	2008-06-09 07:26:23 UTC (rev 90)
@@ -121,6 +121,7 @@
 PSVcalc<-function(samp,tree,compute.var=TRUE){
   # Make samp matrix a pa matrix
   samp[samp>0]<-1
+  
   flag=0
   if (is.null(dim(samp))) #if the samp matrix only has one site
   {
@@ -130,12 +131,17 @@
 
   if(is(tree)[1]=="phylo")
   {
+    tree<-pruneMissing(samp[1,],tree)$tree
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
     Cmatrix<-vcv.phylo(tree,cor=T)
   } else {
     Cmatrix<-tree
+    species<-colnames(samp)
+    preval<-colSums(samp)/sum(samp)
+    species<-species[preval>0]
+    Cmatrix<-Cmatrix[species,species]
     samp<-samp[,colnames(Cmatrix)]
   }
   
@@ -251,12 +257,17 @@
 
   if(is(tree)[1]=="phylo")
   {
+    tree<-pruneMissing(samp[1,],tree)$tree
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
     Cmatrix<-vcv.phylo(tree,cor=T)
   } else {
     Cmatrix<-tree
+    species<-colnames(samp)
+    preval<-colSums(samp)/sum(samp)
+    species<-species[preval>0]
+    Cmatrix<-Cmatrix[species,species]
     samp<-samp[,colnames(Cmatrix)]
   }
   
@@ -311,12 +322,17 @@
 
   if(is(tree)[1]=="phylo")
   {
+    tree<-pruneMissing(samp[1,],tree)$tree
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
     Cmatrix<-vcv.phylo(tree,cor=T)
   } else {
     Cmatrix<-tree
+    species<-colnames(samp)
+    preval<-colSums(samp)/sum(samp)
+    species<-species[preval>0]
+    Cmatrix<-Cmatrix[species,species]
     samp<-samp[,colnames(Cmatrix)]
   }
 
@@ -368,12 +384,17 @@
   }  
   if(is(tree)[1]=="phylo")
   {
+    tree<-pruneMissing(samp[1,],tree)$tree
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
     Cmatrix<-vcv.phylo(tree,cor=T)
   } else {
     Cmatrix<-tree
+    species<-colnames(samp)
+    preval<-colSums(samp)/sum(samp)
+    species<-species[preval>0]
+    Cmatrix<-Cmatrix[species,species]
     samp<-samp[,colnames(Cmatrix)]
   }
   # reduce given Cmatrix to the species observed in samp
@@ -421,4 +442,5 @@
     }
     return(data.frame(PSDout))
   }
-}
\ No newline at end of file
+}
+