[Picante-commits] r99 - in branches/gsoc: R man

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

Author: skembel
Date: 2008-06-11 23:02:44 +0200 (Wed, 11 Jun 2008)
New Revision: 99

Modified:
   branches/gsoc/R/phylodiversity.R
   branches/gsoc/man/psd.Rd
   branches/gsoc/man/specaccum.psr.Rd
Log:
Cleaning up gsoc branch in preparation for merging into trunk

Modified: branches/gsoc/R/phylodiversity.R
===================================================================
--- branches/gsoc/R/phylodiversity.R	2008-06-11 07:45:28 UTC (rev 98)
+++ branches/gsoc/R/phylodiversity.R	2008-06-11 21:02:44 UTC (rev 99)
@@ -135,7 +135,7 @@
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
-    Cmatrix<-vcv.phylo(tree,cor=T)
+    Cmatrix<-vcv.phylo(tree,cor=TRUE)
   } else {
     Cmatrix<-tree
     species<-colnames(samp)
@@ -261,7 +261,7 @@
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
-    Cmatrix<-vcv.phylo(tree,cor=T)
+    Cmatrix<-vcv.phylo(tree,cor=TRUE)
   } else {
     Cmatrix<-tree
     species<-colnames(samp)
@@ -326,7 +326,7 @@
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
-    Cmatrix<-vcv.phylo(tree,cor=T)
+    Cmatrix<-vcv.phylo(tree,cor=TRUE)
   } else {
     Cmatrix<-tree
     species<-colnames(samp)
@@ -388,7 +388,7 @@
     # Make sure that the species line up
     samp<-samp[,tree$tip.label]
     # Make a correlation matrix of the species pool phylogeny
-    Cmatrix<-vcv.phylo(tree,cor=T)
+    Cmatrix<-vcv.phylo(tree,cor=TRUE)
   } else {
     Cmatrix<-tree
     species<-colnames(samp)

Modified: branches/gsoc/man/psd.Rd
===================================================================
--- branches/gsoc/man/psd.Rd	2008-06-11 07:45:28 UTC (rev 98)
+++ branches/gsoc/man/psd.Rd	2008-06-11 21:02:44 UTC (rev 99)
@@ -13,7 +13,7 @@
 psv(samp,tree,compute.var=TRUE)
 psr(samp,tree,compute.var=TRUE)
 pse(samp,tree)
-psc(samp,tree,compute.var=TRUE)
+psc(samp,tree)
 psd(samp,tree,compute.var=TRUE)
 psv.spp(samp,tree)
 }

Modified: branches/gsoc/man/specaccum.psr.Rd
===================================================================
--- branches/gsoc/man/specaccum.psr.Rd	2008-06-11 07:45:28 UTC (rev 98)
+++ branches/gsoc/man/specaccum.psr.Rd	2008-06-11 21:02:44 UTC (rev 99)
@@ -32,6 +32,6 @@
               \cr Helmus M.R., Bland T.J., Williams C.K. & Ives A.R. (2007) Phylogenetic measures of biodiversity. American Naturalist, 169, E68-E83 }
 \author{ Matthew Helmus \email{mrhelmus at gmail.com}
  }
-\seealso{ \code{\link{psr}}, \code{\link{specaccum}}}
+\seealso{ \code{\link{psr}}, \code{\link[vegan]{specaccum}}}
 
 \keyword{univar}