[Picante-commits] r79 - in pkg: . R man

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

Author: skembel
Date: 2008-05-31 09:59:21 +0200 (Sat, 31 May 2008)
New Revision: 79

Modified:
   pkg/DESCRIPTION
   pkg/R/utility.R
   pkg/man/utility.Rd
Log:
Removed phylo2phylog function to eliminate dependency

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-05-31 07:47:07 UTC (rev 78)
+++ pkg/DESCRIPTION	2008-05-31 07:59:21 UTC (rev 79)
@@ -6,6 +6,6 @@
 Author: Steve Kembel <skembel at berkeley.edu>, David Ackerly <dackerly at berkeley.edu>, Simon Blomberg <s.blomberg1 at uq.edu.au>, Peter Cowan <pdc at berkeley.edu>, Cam Webb <cwebb at oeb.harvard.edu>
 Maintainer: Steve Kembel <skembel at berkeley.edu>
 Depends: ape, vegan
-Suggests: circular, ade4
+Suggests: circular
 Description: Phylocom integration, community analyses, null-models, traits and evolution in R
 License: GPL v2

Modified: pkg/R/utility.R
===================================================================
--- pkg/R/utility.R	2008-05-31 07:47:07 UTC (rev 78)
+++ pkg/R/utility.R	2008-05-31 07:59:21 UTC (rev 79)
@@ -69,7 +69,7 @@
 	return(phy)
 	}
 
-`phylo2phylog` <-
+`.phylo2phylog` <-
 function(phy, ...) {
     if(!require(ade4)) {stop("This function requires the ade4 package")}
     newick2phylog(write.tree(phy),...)

Modified: pkg/man/utility.Rd
===================================================================
--- pkg/man/utility.Rd	2008-05-31 07:47:07 UTC (rev 78)
+++ pkg/man/utility.Rd	2008-05-31 07:59:21 UTC (rev 79)
@@ -16,7 +16,6 @@
 df2vec(x, colID=1)
 internal2tips(phy, int.node, return.names = FALSE)
 node.age(phy)
-phylo2phylog(phy, ...)
 pic.variance(x, phy, scaled = TRUE)
 sortColumns(x)
 sortRows(x)
@@ -37,7 +36,6 @@
   \item{df2vec}{A named vector}
   \item{internal2tips}{Vector of tips descended from a node}
   \item{node.age}{Phylo object with phylo\$ages vector of node ages corresponding to phylo\$edge}
-  \item{phylo2phylog}{An ade4 phylog}
   \item{pic.variance}{Variance of independent contrasts}
   \item{sortColumns}{A data.frame or matrix with columns sorted by name}
   \item{sortRows}{A data.frame or matrix with rows sorted by name}