[Picante-commits] r43 - pkg/man

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

Author: skembel
Date: 2008-03-25 19:14:45 +0100 (Tue, 25 Mar 2008)
New Revision: 43

Removed:
   pkg/man/taxaShuffle.Rd
Modified:
   pkg/man/utility.Rd
Log:
Further utility function cleanup and TODO update

Deleted: pkg/man/taxaShuffle.Rd
===================================================================
--- pkg/man/taxaShuffle.Rd	2008-03-25 06:26:26 UTC (rev 42)
+++ pkg/man/taxaShuffle.Rd	2008-03-25 18:14:45 UTC (rev 43)
@@ -1,27 +0,0 @@
-\name{taxaShuffle}
-\alias{taxaShuffle}
-
-\title{ Shuffle taxa names on a dist or matrix object}
-\description{
-  Shuffle taxa names on a dist or matrix object
-}
-\usage{
-taxaShuffle(x, strata)
-}
-
-\arguments{
-  \item{x}{ Matrix or dist object of interspecific distances }
-  \item{strata}{ Strata for randomization }
-}
-\details{
-  Code from \code{\link[vegan]{mantel}}
-}
-\value{
-  Matrix with taxa names shuffled
-}
-
-\seealso{ \code{\link[vegan]{mantel}} }
-
-\author{ Steve Kembel <skembel at berkeley.edu> }
-
-\keyword{manip}

Modified: pkg/man/utility.Rd
===================================================================
--- pkg/man/utility.Rd	2008-03-25 06:26:26 UTC (rev 42)
+++ pkg/man/utility.Rd	2008-03-25 18:14:45 UTC (rev 43)
@@ -6,6 +6,7 @@
 \alias{phylo2phylog}
 \alias{sortColumns}
 \alias{sortRows}
+\alias{taxaShuffle}
 \title{ Picante utility functions }
 \description{
   Picante utility functions for tree and data manipulation
@@ -17,16 +18,18 @@
 phylo2phylog(phy, ...)
 sortColumns(x)
 sortRows(x)
+taxaShuffle(x, strata)
 t2p2t(phy, species)
 }
 
 \arguments{
     \item{phy}{ phylo object }
     \item{species}{ Vector of species names }
-    \item{x}{ A data.frame or matrix }
+    \item{x}{ A data.frame, matrix or dist object }
     \item{colID}{ Numeric or character ID of column to include }
   \item{int.node}{ internal node number }
   \item{return.names}{ TRUE or FALSE }
+  \item{strata}{ Strata for randomization }  
   \item{...}{Additional arguments}
 }
 
@@ -38,8 +41,12 @@
   \item{phylo2phylog}{An ade4 phylog}
   \item{sortColumns}{A data.frame or matrix with columns sorted by name}
   \item{sortRows}{A data.frame or matrix with rows sorted by name}
-  
+    \item{taxaShuffle}{Matrix with taxa names shuffled}
 }
 
+\details{
+  Various utility functions. \code{taxaShuffle} code taken from \code{\link[vegan]{mantel}}
+}
+
 \author{ Steven Kembel <skembel at berkeley.edu>, David Ackerly <dackerly at berkeley.edu> }
 \keyword{manip}