Change some man pages & correct DESCRIPTION file

DESCRIPTION

 Package: amap
-Version: 0.7-1
-Date: 2006-20-01
+Version: 0.7-2
+Date: 2006-12-17
+Suggests: Biobase
 Title: Another Multidimensional Analysis Package 
 Author: Antoine Lucas 
-Maintainer: Antoine Lucas <antoinelucas@libertysurf.fr>
+Maintainer: Antoine Lucas <antoinelucas@free.fr>
 Description: Tools for Clustering and Principal 
         Component Analysis (With robusts methods, and 
 	parallelized functions).	
 License: GPL
 URL: http://mulcyber.toulouse.inra.fr/projects/amap/
-Packaged: Sun Nov 27 19:06:18 2005; antoine
+Packaged: Tue Dec 19 19:21:55 2006; antoine

R/zzz.R

@@ -4,17 +4,10 @@
 .onLoad <- .First.lib <- function(lib, pkg)
 {
     library.dynam("amap", pkg, lib)
-    vers <- R.Version()$major
-    if(vers <2)
-      {
-        have.mva <- "package:mva" %in% search()
-        if(!have.mva) require("mva")
-      }
-    else
-      {
-        have.stats <- "package:stats" %in% search()
-        if(!have.stats)   require("stats")
-      }
+
+    have.stats <- "package:stats" %in% search()
+    if(!have.stats)   require("stats")
+  
 
     if("Biobase" %in% .packages(all=TRUE))
       require("Biobase")

man/acp.Rd

+\name{acp}
+\alias{acp}
+\alias{pca}
+\alias{print.acp}
+
+\title{Principal component analysis}
+\description{Principal component analysis}
+\usage{
+acp(x,center=TRUE,reduce=TRUE,wI=rep(1,nrow(x)),wV=rep(1,ncol(x)))
+pca(x,center=TRUE,reduce=TRUE,wI=rep(1,nrow(x)),wV=rep(1,ncol(x)))
+print.acp(x, ...) 
+}
+
+
+\arguments{
+\item{x}{Matrix  / data frame}
+\item{center}{a logical value indicating whether we center data}
+\item{reduce}{a logical value indicating whether we "reduce" data i.e. 
+  divide each column by standard deviation}
+\item{wI,wV}{weigth vector for individuals / variables}
+\item{\dots}{arguments to be passed to or from other methods.}
+}
+
+
+
+
+\value{
+  An object of class \bold{acp} 
+  The object is a list with components:
+
+  \item{sdev}{the standard deviations of the principal components.}
+  \item{loadings}{the matrix of variable loadings (i.e., a matrix
+    whose columns contain the eigenvectors).  This is of class
+    \code{"loadings"}: see \code{\link[stats]{loadings}} for its \code{print}
+    method.}
+  \item{scores}{if \code{scores = TRUE}, the scores of the supplied
+    data on the principal components.}
+  \item{eig}{Eigen values}
+}
+
+\details{
+  This function offer a variant of \code{\link[stats]{princomp}} and
+  \code{\link[stats]{prcomp}} functions, with a slightly different
+  graphic representation (see \code{\link{plot.acp}}).
+  }
+
+
+\references{
+  A. Carlier
+  Analyse des données Multidimensionnelles
+  \url{http://www.lsp.ups-tlse.fr/Carlier/enseignement.html}
+}
+
+
+\examples{
+data(lubisch)
+lubisch <- lubisch[,-c(1,8)]
+p <- acp(lubisch)
+plot(p)
+}
+\keyword{multivariate}
+
+\author{Antoine Lucas, \url{http://mulcyber.toulouse.inra.fr/projects/amap/}}
+\seealso{\link{plot.acp},\link{acpgen}, \link[stats]{princomp} }

man/acpgen.Rd

@@ -117,6 +117,10 @@ class(p)<- "acp"
   Structures by Means of Principal Component Analysis. In Data Science
   and its Applications} (eds Y. Escoufier and C. Hayashi),
   pp. 177-192. Tokyo: Academic Press.
+
+  Antoine Lucas and Sylvain Jasson, \emph{Using amap and ctc Packages
+  for Huge Clustering}, R News, 2006, vol 6, issue 5 pages 58-60.
+
 }
 
 

man/acprob.Rd

@@ -55,6 +55,10 @@ divide each column by standard deviation}
   Structures by Means of Principal Component Analysis. In Data Science
   and its Applications} (eds Y. Escoufier and C. Hayashi),
   pp. 177-192. Tokyo: Academic Press.
+
+  Antoine Lucas and Sylvain Jasson, \emph{Using amap and ctc Packages
+  for Huge Clustering}, R News, 2006, vol 6, issue 5 pages 58-60.
+
 }
 
 \author{Antoine Lucas, \url{http://mulcyber.toulouse.inra.fr/projects/amap/}}

man/distpar.Rd

@@ -34,6 +34,12 @@ distpar(x, method = "euclidean", nbproc = 2, diag = FALSE, upper = FALSE)
 
 }
 
+\references{
+  Antoine Lucas and Sylvain Jasson, \emph{Using amap and ctc Packages
+    for Huge Clustering}, R News, 2006, vol 6, issue 5 pages 58-60.
+  }
+
+
 \seealso{
   \code{\link{Dist}}
 }

man/hcluster.Rd

@@ -90,6 +90,13 @@ hcluster(x, method = "euclidean", diag = FALSE, upper = FALSE,
   \code{\link{Dist}}, \code{\link{hclusterpar}},
   \code{\link[stats]{hclust}}, \code{\link[stats]{kmeans}}.
 }
+
+\references{
+  Antoine Lucas and Sylvain Jasson, \emph{Using amap and ctc Packages
+    for Huge Clustering}, R News, 2006, vol 6, issue 5 pages 58-60.
+  }
+
+
 \examples{
 
 data(USArrests)

man/hclusterpar.Rd

@@ -89,6 +89,13 @@ hclusterpar(x, method = "euclidean", diag = FALSE, upper = FALSE,
 \seealso{
   \code{\link{Dist}}, \code{\link{hcluster}}, \code{\link[stats]{hclust}}, \code{\link[stats]{kmeans}}.
 }
+
+\references{
+  Antoine Lucas and Sylvain Jasson, \emph{Using amap and ctc Packages
+    for Huge Clustering}, R News, 2006, vol 6, issue 5 pages 58-60.
+  }
+
+
 \examples{
 
 data(USArrests)