[adegenet-commits] r852 - in pkg: R man

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

Author: jombart
Date: 2011-03-29 22:25:07 +0200 (Tue, 29 Mar 2011)
New Revision: 852

Modified:
   pkg/R/dapc.R
   pkg/man/dapc.Rd
Log:
argt pca.loadings -> pca.info
Added doc about pca.info.


Modified: pkg/R/dapc.R
===================================================================
--- pkg/R/dapc.R	2011-03-29 20:18:07 UTC (rev 851)
+++ pkg/R/dapc.R	2011-03-29 20:25:07 UTC (rev 852)
@@ -7,7 +7,7 @@
 ## dapc.data.frame
 ###################
 dapc.data.frame <- function(x, grp, n.pca=NULL, n.da=NULL,
-                            center=TRUE, scale=FALSE, pca.loadings=TRUE, var.contrib=TRUE,
+                            center=TRUE, scale=FALSE, var.contrib=TRUE, pca.info=TRUE,
                             pca.select=c("nbEig","percVar"), perc.pca=NULL, ..., dudi=NULL){
 
     ## FIRST CHECKS
@@ -107,7 +107,7 @@
 
 
     ## optional: store loadings of variables
-    if(pca.loadings){
+    if(pca.info){
         res$pca.loadings <- as.matrix(U)
         res$pca.cent <- pcaX$cent
         res$pca.norm <- pcaX$norm
@@ -146,7 +146,7 @@
 ## dapc.genind
 #############
 dapc.genind <- function(x, pop=NULL, n.pca=NULL, n.da=NULL,
-                        scale=FALSE, scale.method=c("sigma", "binom"), truenames=TRUE, pca.loadings=TRUE, var.contrib=TRUE,
+                        scale=FALSE, scale.method=c("sigma", "binom"), truenames=TRUE, var.contrib=TRUE, pca.info=TRUE,
                         pca.select=c("nbEig","percVar"), perc.pca=NULL, ...){
 
     ## FIRST CHECKS
@@ -203,7 +203,7 @@
 ## dapc.genlight
 #################
 dapc.genlight <- function(x, pop=NULL, n.pca=NULL, n.da=NULL,
-                          scale=FALSE,  pca.loadings=TRUE, var.contrib=TRUE,
+                          scale=FALSE,  var.contrib=TRUE, pca.info=TRUE
                           pca.select=c("nbEig","percVar"), perc.pca=NULL, glPca=NULL, ...){
     ## FIRST CHECKS ##
     if(!require(ade4, quiet=TRUE)) stop("ade4 library is required.")
@@ -328,7 +328,7 @@
 
 
     ## optional: store loadings of variables
-    if(pca.loadings){
+    if(pca.info){
         res$pca.loadings <- as.matrix(U)
         res$pca.cent <- glMean(toto,alleleAsUnit=FALSE)
         res$pca.norm <- sqrt(glVar(toto,alleleAsUnit=FALSE))

Modified: pkg/man/dapc.Rd
===================================================================
--- pkg/man/dapc.Rd	2011-03-29 20:18:07 UTC (rev 851)
+++ pkg/man/dapc.Rd	2011-03-29 20:25:07 UTC (rev 852)
@@ -42,17 +42,17 @@
 }
 \usage{
 \method{dapc}{data.frame}(x, grp, n.pca=NULL, n.da=NULL, center=TRUE,
-     scale=FALSE,var.contrib=TRUE, pca.select=c("nbEig","percVar"),
+     scale=FALSE,var.contrib=TRUE, pca.info=TRUE, pca.select=c("nbEig","percVar"),
      perc.pca=NULL, \ldots, dudi=NULL)
 
 \method{dapc}{matrix}(x, \ldots)
 
 \method{dapc}{genind}(x, pop=NULL, n.pca=NULL, n.da=NULL, scale=FALSE,
      scale.method=c("sigma", "binom"), truenames=TRUE, var.contrib=TRUE,
-     pca.select=c("nbEig","percVar"), perc.pca=NULL, \ldots)
+     pca.info=TRUE, pca.select=c("nbEig","percVar"), perc.pca=NULL, \ldots)
 
 \method{dapc}{genlight}(x, pop = NULL, n.pca = NULL, n.da = NULL, scale
-    = FALSE, var.contrib = TRUE, pca.select = c("nbEig", "percVar"),
+    = FALSE, var.contrib = TRUE, pca.info=TRUE, pca.select = c("nbEig", "percVar"),
     perc.pca = NULL, glPca = NULL, \ldots)
 
 \method{dapc}{dudi}(x, grp, \ldots)
@@ -93,6 +93,10 @@
     contribution of original variables (alleles, for \linkS4class{genind} objects)
     should be provided (TRUE, default) or not (FALSE). Such output can be useful,
     but can also create huge matrices when there is a lot of variables.}
+  \item{pca.info}{a \code{logical} indicating whether information about
+    the prior PCA should be stored (TRUE, default) or not (FALSE). This
+    information is required to predict group membership of new
+    individuals using \code{predict}, but makes the object slightly bigger.}
   \item{pca.select}{a \code{character} indicating the mode of selection of PCA
     axes, matching either "nbEig" or "percVar". For "nbEig", the user
     has to specify the number of axes retained (interactively, or via