[adegenet-commits] r1117 - in pkg: R man

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

Author: greatsage
Date: 2013-04-25 18:32:37 +0200 (Thu, 25 Apr 2013)
New Revision: 1117

Modified:
   pkg/R/dapc.R
   pkg/man/dapc.Rd
Log:
fixed classes

Modified: pkg/R/dapc.R
===================================================================
--- pkg/R/dapc.R	2013-04-25 14:56:56 UTC (rev 1116)
+++ pkg/R/dapc.R	2013-04-25 16:32:37 UTC (rev 1117)
@@ -986,7 +986,6 @@
 ## ############
 ## ## crossval
 ## ############
-xval <- function (object, n.pca, n.da, training.set, ...) UseMethod("xval")
 
 xval.dapc <- function(object, n.pca, n.da, training.set = 90, ...){
   training.set = training.set/100
@@ -1010,6 +1009,11 @@
   return(res)
 } # end of xval.dapc
 
+xval <- function (object, n.pca, n.da, training.set, ...) UseMethod("xval")
+xval.genind  <- function(object, n.pca, n.da, training.set = 90, ...){
+  res = xval.dapc(object = object, n.pca = n.pca, n.da = n.da, training.set = training.set)
+  return(res)
+}
 ## ###############
 ## ## randtest.dapc
 ## ###############

Modified: pkg/man/dapc.Rd
===================================================================
--- pkg/man/dapc.Rd	2013-04-25 14:56:56 UTC (rev 1116)
+++ pkg/man/dapc.Rd	2013-04-25 16:32:37 UTC (rev 1117)
@@ -9,8 +9,9 @@
 \alias{print.dapc}
 \alias{summary.dapc}
 \alias{predict.dapc}
+\alias{xval.dapc}
 \alias{xval}
-\alias{xval.dapc}
+\alias{xval.genind}
 \alias{as.lda}
 \alias{as.lda.dapc}
 \title{Discriminant Analysis of Principal Components (DAPC)}
@@ -40,8 +41,11 @@
   - \code{summary.dapc}: extracts useful information from a  \code{dapc} object.\cr
   - \code{predict.dapc}: predicts group memberships based on DAPC results.\cr
   - \code{xval.dapc}: performs cross-validation of DAPC function varying the number of PCs and keeping the number of DAs fixed. 
+  - \code{xval}: performs cross-validation of DAPC function varying the number of PCs and keeping the number of DAs fixed. 
+  - \code{xval.genind}: performs cross-validation of DAPC function varying the number of PCs and keeping the number of DAs fixed. 
 
 
+
   DAPC implementation calls upon \code{\link[ade4]{dudi.pca}} from the
   \code{ade4} package (except for \linkS4class{genlight} objects)
   and \code{\link[MASS]{lda}} from the \code{MASS} package. The
@@ -78,6 +82,8 @@
          method = c("plug-in", "predictive", "debiased"), ...)
 
 \method{xval}{dapc}(object, n.pca, n.da, training.set = 90, \ldots)
+
+\method{xval}{genind}(object, n.pca, n.da, training.set = 90, \ldots)
 }
 \arguments{
   \item{x}{\code{a data.frame}, \code{matrix}, or \code{\linkS4class{genind}}
@@ -192,7 +198,7 @@
   \code{assign.prop} (proportion of overall correct assignment),
   \code{assign.per.pop} (proportion of correct assignment per group),
   \code{prior.grp.size} (prior group sizes), and \code{post.grp.size} (posterior
-  group sizes),  \code{xval.dapc} (returns a list of four lists, each one with as 
+  group sizes),  \code{xval.dapc}, \code{xval.genind} and \code{xval}  (all return a list of four lists, each one with as 
   many items as cross-validation runs.  The first item is a list of \code{assign} components,  
   the secon is a list of \code{posterior} components, the thirs is a list of \code{ind.score}
   components and the fourth is a list of \code{match.prp} items, i.e. the prortion of the validation
@@ -326,6 +332,12 @@
 
 plot(unlist(crossval.test$match.prp))
 
+# the use can also just call  xval:
+crossval.test2 <- xval(microbov, n.pca = 40, n.da = 15, training.set = 90)
+plot(unlist(crossval.test2$match.prp)) 
+
+
+
 }