[adegenet-commits] r857 - in pkg: R man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Mar 30 01:08:58 CEST 2011 

Author: jombart
Date: 2011-03-30 01:08:57 +0200 (Wed, 30 Mar 2011)
New Revision: 857

Modified:
   pkg/R/dapc.R
   pkg/man/auxil.Rd
   pkg/man/dapc.Rd
   pkg/man/genlight.Rd
   pkg/man/seploc.Rd
Log:
PKg passes the check now.
Yepeeee


Modified: pkg/R/dapc.R
===================================================================
--- pkg/R/dapc.R	2011-03-29 22:12:02 UTC (rev 856)
+++ pkg/R/dapc.R	2011-03-29 23:08:57 UTC (rev 857)
@@ -743,7 +743,7 @@
     UseMethod("as.lda")
 }
 
-as.lda.dapc <- function(x){
+as.lda.dapc <- function(x, ...){
     if(!inherits(x,"dapc")) stop("x is not a dapc object")
     res <- list()
 

Modified: pkg/man/auxil.Rd
===================================================================
--- pkg/man/auxil.Rd	2011-03-29 22:12:02 UTC (rev 856)
+++ pkg/man/auxil.Rd	2011-03-29 23:08:57 UTC (rev 857)
@@ -7,12 +7,15 @@
 \alias{.rmspaces}
 \alias{.genlab}
 \alias{.readExt}
+\alias{corner}
+\alias{num2col}
+\alias{transp}
 \title{ Utilities functions for adegenet}
 \description{
-  These functions are mostly used internally in adegenet.
-  The notable exceptions are \code{adegenetWeb} which opens the adegenet
-  website in the default navigator, and \code{adegenetTutorial} which
-  opens online tutorials for adegenet.\cr
+  These functions are mostly used internally in adegenet.  The notable
+  exceptions are \code{adegenetWeb} which opens the adegenet website in
+  the default navigator, \code{adegenetTutorial} which opens online
+  tutorials for adegenet, and a few auxiliary graphical functions.\cr
 
   The other functions are:\cr
   - \code{checkType}: checks the type of markers being used in a
@@ -20,18 +23,41 @@
   - \code{.rmspaces}: remove peripheric spaces in a character string. \cr
   - \code{.genlab}: generate labels in a correct alphanumeric ordering. \cr
   - \code{.readExt}: read the extension of a given file. \cr
- 
+  - \code{corner}: adds text to a corner of a figure. \cr
+  - \code{num2col}: translates a numeric vector into colors. \cr
+  - \code{transp}: adds transparency to a vector of colors. Note that
+  transparent colors are not supported on some graphical devices.\cr
 }
 \usage{
 adegenetWeb()
 adegenetTutorial(which=c("general","spca"))
 .genlab(base, n)
+corner(text, posi="topleft",  inset=0.1, \dots)
+num2col(x, col.pal=heat.colors, reverse=FALSE,
+               x.min=min(x), x.max=max(x), na.col="green")
+transp(col, alpha=.5)
 }
 \arguments{
   \item{which}{a character string being "general" or "spca", indicating
     which tutorial should be opened.}
   \item{base}{a character string forming the base of the labels}
   \item{n}{the number of labels to generate}
+  \item{text}{a character string to be added to the plot}
+  \item{posi}{a character matching any combinations of "top/bottom" and
+    "left/right".}
+  \item{inset}{a vector of two numeric values (recycled if needed)
+    indicating the inset, as a fraction of the plotting region.}
+  \item{\dots}{further arguments to be passed to \code{\link{text}}}
+  \item{x}{a numeric vector}
+  \item{col.pal}{a function generating colors according to a given palette.}
+  \item{reverse}{a logical stating whether the palette should be
+    inverted (TRUE), or not (FALSE, default).}
+  \item{x.min}{the minimal value from which to start the color scale}
+  \item{x.max}{the maximal value from which to start the color scale}
+  \item{na.col}{the color to be used for missing values (NAs)}
+  \item{col}{a vector of colors}
+  \item{alpha}{a numeric value between 0 and 1 representing the alpha
+  coefficient; 0: total transparency; 1: no transparency.}
 }
 \value{
   For \code{.genlab}, a character vector of size "n".

Modified: pkg/man/dapc.Rd
===================================================================
--- pkg/man/dapc.Rd	2011-03-29 22:12:02 UTC (rev 856)
+++ pkg/man/dapc.Rd	2011-03-29 23:08:57 UTC (rev 857)
@@ -11,6 +11,8 @@
 \alias{scatter.dapc}
 \alias{assignplot}
 \alias{predict.dapc}
+\alias{as.lda}
+\alias{as.lda.dapc}
 \title{Discriminant Analysis of Principal Components (DAPC)}
 \description{
   These functions implement the Discriminant Analysis of Principal
@@ -45,6 +47,11 @@
   and \code{\link[MASS]{lda}} from the \code{MASS} package. The
   \code{predict} procedure uses \code{\link[MASS]{predict.lda}} from the
   \code{MASS} package.
+
+  \code{as.lda} is a generic with a method for \code{dapc} object which
+  converts these objects into outputs similar to that of
+  \code{lda.default}.
+  
 }
 \usage{
 \method{dapc}{data.frame}(x, grp, n.pca=NULL, n.da=NULL, center=TRUE,
@@ -76,7 +83,7 @@
         cleg = 1, cgrid = 1, pixmap = NULL, contour = NULL, area = NULL,
         \ldots)
 
-assignplot(x, only.grp=NULL, subset=NULL, cex.lab=.75, pch=3)
+assignplot(x, only.grp=NULL, subset=NULL, new.pred=NULL, cex.lab=.75, pch=3)
 
 \method{predict}{dapc}(object, newdata, prior = object$prior, dimen,
          method = c("plug-in", "predictive", "debiased"), ...)
@@ -148,6 +155,10 @@
   \item{pch}{a \code{numeric} indicating the type of point to be used to indicate
     the prior group of individuals (see \code{\link{points}} documentation for
     more details).}
+  \item{new.pred}{an optional list, as returned by the \code{predict}
+    method for \code{dapc} objects; if provided, the individuals
+    with unknown groups are added at the bottom of the plot. To
+    visualize these individuals only, specify \code{only.grp="unknown"}.}
   \item{dudi}{optionally, a multivariate analysis with the class
     \code{dudi} (from the ade4 package). If provided, prior PCA will be
     ignored, and this object will be used as a prior step for variable

Modified: pkg/man/genlight.Rd
===================================================================
--- pkg/man/genlight.Rd	2011-03-29 22:12:02 UTC (rev 856)
+++ pkg/man/genlight.Rd	2011-03-29 23:08:57 UTC (rev 857)
@@ -115,9 +115,12 @@
       SNPs.}
     \item{\code{loc.all}:}{a vector of characters indicating the alleles
       of each SNP.}
+    \item{\code{chromosome}:}{an optional factor indicating the
+  chromosome to which each SNP belongs.}
+    \item{\code{position}:}{an optional vector of integers indicating the
+      position of the SNPs.}
     \item{\code{ploidy}:}{a vector of integers indicating the ploidy of each individual.}
-    \item{\code{pop}:}{a factor indicating the population of each
-      individual.}
+    \item{\code{pop}:}{a factor indicating the population of each individual.}
     \item{\code{other}:}{a list containing other miscellaneous information.}
   }
 }

Modified: pkg/man/seploc.Rd
===================================================================
--- pkg/man/seploc.Rd	2011-03-29 22:12:02 UTC (rev 856)
+++ pkg/man/seploc.Rd	2011-03-29 23:08:57 UTC (rev 857)
@@ -6,6 +6,7 @@
 \alias{seploc,ANY-method}
 \alias{seploc,genind-method}
 \alias{seploc,genpop-method}
+\alias{seploc,genlight-method}
 \title{ Separate data per locus}
 \description{
   The function \code{seploc} splits an object (\linkS4class{genind} or

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