[adegenet-commits] r195 - in pkg: . data man misc/bug-report.1.2-2.04

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Oct 30 20:12:57 CET 2008 

Author: jombart
Date: 2008-10-30 20:12:57 +0100 (Thu, 30 Oct 2008)
New Revision: 195

Added:
   pkg/data/rupica.RData
   pkg/man/rupica.Rd
   pkg/misc/bug-report.1.2-2.04/unbiased-h.html
Removed:
   pkg/misc/bug-report.1.2-2.04/unbiased h.html
Modified:
   pkg/TODO
Log:
added the rupica dataset.


Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-10-27 17:42:49 UTC (rev 194)
+++ pkg/TODO	2008-10-30 19:12:57 UTC (rev 195)
@@ -29,22 +29,22 @@
 * fix bug 1.2-2.01 (read.structure issue) -- fixed: was due to the default of "onerowperind" argument.
 * fix bug 1.2-2.02 (read.genetix issue)
 * fix bug 1.2-2.03 (monmonier issue)
+* fix request 1.2-2.04 (implement adjusted heretozygosity in summary)
 
-
 # DOCUMENTATION ISSUES:
 =======================
-* make a tutorial for the sPCA
+* make a tutorial for the sPCA -- done (TJ)
 
 
 # NEW IMPLEMENTATIONS:
 =====================
 * color plot for the sPCA results, based on RGB representation of Cavalli-Sforza -- done(TJ)
-* loadingplot for plotting loadings of one axis -- done(TJ)
-* adegenetTutorial function which opens the online tutorials
+* loadingplot for plotting loadings of one axis -- done (TJ)
+* adegenetTutorial function which opens the online tutorials -- done (TJ)
 * allow for the use of na.replace and scaleGen in spca function -- done (TJ)
+* add rupica dataset -- done (TJ)
 
 
-
 # TESTING:
 ==========
 * 

Added: pkg/data/rupica.RData
===================================================================
(Binary files differ)


Property changes on: pkg/data/rupica.RData
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: pkg/man/rupica.Rd
===================================================================
--- pkg/man/rupica.Rd	                        (rev 0)
+++ pkg/man/rupica.Rd	2008-10-30 19:12:57 UTC (rev 195)
@@ -0,0 +1,85 @@
+\encoding{UTF-8}
+\name{rupica}
+\alias{rupica}
+\docType{data}
+\title{Microsatellites genotypes of 335 chamois (Rupicapra
+   rupicapra) from the Bauges mountains (France)}
+\description{
+  This data set contains the genotypes of 335 chamois (\emph{Rupicapra
+    rupicapra}) from the Bauges mountains, in France. No prior
+  clustering about individuals is known. Each genotype is
+  georeferenced. These data also contain a raster map of elevation of
+  the sampling area.
+}
+\usage{data(rupica)}
+\format{
+    \code{rupica} is a genind object with 6 supplementary components
+    inside the \code{@other} slot:
+    \describe{
+        \item{xy}{a matrix containing the spatial coordinates of the genotypes.}
+        \item{sex}{a factor (F: female; M: male) giving the sex of each individual.}
+	\item{age}{an integer giving the age of each individual.}
+	\item{behav}{a factor (resid: resident; disp: likely to
+	  disperse) stating whether an individual is likely to disperse
+	  or not (based on its age and sex).}
+	\item{mnt}{a raster map of elevation, with the \code{asc} format
+	  from the \code{adehabitat} package.}
+	\item{showBauges}{a function to display the map of elevation
+	  with an appropriate legend (use \code{showBauges()}).}
+    }
+}
+\source{
+Daniel Maillard, 'Office National de la Chasse et de la Faune Sauvage'
+(ONCFS), France.
+}
+\references{
+  Cassar S (2008) Organisation spatiale de la variabilité génétique et
+  phénotypique à l'échelle du paysage: le cas du chamois et du
+  chevreuil, en milieu de montagne. PhD Thesis. University Claude
+  Bernard - Lyon 1, France. \cr
+  
+  Cassar S, Jombart T, Loison A, Pontier D, Dufour A-B, Jullien J-M,
+  Chevrier T, Maillard D. Spatial genetic structure of Alpine chamois
+  (\emph{Rupicapra rupicapra}): a consequence of landscape features and
+  social factors? submitted to \emph{Molecular Ecology}.
+}
+\examples{
+if(require(ade4) & require(adehabitat) & require(spdep)){
+
+data(rupica)
+rupica
+
+## see the sampling area
+showBauges <- rupica$other$showBauges
+showBauges()
+points(rupica$other$xy,col="red")
+
+## perform a sPCA
+spca1 <- spca(rupica,type=5,d1=0,d2=2300,plot=FALSE,scannf=FALSE,nfposi=2,nfnega=0)
+barplot(spca1$eig,col=rep(c("black","grey"),c(2,100)),main="sPCA eigenvalues")
+screeplot(spca1,main="sPCA eigenvalues: decomposition")
+
+## data visualization
+showBauges(,labcex=1)
+s.value(spca1$xy,spca1$ls[,1],add.p=TRUE,csize=.5)
+add.scatter.eig(spca1$eig,1,1,1,posi="topleft",sub="Eigenvalues")
+
+showBauges(,labcex=1)
+s.value(spca1$xy,spca1$ls[,2],add.p=TRUE,csize=.5)
+add.scatter.eig(spca1$eig,2,2,2,posi="topleft",sub="Eigenvalues")
+
+rupica$other$showBauges()
+colorplot(spca1$xy,spca1$li,cex=1.5,add.plot=TRUE)
+
+\dontrun{
+## global and local tests
+Gtest <- global.rtest(rupica at tab,spca1$lw,nperm=999)
+Gtest
+plot(Gtest)
+Ltest <- local.rtest(rupica at tab,spca1$lw,nperm=999)
+Ltest
+plot(Ltest)
+}
+}
+}
+\keyword{datasets}

Deleted: pkg/misc/bug-report.1.2-2.04/unbiased h.html
===================================================================
--- pkg/misc/bug-report.1.2-2.04/unbiased h.html	2008-10-27 17:42:49 UTC (rev 194)
+++ pkg/misc/bug-report.1.2-2.04/unbiased h.html	2008-10-30 19:12:57 UTC (rev 195)
@@ -1,16 +0,0 @@
-<html>
-<head>
-<title>unbiased h</title>
-<link rel="important stylesheet" href="chrome://messenger/skin/messageBody.css">
-</head>
-<body>
-<table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part1"><tr><td><b>Subject: </b>unbiased h</td></tr><tr><td><b>From: </b>Julien Varaldi <varaldi at biomserv.univ-lyon1.fr></td></tr><tr><td><b>Date: </b>Mon, 27 Oct 2008 18:01:04 +0100</td></tr></table><table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part2"><tr><td><b>To: </b>Thibaut Jombart <jombart at biomserv.univ-lyon1.fr></td></tr></table><br>
-<div class="moz-text-flowed">Voila la ref pour
-<br>
-<br>Ht=2N/(2N-1) (1-somme p au carre)
-<br>
-<br>Nei. Estimation of Average Heterozygosity and Genetic Distance from a Small Number of Individuals. Genetics (1978) vol. 89 (3) pp. 583-590
-<br>
-<br>
-<br>&nbsp;<br></div></body>
-</html>

Added: pkg/misc/bug-report.1.2-2.04/unbiased-h.html
===================================================================
--- pkg/misc/bug-report.1.2-2.04/unbiased-h.html	                        (rev 0)
+++ pkg/misc/bug-report.1.2-2.04/unbiased-h.html	2008-10-30 19:12:57 UTC (rev 195)
@@ -0,0 +1,16 @@
+<html>
+<head>
+<title>unbiased h</title>
+<link rel="important stylesheet" href="chrome://messenger/skin/messageBody.css">
+</head>
+<body>
+<table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part1"><tr><td><b>Subject: </b>unbiased h</td></tr><tr><td><b>From: </b>Julien Varaldi <varaldi at biomserv.univ-lyon1.fr></td></tr><tr><td><b>Date: </b>Mon, 27 Oct 2008 18:01:04 +0100</td></tr></table><table border=0 cellspacing=0 cellpadding=0 width="100%" class="header-part2"><tr><td><b>To: </b>Thibaut Jombart <jombart at biomserv.univ-lyon1.fr></td></tr></table><br>
+<div class="moz-text-flowed">Voila la ref pour
+<br>
+<br>Ht=2N/(2N-1) (1-somme p au carre)
+<br>
+<br>Nei. Estimation of Average Heterozygosity and Genetic Distance from a Small Number of Individuals. Genetics (1978) vol. 89 (3) pp. 583-590
+<br>
+<br>
+<br>&nbsp;<br></div></body>
+</html>

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