[adegenet-commits] r294 - in www: . files

Thu Apr 2 18:10:11 CEST 2009

Author: jombart
Date: 2009-04-02 18:10:11 +0200 (Thu, 02 Apr 2009)
New Revision: 294

Modified:
   www/acceuil.html
   www/documentation.html
   www/download.html
   www/files/ChangeLog
   www/news.html
Log:
update website for new release (1.2-3)


Modified: www/acceuil.html
===================================================================

--- www/acceuil.html	2009-04-02 15:50:49 UTC (rev 293)
+++ www/acceuil.html	2009-04-02 16:10:11 UTC (rev 294)
@@ -16,12 +16,12 @@
  href="http://www.r-project.org/" target="_top"><img alt=""
  src="images/R.png"
  style="border: 0px solid ; width: 30px; height: 23px;"></a></span>
-package dedicated to the handling of molecular marker data for
-multivariate analysis. This package is related to <a
+package dedicated to the handling and multivariate analysis of genetic
+markers. This package is related to <a
  href="http://pbil.univ-lyon1.fr/ADE-4/home.php?lang=eng" target="_top">ade4</a>,
 a R
 package for multivariate analysis, graphics, phylogeny and spatial
-analysis. It is currently hosted by <a
+analysis. It is kindly hosted by <a
  href="https://r-forge.r-project.org/projects/adegenet/" target="_top">R-Forge</a>.
 adegenet is described in the following application note:<br>
 <span style="font-style: italic;"></span>Jombart T. (<span
@@ -48,17 +48,22 @@
 <small><br>
 </small><span style="text-decoration: underline;">Main features of
 adegenet are:</span><br>
-<br>
+- data representation (<span style="font-weight: bold;">classes</span>)
+suitable for multivariate analysis<br>
 </div>
-- definition of new object <span style="font-weight: bold;">classes</span>
-to facilitate multivariate analysis<br>
 - data <span style="font-weight: bold;">import</span> from GENETIX,
 STRUCTURE, Genepop, Fstat, Easypop, or any dataframe of genotypes<br>
+- data import from <span style="font-weight: bold;">aligned DNA
+sequences</span> to <span style="font-weight: bold;">SNPs</span><br>
 - data <span style="font-weight: bold;">export</span> to the R
 packages genetics, hierfstat, LDheatmap<br>
 - handling of <span style="font-weight: bold;">different levels of
-ploidy</span><br>
-- basic and advanced <span style="font-weight: bold;">data manipulation</span><br>
+ploidy<br>
+</span>- handling of <span style="font-weight: bold;">codominant </span>markers<span
+ style="font-weight: bold;"> </span>and<span style="font-weight: bold;">
+presence/absence</span> data<span style="font-weight: bold;"><br>
+</span>- basic and advanced <span style="font-weight: bold;">data
+manipulation</span><br>
 - basic <span style="font-weight: bold;">data information </span>(heterozygosity,
 numbers of alleles, sample sizes, ...)<br>
 - <span style="font-weight: bold;">HWE</span> and <span
@@ -74,17 +79,16 @@
 genetics: sPCA, </span><span style="font-weight: bold;">tests for
 global and local
 structuring, </span><span style="font-weight: bold;">Monmonier
-algorithm<span style="font-weight: bold;"></span><br>
+algorithm<br>
 <br>
 <br>
-</span>Author: adegenet is developed by <a
- href="http://biomserv.univ-lyon1.fr/%7Ejombart/" target="_top">Thibaut
-Jombart</a>
-(email: jombart AT biomserv DOT univ-lyon1 DOT fr)<br>
+</span>Author: adegenet is developed by Thibaut
+Jombart
+(<a href="http://www1.imperial.ac.uk/medicine/people/t.jombart/">website</a>)<br>
 Contributors: P&eacute;ter
 S&oacute;lymos<br>
 Datasets from: Katayoun Moazami-Goudarzi &amp; Denis Lalo&euml;,
-Dominique Pontier <br>
+Dominique Pontier, Daniel Maillard<br>
 <span style="font-weight: bold;"><br>
 </span>Suggestions, remarks and contributions are greatly encouraged!<br>
 <br>

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2009-04-02 15:50:49 UTC (rev 293)
+++ www/documentation.html	2009-04-02 16:10:11 UTC (rev 294)
@@ -43,8 +43,7 @@
  style="font-weight: bold;">only for diploid</span> genotypes <br>
 - a <span style="font-weight: bold;">sPCA tutorial</span> (<a
  href="files/tutorial-spca.pdf">pdf</a>), showing how to use the
-spatial Principal Component Analysis (Jombart et al. 2008)<img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+spatial Principal Component Analysis (Jombart et al. 2008)<br>
 <span style="text-decoration: underline;"></span><br>
 <span style="color: rgb(255, 0, 0);"></span></div>
 </body>

Modified: www/download.html
===================================================================
--- www/download.html	2009-04-02 15:50:49 UTC (rev 293)
+++ www/download.html	2009-04-02 16:10:11 UTC (rev 294)
@@ -18,15 +18,15 @@
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 The
 <span style="font-weight: bold;">current stable version</span>
-(adegenet_1.2-2)
+(adegenet_1.2-3)
 is available as:<br>
-- <a href="files/adegenet_1.2-2.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-2.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-2.zip">Windows binary</a><br>
+- <a href="files/adegenet_1.2-3.tar.gz">linux/unix sources</a><br>
+- MacOS X binary<br>
+- Windows binary<br>
 <br>
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 The
-<span style="font-weight: bold;">devel version</span> (adegenet_1.2-3)
+<span style="font-weight: bold;">devel version</span> (adegenet_1.2-4)
 is also available
 from <a href="https://r-forge.r-project.org/scm/?group_id=120"
  target="_top">R-Forge's
@@ -48,6 +48,11 @@
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 <span style="font-weight: bold;">Older
 versions</span>:<br>
+adegenet_1.2-2<br>
+- <a href="files/adegenet_1.2-2.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-2.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-2.zip">Windows binary</a><br>
+<br>
 adegenet_1.2-1<br>
 - <a href="files/adegenet_1.2-1.tar.gz">linux/unix sources</a><br>
 - <a href="files/adegenet_1.2-1.tgz">MacOS X binary</a><br>

Modified: www/files/ChangeLog
===================================================================
--- www/files/ChangeLog	2009-04-02 15:50:49 UTC (rev 293)
+++ www/files/ChangeLog	2009-04-02 16:10:11 UTC (rev 294)
@@ -1,3 +1,44 @@
+			CHANGES IN ADEGENET VERSION 1.2-3
+
+
+NEW FEATURES
+
+	o implement handling of presence/absence markers. genind and
+	genpop object now have a 'type' attribute to differentiate between
+	codominant markers (e.g. microsatellite), which is the default
+	type, and presence/absence data (e.g. AFLP). Functions in adegenet
+	now behave according to the type of markers being used.
+
+	o SNP can now be obtained from sequence data, stored as DNAbin
+	(see E. Paradis's package 'ape'). They can be selected to verify
+	any given degree of polymorphism.
+
+	o 'hybridize' can now be used for genotypes having any even degree
+	of ploidy (e.g. tetraploid genotypes).
+
+	o the new function 'isPoly' checks which loci are polymorphic, or
+	which alleles contribute to polymorphism.
+
+	o the new function 'pop' can be used to retrieve and set the pop
+	slot of genind object.
+
+	o the new function 'selPopSize' allows one to select a subset of
+	genotypes belonging to well-sampled populations, as defined by a
+	threshold sample size.
+
+	o the new accessor 'locNames' can be used to retrieve real labels
+	of markers and/or alleles.
+
+	o the loadingplot has been modified to allow specifying x axis, so
+	that scoring SNPs along their sequence is now possible. 
+
+
+BUG FIXES
+
+	o no bug to fix this version!
+
+
+
 			CHANGES IN ADEGENET VERSION 1.2-2
 
 
@@ -12,6 +53,9 @@
 	o a "sep" argument is now handled by df2genind: this allows
 	reading many data formats.
 
+	o implemented a method "scaleGen" for genind / genpop objects,
+	which scales allelic data using different methods.
+
 	o  colorplot: a generic function, with a method for spca
 	objects. Represents up to three principal components based on RGB
 	representation of Cavalli-Sforza.

Modified: www/news.html
===================================================================
--- www/news.html	2009-04-02 15:50:49 UTC (rev 293)
+++ www/news.html	2009-04-02 16:10:11 UTC (rev 294)
@@ -20,15 +20,39 @@
  style="font-weight: bold;"></span><br>
 <span style="font-weight: bold;"></span>Current
 stable version of <span style="color: rgb(255, 0, 0);">adegenet is
-1.2-2 </span>for R.2.8.0.<br>
+1.2-3 </span>for R.2.8.1.<br>
 You can install the devel version from <a
  href="https://r-forge.r-project.org/scm/?group_id=120">R-Forge</a>.<br>
 See the current <a href="files/ChangeLog">ChangeLog</a> for a list of
 all modifications.<br>
 <br>
-<span style="font-weight: bold;">19/012/2008 <img
+<br>
+<span style="font-weight: bold;">02/04/2009 <img
  style="width: 80px; height: 37px;" alt="" src="images/new.png"></span><span
  style="font-weight: bold;"></span><br>
+<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-3</span>)
+has been released for R.2.8.1 !</big><br>
+This is a important<span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"> release, including some significant
+improvements
+(see </span></span><a href="files/ChangeLog">ChangeLog</a><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
+file). The most important new feature is that <span
+ style="color: rgb(255, 0, 0);">presence/absence </span>data like AFLP
+are now handled. A new slot 'type' now distinguishes, in genind and
+genpop objects, codominant markers (type="codom") from presence/absence
+(type="PA"). Also, <span
+ style="color: rgb(255, 0, 0); font-family: monospace;">hybridize</span>
+can now perform hybridization between genotypes with any even degree of
+ploidy. Another noticeable feature is that SNPs can be obtained from
+aligned DNA sequences using <span
+ style="color: rgb(255, 0, 0); font-family: monospace;">DNAbin2genind</span>.This
+time, the tutorial has been updated at the same time as the package
+release!<br>
+<br>
+<br>
+</span></span><span style="font-weight: bold;">19/12/2008 </span><span
+ style="font-weight: bold;"></span><br>
 <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-2</span>)
 has been released for R.2.8.0 !</big><br>
 <span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This

