From noreply at r-forge.r-project.org  Wed Jul  8 17:55:44 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  8 Jul 2015 17:55:44 +0200 (CEST)
Subject: [adegenet-commits] r1200 - in www/images: . gimp
Message-ID: <20150708155544.C3E15187AD8@r-forge.r-project.org>

Author: jombart
Date: 2015-07-08 17:55:44 +0200 (Wed, 08 Jul 2015)
New Revision: 1200

Modified:
   www/images/acceuil.png
   www/images/gimp/acceuil.xcf
Log:
updated image for new release

Modified: www/images/acceuil.png
===================================================================
(Binary files differ)

Modified: www/images/gimp/acceuil.xcf
===================================================================
(Binary files differ)


From noreply at r-forge.r-project.org  Wed Jul  8 18:11:32 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  8 Jul 2015 18:11:32 +0200 (CEST)
Subject: [adegenet-commits] r1201 - www
Message-ID: <20150708161132.4CF061858DF@r-forge.r-project.org>

Author: jombart
Date: 2015-07-08 18:11:32 +0200 (Wed, 08 Jul 2015)
New Revision: 1201

Modified:
   www/acceuil.html
   www/news.html
Log:
updated website

Modified: www/acceuil.html
===================================================================
--- www/acceuil.html	2015-07-08 15:55:44 UTC (rev 1200)
+++ www/acceuil.html	2015-07-08 16:11:32 UTC (rev 1201)
@@ -24,16 +24,22 @@
       <br>
       <br>
       <br>
-      <div style="text-align: left;"> <span style="font-weight: bold;">adegenet</span>
-        is an <span style="text-decoration: underline;"><a
-            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
-        exploratory analysis of genetic data. It implements a set of
-        tools ranging from multivariate methods to spatial genetics and
-        genome-wise SNP data analysis. <br>
+      <div style="text-align: left;"> <span style="font-weight: bold;">NOTE:
+          this website will soon be replaced by a new github page.
+          Meanwhile, up-to-date information on adegenet can be found on
+          github:<br>
+          <a href="https://github.com/thibautjombart/adegenet/wiki">https://github.com/thibautjombart/adegenet/wiki</a><br>
+          <br>
+          adegenet</span> is an <span style="text-decoration:
+          underline;"><a 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 exploratory analysis of genetic data. It implements a set
+        of tools ranging from multivariate methods to spatial genetics
+        and genome-wise SNP data analysis. <br>
         <br>
-        It is developed on <a href="http://sourceforge.net/p/adegenet">Sourceforge</a>
+        It is developed on <a
+          href="https://github.com/thibautjombart/adegenet">Github</a>
         by <a href="http://sites.google.com/site/thibautjombart/">Thibaut
 
 
@@ -41,17 +47,12 @@
 
 
 
-          Jombart</a>, <a
-          href="https://sites.google.com/site/caitlincollinswebpage/home">Caitlin
 
-          Collins</a>, Ismail Ahmed, <a
-          href="http://www.federicocalboli.com/">Federico Calboli</a>, <a
-          href="http://www1.imperial.ac.uk/medicine/people/a.cori/">Anne
-          Cori</a>, Tobias Erik Reiners, and <a
-          href="https://sites.google.com/site/psolymos/">P?ter S?lymos</a>,
-        and officially released on <a href="http://cran.r-project.org">CRAN</a>
-        periodically. <br>
+          Jombart</a>, Caitlin Collins, Zhian N Kamvar, Roman Lustrik,
+        Ismail Ahmed, Federico Calboli, Anne Cori, Tobias Erik Reiners,
+        and P?ter S?lymos, and officially released on CRAN periodically.
         <br>
+        <br>
         adegenet is described in the following publications:<br>
         <ul>
           <li> Jombart T. (2008) adegenet: a R package for the
@@ -78,6 +79,7 @@
 
 
 
+
               the bublisher's website</a>]<br>
           </li>
         </ul>
@@ -106,6 +108,7 @@
 
 
 
+
                 DNA sequences</span> to <span style="font-weight:
                 bold;">SNPs</span></li>
             <li> data import from <span style="font-weight: bold;">aligned
@@ -113,6 +116,7 @@
 
 
 
+
                 protein sequences</span> to polymorphic sites </li>
             <li> data <span style="font-weight: bold;">export</span> to
               the R packages genetics, hierfstat, LDheatmap</li>
@@ -131,6 +135,7 @@
 
 
 
+
                 manipulation</span></li>
             <li> basic <span style="font-weight: bold;">data
                 information </span>(heterozygosity, numbers of alleles,
@@ -151,6 +156,7 @@
 
 
 
+
                 Fst </span></li>
             <li> simulation of <span style="font-weight: bold;">hybridization</span></li>
             <li>methods for <span style="font-weight: bold;">spatial
@@ -158,6 +164,7 @@
 
 
 
+
                 for global and local structuring, </span><span
                 style="font-weight: bold;">Monmonier algorithm</span></li>
             <li>the <span style="font-style: italic; font-weight:
@@ -171,6 +178,7 @@
 
 
 
+
               </span>for reconstructing genealogies of haplotypes</li>
             <li>simulation of <span style="font-weight: bold;">genealogies
 
@@ -182,6 +190,7 @@
 
 
 
+
                 of haplotypes</span></li>
             <li> Discriminant Analysis of Principal Components (<span
                 style="font-weight: bold;">DAPC</span>)</li>
@@ -214,6 +223,7 @@
 
 
 
+
         Collins (<a href="mailto:caitiecollins17 at gmail.com">caitiecollins at gmail.com</a>),
 
 
@@ -224,11 +234,13 @@
 
 
 
+
         Isma?l Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
 
 
 
 
+
         Federico Calboli (<a href="mailto:f.calboli at imperial.ac.uk">f.calboli at imperial.ac.uk</a>),
 
 
@@ -237,6 +249,7 @@
 
 
 
+
         Anne Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>),
 Tobias
 
@@ -248,6 +261,7 @@
 
 
 
+
         Erik Reiners (<a href="mailto:Tobias.Reiners at Senckenberg.de">Tobias.Reiners at Senckenberg.de</a>),
 
 
@@ -258,6 +272,7 @@
 
 
 
+
         P?ter S?lymos (<a href="mailto:solymos at ualberta.ca">solymos at ualberta.ca</a>)<br>
         <span style="text-decoration: underline;">Contributors
           (datasets/ideas):</span> Christophe Fraser, Katayoun

Modified: www/news.html
===================================================================
--- www/news.html	2015-07-08 15:55:44 UTC (rev 1200)
+++ www/news.html	2015-07-08 16:11:32 UTC (rev 1201)
@@ -37,15 +37,32 @@
         style="font-weight: bold;"></span><span 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 1.4-2 </span>for
-      R.3.1.0.<br>
+      <span style="color: rgb(255, 0, 0);">adegenet is 2.0.0 </span>for
+      R.3.2.1.<br>
       See the current <a
         href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a>
       for a list of all modifications.<br>
       <br>
       <br>
-      13/05/2014 <img style=" width: 80px; height: 37px;" alt=""
-        src="images/new.png"><br>
+      07/07/2015 <img style=" width: 80px; height: 37px;" alt=""
+        src="images/new.png" height="37" width="80"><br>
+      <big>New adegenet version (<span style="color: rgb(255, 0, 0);">2.0.0</span>)
+        has been released for R-3.2.1!</big> <span style="color:
+        rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
+        style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
+          0);">This is a new major release, which implements a lot of
+          improvements over previous versions, including support for
+          varying ploidy in a single dataset, simplified data
+          structures, hierarchical stucture storage and manipulation,
+          and more. </span><span style="color: rgb(0, 0, 0);">See the </span></span><span
+        style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
+          0);"></span></span><a
+        href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
+        style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
+          0);"></span></span><span style="color: rgb(255, 0, 0);"><span
+          style="color: rgb(0, 0, 0);"> file for more details.</span></span><br>
+      <br>
+      13/05/2014 <br>
       <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.4-2</span>)
         has been released for R-3.1.0!</big> <span style="color:
         rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
@@ -101,6 +118,7 @@
 
 
 
+
           and DAPC-based feature selection (</span></span><span
         style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
           0);"><span style="color: rgb(255, 0, 0); font-family:
@@ -111,6 +129,7 @@
 
 
 
+
         </span><span style="color: rgb(0, 0, 0);">See the </span></span><span
         style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
           0);"></span></span><a
@@ -238,10 +257,10 @@
         style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
           0);">download and installed size (respectively 4-5MB and
           6-7MB). Many examples have been 'inactivated' to comply with
-          CRAN check runtime policy, meaning these won't be run by 'example(myFunction)'
-          anymore, but will still be available in the documentation. See
-          the </span></span><span style="color: rgb(255, 0, 0);"><span
-          style="color: rgb(0, 0, 0);"></span></span><a
+          CRAN check runtime policy, meaning these won't be run by
+          'example(myFunction)' anymore, but will still be available in
+          the documentation. See the </span></span><span style="color:
+        rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><a
         href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
         style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
           0);"></span></span><span style="color: rgb(255, 0, 0);"><span
@@ -524,6 +543,7 @@
           loci in an analysis.&nbsp; A new georeferenced genetic dataset
           is also available (dataset <span style="color: rgb(255, 0,
             0);">rupica</span>). And... <a href="files/ChangeLog">several
+
             other things</a>!<br>
         </span></span><br>
       <br>
@@ -674,6 +694,7 @@
 
 
 
+
       Principal Component Analysis (Jombart et al, submitted to
       Heredity), two multivariate spatial tests, and new functionalities
       for Monmonier's algorithm.<br>
@@ -698,6 +719,7 @@
 
 
 
+
         manipulation:</span> new function to separate data by
       population. Accessors to genind and genpop object like with
       matrices using 'foo[ chosenGenotypes, chosenAlleles]'.<br>
@@ -752,6 +774,7 @@
 
 
 
+
       using <span style="color: rgb(255, 0, 0);">sim2pop</span><span
         style="color: rgb(255, 0, 0);"> </span>data.<br>
       <span style="font-weight: bold;"><br>


From noreply at r-forge.r-project.org  Wed Jul  8 18:29:03 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  8 Jul 2015 18:29:03 +0200 (CEST)
Subject: [adegenet-commits] r1202 - www
Message-ID: <20150708162903.2FEE4187B12@r-forge.r-project.org>

Author: jombart
Date: 2015-07-08 18:29:02 +0200 (Wed, 08 Jul 2015)
New Revision: 1202

Modified:
   www/acceuil.html
Log:
fixing link

Modified: www/acceuil.html
===================================================================
--- www/acceuil.html	2015-07-08 16:11:32 UTC (rev 1201)
+++ www/acceuil.html	2015-07-08 16:29:02 UTC (rev 1202)
@@ -25,10 +25,12 @@
       <br>
       <br>
       <div style="text-align: left;"> <span style="font-weight: bold;">NOTE:
+
           this website will soon be replaced by a new github page.
           Meanwhile, up-to-date information on adegenet can be found on
           github:<br>
-          <a href="https://github.com/thibautjombart/adegenet/wiki">https://github.com/thibautjombart/adegenet/wiki</a><br>
+          <a target="_top"
+            href="https://github.com/thibautjombart/adegenet/wiki">https://github.com/thibautjombart/adegenet/wiki</a><br>
           <br>
           adegenet</span> is an <span style="text-decoration:
           underline;"><a href="http://www.r-project.org/" target="_top"><img
@@ -48,6 +50,7 @@
 
 
 
+
           Jombart</a>, Caitlin Collins, Zhian N Kamvar, Roman Lustrik,
         Ismail Ahmed, Federico Calboli, Anne Cori, Tobias Erik Reiners,
         and P?ter S?lymos, and officially released on CRAN periodically.
@@ -80,6 +83,7 @@
 
 
 
+
               the bublisher's website</a>]<br>
           </li>
         </ul>
@@ -109,6 +113,7 @@
 
 
 
+
                 DNA sequences</span> to <span style="font-weight:
                 bold;">SNPs</span></li>
             <li> data import from <span style="font-weight: bold;">aligned
@@ -117,6 +122,7 @@
 
 
 
+
                 protein sequences</span> to polymorphic sites </li>
             <li> data <span style="font-weight: bold;">export</span> to
               the R packages genetics, hierfstat, LDheatmap</li>
@@ -136,6 +142,7 @@
 
 
 
+
                 manipulation</span></li>
             <li> basic <span style="font-weight: bold;">data
                 information </span>(heterozygosity, numbers of alleles,
@@ -157,6 +164,7 @@
 
 
 
+
                 Fst </span></li>
             <li> simulation of <span style="font-weight: bold;">hybridization</span></li>
             <li>methods for <span style="font-weight: bold;">spatial
@@ -165,6 +173,7 @@
 
 
 
+
                 for global and local structuring, </span><span
                 style="font-weight: bold;">Monmonier algorithm</span></li>
             <li>the <span style="font-style: italic; font-weight:
@@ -179,6 +188,7 @@
 
 
 
+
               </span>for reconstructing genealogies of haplotypes</li>
             <li>simulation of <span style="font-weight: bold;">genealogies
 
@@ -191,6 +201,7 @@
 
 
 
+
                 of haplotypes</span></li>
             <li> Discriminant Analysis of Principal Components (<span
                 style="font-weight: bold;">DAPC</span>)</li>
@@ -224,6 +235,7 @@
 
 
 
+
         Collins (<a href="mailto:caitiecollins17 at gmail.com">caitiecollins at gmail.com</a>),
 
 
@@ -235,12 +247,14 @@
 
 
 
+
         Isma?l Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
 
 
 
 
 
+
         Federico Calboli (<a href="mailto:f.calboli at imperial.ac.uk">f.calboli at imperial.ac.uk</a>),
 
 
@@ -250,6 +264,7 @@
 
 
 
+
         Anne Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>),
 Tobias
 
@@ -262,6 +277,7 @@
 
 
 
+
         Erik Reiners (<a href="mailto:Tobias.Reiners at Senckenberg.de">Tobias.Reiners at Senckenberg.de</a>),
 
 
@@ -273,6 +289,7 @@
 
 
 
+
         P?ter S?lymos (<a href="mailto:solymos at ualberta.ca">solymos at ualberta.ca</a>)<br>
         <span style="text-decoration: underline;">Contributors
           (datasets/ideas):</span> Christophe Fraser, Katayoun


From noreply at r-forge.r-project.org  Tue Jul 14 12:01:24 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 14 Jul 2015 12:01:24 +0200 (CEST)
Subject: [adegenet-commits] r1203 - www
Message-ID: <20150714100124.3E44C184FA3@r-forge.r-project.org>

Author: jombart
Date: 2015-07-14 12:01:23 +0200 (Tue, 14 Jul 2015)
New Revision: 1203

Modified:
   www/documentation.html
Log:
updating link to tutorials

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2015-07-08 16:29:02 UTC (rev 1202)
+++ www/documentation.html	2015-07-14 10:01:23 UTC (rev 1203)
@@ -79,6 +79,7 @@
 
 
 
+
         engine</a><span style="font-family: Helvetica,Arial,sans-serif;">.
       </span><br style="font-family: Helvetica,Arial,sans-serif;">
       <br style="font-family: Helvetica,Arial,sans-serif;">
@@ -99,49 +100,15 @@
       <br style="font-family: Helvetica,Arial,sans-serif;">
       <br style="font-family: Helvetica,Arial,sans-serif;">
       <span style="color: rgb(0, 102, 0); font-weight: bold;
-        font-family: Helvetica,Arial,sans-serif;">Tutorials*</span>
-      <ul>
-        <li><a style="font-family: Helvetica,Arial,sans-serif;"
-            href="files/tutorial-basics.pdf"><span style="font-style:
-              italic;">tutorial-basics</span></a><span
-            style="font-family: Helvetica,Arial,sans-serif;">:
-            introduction to the package: data classes, inputs/outputs,
-            basic population genetics, and exploratory analyses;
-            accessible from R by typing </span><span style="color:
-            rgb(255, 0, 0); font-family: Helvetica,Arial,sans-serif;"></span><span
-            style="font-family: monospace; color: rgb(255, 0, 0);">adegenetTutorial("basics")</span>.</li>
-        <li><a style="font-family: Helvetica,Arial,sans-serif;"
-            href="files/tutorial-dapc.pdf"><span style="font-style:
-              italic;">tutorial-dapc</span></a><span style="font-family:
-            Helvetica,Arial,sans-serif;">: a tutorial for the analysis
-            of population diversity using Discriminant Analysis of
-            Principal Components (DAPC); accessible from R by typing</span>&nbsp;<span
-            style="font-family: monospace; color: rgb(255, 0, 0);"><span
-              style="font-family: monospace; color: rgb(255, 0, 0);">adegenetTutorial</span>("dapc")</span>.</li>
-        <li><a style="font-family: Helvetica,Arial,sans-serif;"
-            href="files/tutorial-genomics.pdf"><span style="font-style:
-              italic;">tutorial-genomics</span></a><span
-            style="font-family: Helvetica,Arial,sans-serif;">:
-            introduction to the genlight class for storing and handling
-            large genome-wide SNP data; accessible from R by typing</span>
-          <span style="font-family: monospace;"></span><span
-            style="font-family: monospace; color: rgb(255, 0, 0);">adegenetTutorial("genomics")</span>.</li>
-        <li><a style="font-family: Helvetica,Arial,sans-serif;"
-            href="files/tutorial-spca.pdf"><span style="font-style:
-              italic;">tutorial-spca</span></a><span style="font-family:
-            Helvetica,Arial,sans-serif;">: introduction to spatial
-            multivariate analysis using the spatial Principal Component
-            Analysis (sPCA); accessible from R by typing</span>&nbsp;<span
-            style="font-family: monospace; color: rgb(255, 0, 0);">adegenetTutorial</span><span
-            style="font-family: monospace; color: rgb(255, 0, 0);">("spca")</span>.</li>
-      </ul>
-    </div>
-    <div style="margin-left: 40px;"> <span style="color: rgb(0, 102,
-        0);"><small>*(note: since adegenet 1.4-0, these tutorials
-          replace the vignettes which used to be part of the package)</small></span><br>
-      &nbsp;&nbsp;&nbsp;&nbsp; <br>
+        font-family: Helvetica,Arial,sans-serif;">Tutorials*</span><br>
+      <font face="Helvetica, Arial, sans-serif">Up-to-date tutorials are
+        now hosted on Github:<br>
+        <a target="_top"
+          href="https://github.com/thibautjombart/adegenet/wiki/Tutorials">https://github.com/thibautjombart/adegenet/wiki/Tutorials</a>&nbsp;&nbsp;&nbsp;&nbsp;
+      </font><br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);
         font-family: Helvetica,Arial,sans-serif;"><br>
+        <br>
         Lectures and practicals</span><br style="font-family:
         Helvetica,Arial,sans-serif;">
       <ul style="font-family: Helvetica,Arial,sans-serif;">
@@ -235,6 +202,7 @@
 
 
 
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to phylogenetics</span>
           (last updated on the 15/13/2013)</li>
@@ -284,6 +252,7 @@
 
 
 
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to multivariate
             analysis / bacterial GWAS</span> (last updated on the
@@ -328,6 +297,7 @@
 
 
 
+
           </b><b><i>outbreaker</i></b></li>
         <ul>
           <li><a href="files/GenEpiTalk.1.0.pdf">talk</a></li>
@@ -359,6 +329,7 @@
 
 
 
+
             analysis using <span style="font-style: italic;">ape,
               adegenet,</span> </span><b>and </b><b><i>outbreaker</i></b></li>
         <ul>
@@ -423,6 +394,7 @@
               href="files/Leuven2014/practical-MVAgroups-allCmd.1.2.pdf">practical
 
 
+
               all commands</a>]</li>
           <li>An introduction to Genome Wise Association Studies (GWAS)
             [<a


From noreply at r-forge.r-project.org  Tue Jul 14 13:07:20 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 14 Jul 2015 13:07:20 +0200 (CEST)
Subject: [adegenet-commits] r1204 - www/files
Message-ID: <20150714110720.DF17D187A34@r-forge.r-project.org>

Author: jombart
Date: 2015-07-14 13:07:19 +0200 (Tue, 14 Jul 2015)
New Revision: 1204

Modified:
   www/files/tutorial-basics.pdf
   www/files/tutorial-dapc.pdf
   www/files/tutorial-genomics.pdf
   www/files/tutorial-spca.pdf
Log:
updating tutorials

Modified: www/files/tutorial-basics.pdf
===================================================================
--- www/files/tutorial-basics.pdf	2015-07-14 10:01:23 UTC (rev 1203)
+++ www/files/tutorial-basics.pdf	2015-07-14 11:07:19 UTC (rev 1204)
@@ -1,1006 +1,317 @@
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+%PDF-1.5
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To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1204

From noreply at r-forge.r-project.org  Wed Jul 29 15:50:13 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 29 Jul 2015 15:50:13 +0200 (CEST)
Subject: [adegenet-commits] r1205 - www/files
Message-ID: <20150729135013.4577A18517B@r-forge.r-project.org>

Author: jombart
Date: 2015-07-29 15:50:12 +0200 (Wed, 29 Jul 2015)
New Revision: 1205

Modified:
   www/files/tutorial-basics.pdf
Log:
fixed typos in basics tuto

Modified: www/files/tutorial-basics.pdf
===================================================================
--- www/files/tutorial-basics.pdf	2015-07-14 11:07:19 UTC (rev 1204)
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From noreply at r-forge.r-project.org  Thu Jul 30 16:53:44 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 Jul 2015 16:53:44 +0200 (CEST)
Subject: [adegenet-commits] r1206 - in www/files: . Glasgow2015
Message-ID: <20150730145344.97F7C187ADD@r-forge.r-project.org>

Author: jombart
Date: 2015-07-30 16:53:43 +0200 (Thu, 30 Jul 2015)
New Revision: 1206

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Log:
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+????b?/?W?"?	?????]|?~>??	?c???9?E???{?L`L?A&??y?????Za?`??3?????Lk&?8Z???u??p Np'??H??X?
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1206

From noreply at r-forge.r-project.org  Thu Jul 30 17:02:19 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 Jul 2015 17:02:19 +0200 (CEST)
Subject: [adegenet-commits] r1207 - www/files/Glasgow2015
Message-ID: <20150730150219.3500E187ADD@r-forge.r-project.org>

Author: jombart
Date: 2015-07-30 17:02:18 +0200 (Thu, 30 Jul 2015)
New Revision: 1207

Modified:
   www/files/Glasgow2015/Enonsensicus1.RData
   www/files/Glasgow2015/Enonsensicus2.RData
Log:
fixed datasets

Modified: www/files/Glasgow2015/Enonsensicus1.RData
===================================================================
(Binary files differ)

Modified: www/files/Glasgow2015/Enonsensicus2.RData
===================================================================
(Binary files differ)


From noreply at r-forge.r-project.org  Thu Jul 30 17:03:19 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 Jul 2015 17:03:19 +0200 (CEST)
Subject: [adegenet-commits] r1208 - www/files/Glasgow2015
Message-ID: <20150730150319.B3849183E9F@r-forge.r-project.org>

Author: jombart
Date: 2015-07-30 17:03:19 +0200 (Thu, 30 Jul 2015)
New Revision: 1208

Removed:
   www/files/Glasgow2015/Lecture-Day4- Genome-Wide Association Studies.pptx
   www/files/Glasgow2015/Refresh-R.pdf
   www/files/Glasgow2015/Refresh-R.pptx
   www/files/Glasgow2015/lecture-MVA.1.1.pdf
   www/files/Glasgow2015/lecture-MVAgroups.1.1.pdf
   www/files/Glasgow2015/lecture-MVAspatial.1.1.pdf
   www/files/Glasgow2015/lecture-phylo.1.3.pdf
   www/files/Glasgow2015/practical-GWAS.pdf
   www/files/Glasgow2015/practical-MVAgroups-allCmd.1.2.pdf
   www/files/Glasgow2015/practical-MVAgroups.1.0.pdf
   www/files/Glasgow2015/practical-MVAgroups.1.2.pdf
   www/files/Glasgow2015/practical-MVAintro.1.0.pdf
   www/files/Glasgow2015/practical-MVAspatial.1.0.pdf
   www/files/Glasgow2015/practical-introphylo.1.1.pdf
Log:
cleaning directory

Deleted: www/files/Glasgow2015/Lecture-Day4- Genome-Wide Association Studies.pptx
===================================================================
(Binary files differ)

Deleted: www/files/Glasgow2015/Refresh-R.pdf
===================================================================
(Binary files differ)

Deleted: www/files/Glasgow2015/Refresh-R.pptx
===================================================================
(Binary files differ)

Deleted: www/files/Glasgow2015/lecture-MVA.1.1.pdf
===================================================================
--- www/files/Glasgow2015/lecture-MVA.1.1.pdf	2015-07-30 15:02:18 UTC (rev 1207)
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1208

From noreply at r-forge.r-project.org  Thu Jul 30 17:21:06 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 Jul 2015 17:21:06 +0200 (CEST)
Subject: [adegenet-commits] r1209 - www/files/Glasgow2015
Message-ID: <20150730152106.7039E18688C@r-forge.r-project.org>

Author: jombart
Date: 2015-07-30 17:21:06 +0200 (Thu, 30 Jul 2015)
New Revision: 1209

Modified:
   www/files/Glasgow2015/unknown1.RData
   www/files/Glasgow2015/unknown2.RData
Log:
fixing datasetse

Modified: www/files/Glasgow2015/unknown1.RData
===================================================================
(Binary files differ)

Modified: www/files/Glasgow2015/unknown2.RData
===================================================================
(Binary files differ)


From noreply at r-forge.r-project.org  Thu Jul 30 21:33:17 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 Jul 2015 21:33:17 +0200 (CEST)
Subject: [adegenet-commits] r1210 - www/files/Glasgow2015
Message-ID: <20150730193317.A5C63187A9A@r-forge.r-project.org>

Author: jombart
Date: 2015-07-30 21:33:17 +0200 (Thu, 30 Jul 2015)
New Revision: 1210

Added:
   www/files/Glasgow2015/lecture-MVA.1.0.pdf
   www/files/Glasgow2015/lecture-MVAgroups.1.0.pdf
   www/files/Glasgow2015/lecture-MVAspatial.1.0.pdf
   www/files/Glasgow2015/lecture-phylo.1.0.pdf
Log:
adding the slides of lectures for days 1,2,3, and 5

Added: www/files/Glasgow2015/lecture-MVA.1.0.pdf
===================================================================
(Binary files differ)


Property changes on: www/files/Glasgow2015/lecture-MVA.1.0.pdf
___________________________________________________________________
Added: svn:mime-type
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Added: www/files/Glasgow2015/lecture-MVAgroups.1.0.pdf
===================================================================
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1210

From noreply at r-forge.r-project.org  Thu Jul 30 21:34:13 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 Jul 2015 21:34:13 +0200 (CEST)
Subject: [adegenet-commits] r1211 - www/files/Glasgow2015
Message-ID: <20150730193413.54E27183C5C@r-forge.r-project.org>

Author: jombart
Date: 2015-07-30 21:34:13 +0200 (Thu, 30 Jul 2015)
New Revision: 1211

Added:
   www/files/Glasgow2015/practical-MVAgroups.1.0.pdf
   www/files/Glasgow2015/practical-MVAintro.1.0.pdf
   www/files/Glasgow2015/practical-MVAspatial.1.0.pdf
   www/files/Glasgow2015/practical-introphylo.1.0.pdf
Log:
 Adding practicals for days 1,2,3 and 5

Added: www/files/Glasgow2015/practical-MVAgroups.1.0.pdf
===================================================================
(Binary files differ)


Property changes on: www/files/Glasgow2015/practical-MVAgroups.1.0.pdf
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: www/files/Glasgow2015/practical-MVAintro.1.0.pdf
===================================================================
(Binary files differ)


Property changes on: www/files/Glasgow2015/practical-MVAintro.1.0.pdf
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: www/files/Glasgow2015/practical-MVAspatial.1.0.pdf
===================================================================
(Binary files differ)


Property changes on: www/files/Glasgow2015/practical-MVAspatial.1.0.pdf
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: www/files/Glasgow2015/practical-introphylo.1.0.pdf
===================================================================
(Binary files differ)


Property changes on: www/files/Glasgow2015/practical-introphylo.1.0.pdf
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream


From noreply at r-forge.r-project.org  Thu Jul 30 21:40:53 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 Jul 2015 21:40:53 +0200 (CEST)
Subject: [adegenet-commits] r1212 - www
Message-ID: <20150730194053.B02AC1878CF@r-forge.r-project.org>

Author: jombart
Date: 2015-07-30 21:40:53 +0200 (Thu, 30 Jul 2015)
New Revision: 1212

Modified:
   www/documentation.html
Log:
updating website for new workshop

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2015-07-30 19:34:13 UTC (rev 1211)
+++ www/documentation.html	2015-07-30 19:40:53 UTC (rev 1212)
@@ -80,6 +80,7 @@
 
 
 
+
         engine</a><span style="font-family: Helvetica,Arial,sans-serif;">.
       </span><br style="font-family: Helvetica,Arial,sans-serif;">
       <br style="font-family: Helvetica,Arial,sans-serif;">
@@ -100,11 +101,13 @@
       <br style="font-family: Helvetica,Arial,sans-serif;">
       <br style="font-family: Helvetica,Arial,sans-serif;">
       <span style="color: rgb(0, 102, 0); font-weight: bold;
-        font-family: Helvetica,Arial,sans-serif;">Tutorials*</span><br>
+        font-family: Helvetica,Arial,sans-serif;">Tutorials*</span> <img
+        alt="new" src="images/new.png" height="37" width="80"><br>
       <font face="Helvetica, Arial, sans-serif">Up-to-date tutorials are
         now hosted on Github:<br>
         <a target="_top"
           href="https://github.com/thibautjombart/adegenet/wiki/Tutorials">https://github.com/thibautjombart/adegenet/wiki/Tutorials</a>&nbsp;&nbsp;&nbsp;&nbsp;
+
       </font><br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);
         font-family: Helvetica,Arial,sans-serif;"><br>
@@ -203,6 +206,7 @@
 
 
 
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to phylogenetics</span>
           (last updated on the 15/13/2013)</li>
@@ -253,6 +257,7 @@
 
 
 
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to multivariate
             analysis / bacterial GWAS</span> (last updated on the
@@ -261,6 +266,7 @@
           <li><a href="files/simGWAS/lecture-MSc-MVA.1.2.pdf">lecture</a></li>
           <li><a href="files/simGWAS/MSc-GWAS-1.1.pdf">practical</a></li>
           <li>data (<a href="files/simGWAS/simGWAS.RData">simGWAS.RData</a>)<br>
+            <br>
           </li>
         </ul>
       </ul>
@@ -298,6 +304,7 @@
 
 
 
+
           </b><b><i>outbreaker</i></b></li>
         <ul>
           <li><a href="files/GenEpiTalk.1.0.pdf">talk</a></li>
@@ -330,6 +337,7 @@
 
 
 
+
             analysis using <span style="font-style: italic;">ape,
               adegenet,</span> </span><b>and </b><b><i>outbreaker</i></b></li>
         <ul>
@@ -338,6 +346,7 @@
           <li>data (<a href="files/fakeOutbreak/cases.csv">cases.csv</a>,
             <a href="files/fakeOutbreak/alignment.fa">alignment.fa</a>,
             <a href="files/fakeOutbreak/update.csv">update.csv</a>)<br>
+            <br>
           </li>
         </ul>
       </ul>
@@ -360,6 +369,7 @@
               href="files/montpellier/lecture-MVAspatial.1.0.pdf">lecture</a>,
             <a href="files/montpellier/practical-MVAspatial.1.0.pdf">practical</a>]<br>
             <br>
+            <br>
           </li>
         </ul>
         <li>XXIV International Symposium of Statistics, Bogota, Colombia
@@ -368,46 +378,105 @@
         <ul>
           <li><a href="files/lectureBogota2014-MVA.1.1.pdf">slides</a>
             of the lecture<br>
+          </li>
+          <li>Workshop "<span style="font-weight: bold;">Genetic data
+              analysis using R</span>" - Leuven (October 2014)</li>
+          <li>Short R refresher [<a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/Refresh-R.pdf">lecture</a>]<br>
+          </li>
+          <li>Introduction to phylogenetics [<a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-phylo.1.3.pdf">lecture</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-introphylo.1.1.pdf">practical</a>]
+          </li>
+          <li>Multivariate analysis of genetic data: an introduction [<a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-MVA.1.1.pdf">lecture</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAintro.1.0.pdf">practical</a>]
+          </li>
+          <li>Multivariate analysis of genetic data: exploring group
+            diversity [<a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-MVAgroups.1.1.pdf">lecture</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAgroups.1.2.pdf">practical</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAgroups-allCmd.1.2.pdf">practical
+
+
+
+
+              all commands</a>]</li>
+          <li>An introduction to Genome Wise Association Studies (GWAS)
+            [<a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/Lecture-Day4-%20Genome-Wide%20Association%20Studies.pptx">lecture</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-GWAS.pdf">practical</a>]</li>
+          <li>Multivariate analysis of genetic data: uncovering spatial
+            structures [<a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-MVAspatial.1.1.pdf">lecture</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAspatial.1.0.pdf">practical</a>]<br>
             <br>
           </li>
         </ul>
+      </ul>
+      <ul style="font-family: Helvetica,Arial,sans-serif;">
         <li>Workshop "<span style="font-weight: bold;">Genetic data
-            analysis using R</span>" - Leuven (October 2014)&nbsp;<img
-            alt="" src="images/new.png" height="37" width="80"></li>
+            analysis using R</span>" - Leuven (October 2014)</li>
         <ul>
           <li>Short R refresher [<a
-              href="files/Leuven2014/Refresh-R.pdf">lecture</a>]<br>
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/Refresh-R.pdf">lecture</a>]<br>
           </li>
           <li>Introduction to phylogenetics [<a
-              href="files/Leuven2014/lecture-phylo.1.3.pdf">lecture</a>,
-            <a href="files/Leuven2014/practical-introphylo.1.1.pdf">practical</a>]
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-phylo.1.3.pdf">lecture</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-introphylo.1.1.pdf">practical</a>]
           </li>
           <li>Multivariate analysis of genetic data: an introduction [<a
-              href="files/Leuven2014/lecture-MVA.1.1.pdf">lecture</a>, <a
-              href="files/Leuven2014/practical-MVAintro.1.0.pdf">practical</a>]
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-MVA.1.1.pdf">lecture</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAintro.1.0.pdf">practical</a>]
           </li>
           <li>Multivariate analysis of genetic data: exploring group
             diversity [<a
-              href="files/Leuven2014/lecture-MVAgroups.1.1.pdf">lecture</a>,
-            <a href="files/Leuven2014/practical-MVAgroups.1.2.pdf">practical</a>,
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-MVAgroups.1.1.pdf">lecture</a>,
             <a
-              href="files/Leuven2014/practical-MVAgroups-allCmd.1.2.pdf">practical
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAgroups.1.2.pdf">practical</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAgroups-allCmd.1.2.pdf">practical
 
 
 
+
               all commands</a>]</li>
           <li>An introduction to Genome Wise Association Studies (GWAS)
             [<a
-href="files/Leuven2014/Lecture-Day4-%20Genome-Wide%20Association%20Studies.pptx">lecture</a>,
-            <a href="files/Leuven2014/practical-GWAS.pdf">practical</a>]</li>
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/Lecture-Day4-%20Genome-Wide%20Association%20Studies.pptx">lecture</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-GWAS.pdf">practical</a>]</li>
           <li>Multivariate analysis of genetic data: uncovering spatial
             structures [<a
-              href="files/Leuven2014/lecture-MVAspatial.1.1.pdf">lecture</a>,
-            <a href="files/Leuven2014/practical-MVAspatial.1.0.pdf">practical</a>]<br>
-            <br>
-          </li>
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-MVAspatial.1.1.pdf">lecture</a>,
+            <a
+href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAspatial.1.0.pdf">practical</a>]</li>
         </ul>
+      </ul>
+      <ul style="font-family: Helvetica,Arial,sans-serif;">
+        <li>Workshop "<span style="font-weight: bold;">Genetic data
+            analysis with R</span>" - Glasgow (August 2015) <img
+            alt="new" src="images/new.png" height="37" width="80"></li>
         <ul>
+          <li>Short R refresher [lecture]<br>
+          </li>
+          <li>Introduction to phylogenetics [lecture, practical] </li>
+          <li>Multivariate analysis of genetic data: an introduction [lecture,
+            practical] </li>
+          <li>Multivariate analysis of genetic data: exploring group
+            diversity [lecture, practical]</li>
+          <li>An introduction to Genome Wise Association Studies (GWAS)
+            [lecture, practical]</li>
+          <li>Multivariate analysis of genetic data: uncovering spatial
+            structures [lecture, practical]</li>
         </ul>
       </ul>
       <br style="font-family: Helvetica,Arial,sans-serif;">
@@ -447,21 +516,7 @@
         style="font-family: Helvetica,Arial,sans-serif;">
       <br style="font-family: Helvetica,Arial,sans-serif;">
       <br style="font-family: Helvetica,Arial,sans-serif;">
-      <span style="font-weight: bold; color: rgb(0, 102, 0);
-        font-family: Helvetica,Arial,sans-serif;">Miscellaneous<br>
-      </span><span style="font-family: Helvetica,Arial,sans-serif;">- </span><a
-        style="font-family: Helvetica,Arial,sans-serif;"
-        href="files/worksOnlyInDiploids.txt">worksOnyInDiploids.txt</a><span
-        style="font-family: Helvetica,Arial,sans-serif;">: the list of </span><span
-        style="font-weight: bold; font-family:
-        Helvetica,Arial,sans-serif;">functions</span><span
-        style="font-family: Helvetica,Arial,sans-serif;"> working </span><span
-        style="font-weight: bold; font-family:
-        Helvetica,Arial,sans-serif;">only for diploid</span><span
-        style="font-family: Helvetica,Arial,sans-serif;"> genotypes </span><br
-        style="font-family: Helvetica,Arial,sans-serif;">
       <br style="font-family: Helvetica,Arial,sans-serif;">
-      <br style="font-family: Helvetica,Arial,sans-serif;">
       <span style="font-weight: bold; color: rgb(0, 102, 0);
         font-family: Helvetica,Arial,sans-serif;"></span><br
         style="font-family: Helvetica,Arial,sans-serif;">


From noreply at r-forge.r-project.org  Thu Jul 30 21:41:42 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 Jul 2015 21:41:42 +0200 (CEST)
Subject: [adegenet-commits] r1213 - www
Message-ID: <20150730194142.F0F881872EE@r-forge.r-project.org>

Author: jombart
Date: 2015-07-30 21:41:42 +0200 (Thu, 30 Jul 2015)
New Revision: 1213

Modified:
   www/documentation.html
Log:
updating website for new workshop

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2015-07-30 19:40:53 UTC (rev 1212)
+++ www/documentation.html	2015-07-30 19:41:42 UTC (rev 1213)
@@ -81,6 +81,7 @@
 
 
 
+
         engine</a><span style="font-family: Helvetica,Arial,sans-serif;">.
       </span><br style="font-family: Helvetica,Arial,sans-serif;">
       <br style="font-family: Helvetica,Arial,sans-serif;">
@@ -108,6 +109,7 @@
         <a target="_top"
           href="https://github.com/thibautjombart/adegenet/wiki/Tutorials">https://github.com/thibautjombart/adegenet/wiki/Tutorials</a>&nbsp;&nbsp;&nbsp;&nbsp;
 
+
       </font><br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);
         font-family: Helvetica,Arial,sans-serif;"><br>
@@ -207,6 +209,7 @@
 
 
 
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to phylogenetics</span>
           (last updated on the 15/13/2013)</li>
@@ -258,6 +261,7 @@
 
 
 
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to multivariate
             analysis / bacterial GWAS</span> (last updated on the
@@ -305,6 +309,7 @@
 
 
 
+
           </b><b><i>outbreaker</i></b></li>
         <ul>
           <li><a href="files/GenEpiTalk.1.0.pdf">talk</a></li>
@@ -338,6 +343,7 @@
 
 
 
+
             analysis using <span style="font-style: italic;">ape,
               adegenet,</span> </span><b>and </b><b><i>outbreaker</i></b></li>
         <ul>
@@ -378,44 +384,6 @@
         <ul>
           <li><a href="files/lectureBogota2014-MVA.1.1.pdf">slides</a>
             of the lecture<br>
-          </li>
-          <li>Workshop "<span style="font-weight: bold;">Genetic data
-              analysis using R</span>" - Leuven (October 2014)</li>
-          <li>Short R refresher [<a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/Refresh-R.pdf">lecture</a>]<br>
-          </li>
-          <li>Introduction to phylogenetics [<a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-phylo.1.3.pdf">lecture</a>,
-            <a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-introphylo.1.1.pdf">practical</a>]
-          </li>
-          <li>Multivariate analysis of genetic data: an introduction [<a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-MVA.1.1.pdf">lecture</a>,
-            <a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAintro.1.0.pdf">practical</a>]
-          </li>
-          <li>Multivariate analysis of genetic data: exploring group
-            diversity [<a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-MVAgroups.1.1.pdf">lecture</a>,
-            <a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAgroups.1.2.pdf">practical</a>,
-            <a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAgroups-allCmd.1.2.pdf">practical
-
-
-
-
-              all commands</a>]</li>
-          <li>An introduction to Genome Wise Association Studies (GWAS)
-            [<a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/Lecture-Day4-%20Genome-Wide%20Association%20Studies.pptx">lecture</a>,
-            <a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-GWAS.pdf">practical</a>]</li>
-          <li>Multivariate analysis of genetic data: uncovering spatial
-            structures [<a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/lecture-MVAspatial.1.1.pdf">lecture</a>,
-            <a
-href="file:///home/thibaut/dev/adegenet/www/files/Leuven2014/practical-MVAspatial.1.0.pdf">practical</a>]<br>
             <br>
           </li>
         </ul>
@@ -448,6 +416,7 @@
 
 
 
+
               all commands</a>]</li>
           <li>An introduction to Genome Wise Association Studies (GWAS)
             [<a
@@ -469,8 +438,8 @@
           <li>Short R refresher [lecture]<br>
           </li>
           <li>Introduction to phylogenetics [lecture, practical] </li>
-          <li>Multivariate analysis of genetic data: an introduction [lecture,
-            practical] </li>
+          <li>Multivariate analysis of genetic data: an introduction
+            [lecture, practical] </li>
           <li>Multivariate analysis of genetic data: exploring group
             diversity [lecture, practical]</li>
           <li>An introduction to Genome Wise Association Studies (GWAS)


From noreply at r-forge.r-project.org  Thu Jul 30 21:46:20 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 30 Jul 2015 21:46:20 +0200 (CEST)
Subject: [adegenet-commits] r1214 - www
Message-ID: <20150730194620.4750B18784F@r-forge.r-project.org>

Author: jombart
Date: 2015-07-30 21:46:19 +0200 (Thu, 30 Jul 2015)
New Revision: 1214

Modified:
   www/acceuil.html
Log:
updating website for new workshop

Modified: www/acceuil.html
===================================================================
--- www/acceuil.html	2015-07-30 19:41:42 UTC (rev 1213)
+++ www/acceuil.html	2015-07-30 19:46:19 UTC (rev 1214)
@@ -26,6 +26,7 @@
       <br>
       <div style="text-align: left;"> <span style="font-weight: bold;">NOTE:
 
+
           this website will soon be replaced by a new github page.
           Meanwhile, up-to-date information on adegenet can be found on
           github:<br>
@@ -40,17 +41,10 @@
         of tools ranging from multivariate methods to spatial genetics
         and genome-wise SNP data analysis. <br>
         <br>
-        It is developed on <a
+        It is developed on <a target="_top"
           href="https://github.com/thibautjombart/adegenet">Github</a>
-        by <a href="http://sites.google.com/site/thibautjombart/">Thibaut
-
-
-
-
-
-
-
-
+        by <a target="_top"
+          href="http://sites.google.com/site/thibautjombart/">Thibaut
           Jombart</a>, Caitlin Collins, Zhian N Kamvar, Roman Lustrik,
         Ismail Ahmed, Federico Calboli, Anne Cori, Tobias Erik Reiners,
         and P?ter S?lymos, and officially released on CRAN periodically.
@@ -84,6 +78,7 @@
 
 
 
+
               the bublisher's website</a>]<br>
           </li>
         </ul>
@@ -114,6 +109,7 @@
 
 
 
+
                 DNA sequences</span> to <span style="font-weight:
                 bold;">SNPs</span></li>
             <li> data import from <span style="font-weight: bold;">aligned
@@ -123,14 +119,16 @@
 
 
 
+
                 protein sequences</span> to polymorphic sites </li>
             <li> data <span style="font-weight: bold;">export</span> to
               the R packages genetics, hierfstat, LDheatmap</li>
             <li> handling of <span style="font-weight: bold;">different
-                levels of ploidy</span></li>
+                levels of ploidy<br>
+              </span></li>
             <li>handling of <span style="font-weight: bold;">codominant
-              </span>markersand<span style="font-weight: bold;">presence/absence</span>
-              data</li>
+              </span>markers and<span style="font-weight: bold;">
+                presence/absence</span> data</li>
             <li>basic and advanced <span style="font-weight: bold;">data
 
 
@@ -143,30 +141,14 @@
 
 
 
+
                 manipulation</span></li>
             <li> basic <span style="font-weight: bold;">data
                 information </span>(heterozygosity, numbers of alleles,
               sample sizes, ...)</li>
-            <li> <span style="font-weight: bold;">HWE</span> and <span
-                style="font-weight: bold;">G-statistic</span> <span
-                style="font-weight: bold;">tests</span>, F statistics
-              implemented for adegenet objects</li>
             <li> computation of <span style="font-weight: bold;">genetic</span>
               <span style="font-weight: bold;">distances</span></li>
-            <li>computation of <span style="font-weight: bold;">pairwise
-
-
-
-
-
-
-
-
-
-
-
-                Fst </span></li>
-            <li> simulation of <span style="font-weight: bold;">hybridization</span></li>
+            <li>simulation of <span style="font-weight: bold;">hybridization</span></li>
             <li>methods for <span style="font-weight: bold;">spatial
                 genetics: sPCA, </span><span style="font-weight: bold;">tests
 
@@ -174,22 +156,13 @@
 
 
 
+
                 for global and local structuring, </span><span
                 style="font-weight: bold;">Monmonier algorithm</span></li>
             <li>the <span style="font-style: italic; font-weight:
-                bold;">seqTrack</span><span style="font-weight: bold;">algorithm
-
-
-
-
-
-
-
-
-
-
-
-              </span>for reconstructing genealogies of haplotypes</li>
+                bold;">seqTrack</span><span style="font-weight: bold;">
+                algorithm </span>for reconstructing genealogies of
+              haplotypes</li>
             <li>simulation of <span style="font-weight: bold;">genealogies
 
 
@@ -202,6 +175,7 @@
 
 
 
+
                 of haplotypes</span></li>
             <li> Discriminant Analysis of Principal Components (<span
                 style="font-weight: bold;">DAPC</span>)</li>
@@ -212,13 +186,10 @@
             <li> identification of mutations between pairs of sequences
             </li>
             <li><b>visualization of SNPs density</b> and test for the
-              randomness of their distribution<img style="width: 80px;
-                height: 37px;" alt="" src="images/new.png" height="37"
-                width="80"></li>
+              randomness of their distribution</li>
             <li><b>web interface for DAPC</b>, including feature
-              selection and cross validation <img style="width: 80px;
-                height: 37px;" alt="" src="images/new.png" height="37"
-                width="80"><br>
+              selection and cross validation&nbsp;</li>
+            <li>and more...<br>
             </li>
           </ul>
         </div>
@@ -227,76 +198,7 @@
           style="text-decoration: underline; font-weight: bold;">:</span>
         Thibaut Jombart (<a target="_new"
           href="http://sites.google.com/site/thibautjombart/">website</a>)<br>
-        <span style="text-decoration: underline;">Developers:</span>
-        Thibaut Jombart (<a href="mailto:tjombart at imperial.ac.uk">tjombart at imperial.ac.uk</a>),
-Caitlin
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-        Collins (<a href="mailto:caitiecollins17 at gmail.com">caitiecollins at gmail.com</a>),
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-        Isma?l Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
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-        Federico Calboli (<a href="mailto:f.calboli at imperial.ac.uk">f.calboli at imperial.ac.uk</a>),
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-        Anne Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>),
-Tobias
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-        Erik Reiners (<a href="mailto:Tobias.Reiners at Senckenberg.de">Tobias.Reiners at Senckenberg.de</a>),
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-        P?ter S?lymos (<a href="mailto:solymos at ualberta.ca">solymos at ualberta.ca</a>)<br>
-        <span style="text-decoration: underline;">Contributors
-          (datasets/ideas):</span> Christophe Fraser, Katayoun
-        Moazami-Goudarzi, Denis Lalo?, Francois Balloux, Dominique
-        Pontier, Daniel Maillard<span style="font-weight: bold;"><br>
-          <br>
-          <br style="font-weight: bold;">
+        <span style="font-weight: bold;"><br style="font-weight: bold;">
           Suggestions, comments and contributions are most welcome!</span><br>
         <br>
         <br>