From noreply at r-forge.r-project.org  Sun Aug  2 17:58:45 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  2 Aug 2015 17:58:45 +0200 (CEST)
Subject: [adegenet-commits] r1215 - www
Message-ID: <20150802155845.54936187A97@r-forge.r-project.org>

Author: jombart
Date: 2015-08-02 17:58:44 +0200 (Sun, 02 Aug 2015)
New Revision: 1215

Modified:
   www/documentation.html
Log:
added links to documents for Glasgow

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2015-07-30 19:46:19 UTC (rev 1214)
+++ www/documentation.html	2015-08-02 15:58:44 UTC (rev 1215)
@@ -82,6 +82,8 @@
 
 
 
+
+
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@@ -110,6 +112,8 @@
           href="https://github.com/thibautjombart/adegenet/wiki/Tutorials">https://github.com/thibautjombart/adegenet/wiki/Tutorials</a>&nbsp;&nbsp;&nbsp;&nbsp;
 
 
+
+
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       <span style="font-weight: bold; color: rgb(0, 102, 0);
         font-family: Helvetica,Arial,sans-serif;"><br>
@@ -210,6 +214,8 @@
 
 
 
+
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to phylogenetics</span>
           (last updated on the 15/13/2013)</li>
@@ -262,6 +268,8 @@
 
 
 
+
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to multivariate
             analysis / bacterial GWAS</span> (last updated on the
@@ -310,6 +318,8 @@
 
 
 
+
+
           </b><b><i>outbreaker</i></b></li>
         <ul>
           <li><a href="files/GenEpiTalk.1.0.pdf">talk</a></li>
@@ -344,6 +354,8 @@
 
 
 
+
+
             analysis using <span style="font-style: italic;">ape,
               adegenet,</span> </span><b>and </b><b><i>outbreaker</i></b></li>
         <ul>
@@ -417,6 +429,8 @@
 
 
 
+
+
               all commands</a>]</li>
           <li>An introduction to Genome Wise Association Studies (GWAS)
             [<a
@@ -437,15 +451,24 @@
         <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>Introduction to phylogenetics [<a
+              href="files/Glasgow2015/lecture-phylo.1.0.pdf">lecture</a>,
+            <a href="files/Glasgow2015/practical-introphylo.1.0.pdf">practical</a>]
+          </li>
+          <li>Multivariate analysis of genetic data: an introduction [<a
+              href="files/Glasgow2015/lecture-MVA.1.0.pdf">lecture</a>,
+            <a href="files/Glasgow2015/practical-MVAintro.1.0.pdf">practical</a>]
+          </li>
           <li>Multivariate analysis of genetic data: exploring group
-            diversity [lecture, practical]</li>
+            diversity [<a
+              href="files/Glasgow2015/lecture-MVAgroups.1.0.pdf">lecture</a>,
+            <a href="files/Glasgow2015/practical-MVAgroups.1.0.pdf">practical</a>]</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>
+            structures [<a
+              href="files/Glasgow2015/lecture-MVAspatial.1.0.pdf">lecture</a>,
+            <a href="files/Glasgow2015/practical-MVAspatial.1.0.pdf">practical</a>]</li>
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From noreply at r-forge.r-project.org  Tue Aug  4 23:47:51 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  4 Aug 2015 23:47:51 +0200 (CEST)
Subject: [adegenet-commits] r1216 - in www: . files/Glasgow2015
Message-ID: <20150804214751.1B3D11874D5@r-forge.r-project.org>

Author: jombart
Date: 2015-08-04 23:47:50 +0200 (Tue, 04 Aug 2015)
New Revision: 1216

Added:
   www/files/Glasgow2015/practical-MVAintro-allCmd.1.0.pdf
Modified:
   www/documentation.html
Log:
added the MVA practical with all commands and link

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2015-08-02 15:58:44 UTC (rev 1215)
+++ www/documentation.html	2015-08-04 21:47:50 UTC (rev 1216)
@@ -84,6 +84,7 @@
 
 
 
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@@ -114,6 +115,7 @@
 
 
 
+
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       <span style="font-weight: bold; color: rgb(0, 102, 0);
         font-family: Helvetica,Arial,sans-serif;"><br>
@@ -216,6 +218,7 @@
 
 
 
+
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             style="font-weight: bold;">Introduction to phylogenetics</span>
           (last updated on the 15/13/2013)</li>
@@ -270,6 +273,7 @@
 
 
 
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to multivariate
             analysis / bacterial GWAS</span> (last updated on the
@@ -320,6 +324,7 @@
 
 
 
+
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         <ul>
           <li><a href="files/GenEpiTalk.1.0.pdf">talk</a></li>
@@ -356,6 +361,7 @@
 
 
 
+
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               adegenet,</span> </span><b>and </b><b><i>outbreaker</i></b></li>
         <ul>
@@ -431,6 +437,7 @@
 
 
 
+
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           <li>An introduction to Genome Wise Association Studies (GWAS)
             [<a
@@ -457,8 +464,10 @@
           </li>
           <li>Multivariate analysis of genetic data: an introduction [<a
               href="files/Glasgow2015/lecture-MVA.1.0.pdf">lecture</a>,
-            <a href="files/Glasgow2015/practical-MVAintro.1.0.pdf">practical</a>]
-          </li>
+            <a href="files/Glasgow2015/practical-MVAintro.1.0.pdf">practical</a>,
+            <a
+              href="files/Glasgow2015/practical-MVAintro-allCmd.1.0.pdf">practical
+              with all commands</a>] </li>
           <li>Multivariate analysis of genetic data: exploring group
             diversity [<a
               href="files/Glasgow2015/lecture-MVAgroups.1.0.pdf">lecture</a>,

Added: www/files/Glasgow2015/practical-MVAintro-allCmd.1.0.pdf
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From noreply at r-forge.r-project.org  Thu Aug  6 10:46:35 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  6 Aug 2015 10:46:35 +0200 (CEST)
Subject: [adegenet-commits] r1217 - in www: . files/Glasgow2015
Message-ID: <20150806084635.B821A187393@r-forge.r-project.org>

Author: jombart
Date: 2015-08-06 10:46:35 +0200 (Thu, 06 Aug 2015)
New Revision: 1217

Added:
   www/files/Glasgow2015/PRESENTATION- Genome-Wide Association Studies.pdf
   www/files/Glasgow2015/practical-GWAS_day4.pdf
   www/files/Glasgow2015/simGWAS.Rdata
Modified:
   www/documentation.html
Log:
finally adding material for day4

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2015-08-04 21:47:50 UTC (rev 1216)
+++ www/documentation.html	2015-08-06 08:46:35 UTC (rev 1217)
@@ -85,6 +85,7 @@
 
 
 
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@@ -116,6 +117,7 @@
 
 
 
+
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         font-family: Helvetica,Arial,sans-serif;"><br>
@@ -219,6 +221,7 @@
 
 
 
+
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             style="font-weight: bold;">Introduction to phylogenetics</span>
           (last updated on the 15/13/2013)</li>
@@ -274,6 +277,7 @@
 
 
 
+
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             style="font-weight: bold;">Introduction to multivariate
             analysis / bacterial GWAS</span> (last updated on the
@@ -325,6 +329,7 @@
 
 
 
+
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@@ -362,6 +367,7 @@
 
 
 
+
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         <ul>
@@ -438,6 +444,7 @@
 
 
 
+
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+
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           <li>Multivariate analysis of genetic data: uncovering spatial
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1217

From noreply at r-forge.r-project.org  Thu Aug  6 11:18:25 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  6 Aug 2015 11:18:25 +0200 (CEST)
Subject: [adegenet-commits] r1218 - in www: . files/Glasgow2015
Message-ID: <20150806091825.CCA38187269@r-forge.r-project.org>

Author: jombart
Date: 2015-08-06 11:18:25 +0200 (Thu, 06 Aug 2015)
New Revision: 1218

Added:
   www/files/Glasgow2015/practical-MVAgroups.1.0-allCmds.pdf
Modified:
   www/documentation.html
Log:
adding version with all commands for day3 practical

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2015-08-06 08:46:35 UTC (rev 1217)
+++ www/documentation.html	2015-08-06 09:18:25 UTC (rev 1218)
@@ -86,6 +86,7 @@
 
 
 
+
         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;">
@@ -118,6 +119,7 @@
 
 
 
+
       </font><br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);
         font-family: Helvetica,Arial,sans-serif;"><br>
@@ -222,6 +224,7 @@
 
 
 
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to phylogenetics</span>
           (last updated on the 15/13/2013)</li>
@@ -278,6 +281,7 @@
 
 
 
+
             Epidemiology</span> / <i>Public Health</i>: <span
             style="font-weight: bold;">Introduction to multivariate
             analysis / bacterial GWAS</span> (last updated on the
@@ -330,6 +334,7 @@
 
 
 
+
           </b><b><i>outbreaker</i></b></li>
         <ul>
           <li><a href="files/GenEpiTalk.1.0.pdf">talk</a></li>
@@ -368,6 +373,7 @@
 
 
 
+
             analysis using <span style="font-style: italic;">ape,
               adegenet,</span> </span><b>and </b><b><i>outbreaker</i></b></li>
         <ul>
@@ -445,6 +451,7 @@
 
 
 
+
               all commands</a>]</li>
           <li>An introduction to Genome Wise Association Studies (GWAS)
             [<a
@@ -473,11 +480,16 @@
             <a
               href="files/Glasgow2015/practical-MVAintro-allCmd.1.0.pdf">practical
 
+
               with all commands</a>] </li>
           <li>Multivariate analysis of genetic data: exploring group
             diversity [<a
               href="files/Glasgow2015/lecture-MVAgroups.1.0.pdf">lecture</a>,
-            <a href="files/Glasgow2015/practical-MVAgroups.1.0.pdf">practical</a>]</li>
+            <a href="files/Glasgow2015/practical-MVAgroups.1.0.pdf">practical</a>,
+            <a
+              href="files/Glasgow2015/practical-MVAgroups.1.0-allCmds.pdf">practical
+              with all commands</a>]<br>
+          </li>
           <li>An introduction to Genome Wise Association Studies (GWAS)
             [<a
 href="files/Glasgow2015/PRESENTATION-%20Genome-Wide%20Association%20Studies.pdf">lecture</a>,

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


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


From noreply at r-forge.r-project.org  Wed Aug 12 13:45:11 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 12 Aug 2015 13:45:11 +0200 (CEST)
Subject: [adegenet-commits] r1219 - www
Message-ID: <20150812114511.98C1C1873CA@r-forge.r-project.org>

Author: jombart
Date: 2015-08-12 13:45:11 +0200 (Wed, 12 Aug 2015)
New Revision: 1219

Modified:
   www/acceuil.html
Log:
added link to author

Modified: www/acceuil.html
===================================================================
--- www/acceuil.html	2015-08-06 09:18:25 UTC (rev 1218)
+++ www/acceuil.html	2015-08-12 11:45:11 UTC (rev 1219)
@@ -27,6 +27,7 @@
       <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>
@@ -45,11 +46,12 @@
           href="https://github.com/thibautjombart/adegenet">Github</a>
         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.
+          Jombart</a>, <a target="_top"
+          href="https://github.com/zkamvar">Zhian N Kamvar</a>, Caitlin
+        Collins, Roman Lustrik, Ismail Ahmed, Federico Calboli, Anne
+        Cori, Tobias Erik Reiners, and P?ter S?lymos, and officially
+        released on CRAN periodically. <br>
         <br>
-        <br>
         adegenet is described in the following publications:<br>
         <ul>
           <li> Jombart T. (2008) adegenet: a R package for the
@@ -79,6 +81,7 @@
 
 
 
+
               the bublisher's website</a>]<br>
           </li>
         </ul>
@@ -110,6 +113,7 @@
 
 
 
+
                 DNA sequences</span> to <span style="font-weight:
                 bold;">SNPs</span></li>
             <li> data import from <span style="font-weight: bold;">aligned
@@ -120,6 +124,7 @@
 
 
 
+
                 protein sequences</span> to polymorphic sites </li>
             <li> data <span style="font-weight: bold;">export</span> to
               the R packages genetics, hierfstat, LDheatmap</li>
@@ -142,6 +147,7 @@
 
 
 
+
                 manipulation</span></li>
             <li> basic <span style="font-weight: bold;">data
                 information </span>(heterozygosity, numbers of alleles,
@@ -157,6 +163,7 @@
 
 
 
+
                 for global and local structuring, </span><span
                 style="font-weight: bold;">Monmonier algorithm</span></li>
             <li>the <span style="font-style: italic; font-weight:
@@ -176,6 +183,7 @@
 
 
 
+
                 of haplotypes</span></li>
             <li> Discriminant Analysis of Principal Components (<span
                 style="font-weight: bold;">DAPC</span>)</li>