[adegenet-commits] r1162 - in www: . files

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Mar 19 13:13:10 CET 2014 

Author: jombart
Date: 2014-03-19 13:13:09 +0100 (Wed, 19 Mar 2014)
New Revision: 1162

Added:
   www/files/tutorial-basics.pdf
   www/files/tutorial-dapc.pdf
   www/files/tutorial-genomics.pdf
   www/files/tutorial-spca.pdf
Removed:
   www/files/tutorial-basics.pdf
   www/files/tutorial-dapc.pdf
   www/files/tutorial-spca.pdf
Modified:
   www/acceuil.html
   www/documentation.html
Log:
adding new genomics vignette

Modified: www/acceuil.html
===================================================================
--- www/acceuil.html	2014-03-18 19:02:13 UTC (rev 1161)
+++ www/acceuil.html	2014-03-19 12:13:09 UTC (rev 1162)
@@ -39,7 +39,10 @@
 
 
 
-          Jombart</a>, Caitlin Collins, Ismail Ahmed, <a
+
+          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
@@ -71,6 +74,7 @@
 
 
 
+
               the bublisher's website</a>]<br>
           </li>
         </ul>
@@ -97,11 +101,13 @@
               dataframe of genotypes</li>
             <li>data import from <span style="font-weight: bold;">aligned
 
+
                 DNA sequences</span> to <span style="font-weight:
                 bold;">SNPs</span></li>
             <li> data import from <span style="font-weight: bold;">aligned
 
 
+
                 protein sequences</span> to polymorphic sites </li>
             <li> data <span style="font-weight: bold;">export</span> to
               the R packages genetics, hierfstat, LDheatmap</li>
@@ -118,6 +124,7 @@
 
 
 
+
                 manipulation</span></li>
             <li> basic <span style="font-weight: bold;">data
                 information </span>(heterozygosity, numbers of alleles,
@@ -136,11 +143,13 @@
 
 
 
+
                 Fst </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
 
+
                 for global and local structuring, </span><span
                 style="font-weight: bold;">Monmonier algorithm</span></li>
             <li>the <span style="font-style: italic; font-weight:
@@ -152,6 +161,7 @@
 
 
 
+
               </span>for reconstructing genealogies of haplotypes</li>
             <li>simulation of <span style="font-weight: bold;">genealogies
 
@@ -161,6 +171,7 @@
 
 
 
+
                 of haplotypes</span></li>
             <li> Discriminant Analysis of Principal Components (<span
                 style="font-weight: bold;">DAPC</span>)</li>
@@ -191,6 +202,7 @@
 Caitlin
 
 
+
         Collins (<a href="mailto:caitiecollins17 at gmail.com">caitiecollins at gmail.com</a>),
 
 
@@ -199,15 +211,18 @@
 
 
 
+
         Ismaïl 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>),
 
 
 
 
 
+
         Anne Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>),
 Tobias
 
@@ -217,6 +232,7 @@
 
 
 
+
         Erik Reiners (<a href="mailto:Tobias.Reiners at Senckenberg.de">Tobias.Reiners at Senckenberg.de</a>),
 
 
@@ -225,6 +241,7 @@
 
 
 
+
         Péter Sólymos (<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/documentation.html
===================================================================
--- www/documentation.html	2014-03-18 19:02:13 UTC (rev 1161)
+++ www/documentation.html	2014-03-19 12:13:09 UTC (rev 1162)
@@ -50,6 +50,8 @@
 
 
 
+
+
         engine</a>. <br>
       <br>
       <br>
@@ -62,42 +64,41 @@
 
 
 
+
+
       which compiles all the manpages of the package.<br>
       <br>
       <br>
       <span style="color: rgb(0, 102, 0); font-weight: bold;">Tutorials*</span><br>
       <ul>
-        <li><a
-href="http://cran.r-project.org/web/packages/adegenet/vignettes/tutorial-basics.pdf"><span
-              style="font-style: italic;">tutorial-basics</span></a>:
-          introduction to the package: data classes, inputs/outputs,
-          basic population genetics, and exploratory analyses;
-          accessible from R by typing <span style="font-family:
-            monospace; color: rgb(255, 0, 0);">adegenetTutorial("basics")</span>.<img
+        <li><a href="files/tutorial-basics.pdf"><span style="font-style:
+              italic;">tutorial-basics</span></a>: introduction to the
+          package: data classes, inputs/outputs, basic population
+          genetics, and exploratory analyses; accessible from R by
+          typing <span style="font-family: monospace; color: rgb(255,
+            0, 0);">adegenetTutorial("basics")</span>.<img alt=""
+            src="images/new.png" height="37" width="80"></li>
+        <li><a href="files/tutorial-dapc.pdf"><span style="font-style:
+              italic;">tutorial-dapc</span></a>: a tutorial for the
+          analysis of population diversity using Discriminant Analysis
+          of Principal Components (DAPC); accessible from R by
+          typing <span style="font-family: monospace; color:
+            rgb(255, 0, 0);"><span style="font-family: monospace; color:
+              rgb(255, 0, 0);">adegenetTutorial</span>("dapc")</span>.<img
             alt="" src="images/new.png" height="37" width="80"></li>
-        <li><a
-href="http://cran.r-project.org/web/packages/adegenet/vignettes/tutorial-dapc.pdf"><span
-              style="font-style: italic;">tutorial-dapc</span></a>:
-          a tutorial for the analysis of population diversity using
-          Discriminant Analysis of Principal Components (DAPC);
-          accessible from R by typing <span style="font-family:
-            monospace; color: rgb(255, 0, 0);"><span style="font-family:
-              monospace; color: rgb(255, 0, 0);">adegenetTutorial</span>("dapc")</span>.<img
-            alt="" src="images/new.png" height="37" width="80"></li>
-        <li><a
-href="http://cran.r-project.org/web/packages/adegenet/vignettes/adegenet-spca.pdf"><span
-              style="font-style: italic;">adegenet-spca</span></a>:
-          spatial multivariate analysis using adegenet; includes an
-          introduction to spatial PCA (sPCA); accessible from R by
-          typing <span style="font-family: monospace; color: rgb(255,
-            0, 0);">vignette("adegenet-spca")</span>.</li>
-        <li><a
-href="http://cran.r-project.org/web/packages/adegenet/vignettes/adegenet-genomics.pdf"><span
-              style="font-style: italic;">adegenet-genomics</span></a>:
-          introduction to the handling of genome-wide SNP data using
-          adegenet; accessible from R by typing <span
-            style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-genomics")</span>.<br>
-        </li>
+        <li><a href="files/tutorial-genomics.pdf"><span
+              style="font-style: italic;">tutorial-genomics</span></a>:
+          introduction to the genlight class for storing and handling
+          large genome-wide SNP data; accessible from R by typing <span
+            style="font-family: monospace;"></span><span
+            style="font-family: monospace; color: rgb(255, 0, 0);">adegenetTutorial("genomics")</span>.<img
+            style=" width: 80px; height: 37px;" alt=""
+            src="images/new.png"></li>
+        <li><a href="files/tutorial-spca.pdf"><span style="font-style:
+              italic;">adegenet-spca</span></a>: spatial multivariate
+          analysis using adegenet; includes an introduction to spatial
+          PCA (sPCA); accessible from R by typing <span
+            style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-spca")</span>.</li>
       </ul>
     </div>
     <div style="margin-left: 40px;"> <span style="color: rgb(0, 102,
@@ -138,6 +139,8 @@
 
 
 
+
+
         1</a> [<a href="files/practical-day1.1.2-allcmd.pdf">version
         with all commands</a>]<br>
           > <a href="files/practical-day2.1.3.pdf">practical
@@ -157,6 +160,8 @@
 
 
 
+
+
         2</a> [<a href="files/practical-day2.1.3-allcmd.pdf">version
         with all commands</a>]<br>
           > <a href="files/practical-day3.1.2.pdf">practical
@@ -176,6 +181,8 @@
 
 
 
+
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
@@ -211,6 +218,8 @@
 
 
 
+
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to phylogenetics</span>.<br>
       (last updated on the 15/13/2013)<br>
@@ -234,6 +243,8 @@
 
 
 
+
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to multivariate analysis
         / bacterial GWAS</span>.<br>
@@ -255,6 +266,8 @@
 
 
 
+
+
       </b><b><i>outbreaker</i></b> <br>
           > <a href="files/GenEpiTalk.1.0.pdf">talk</a><br>
           > <a href="files/outbreakPractical.1.3.pdf">practical</a><br>
@@ -294,6 +307,8 @@
 
 
 
+
+
       <a href="files/hackLib/README">README</a> <br>
       <br>
       <br>

Deleted: www/files/tutorial-basics.pdf
===================================================================
--- www/files/tutorial-basics.pdf	2014-03-18 19:02:13 UTC (rev 1161)
+++ www/files/tutorial-basics.pdf	2014-03-19 12:13:09 UTC (rev 1162)
@@ -1,13610 +0,0 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1162

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