[adegenet-commits] r1160 - in www: . files

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Mar 18 16:41:44 CET 2014 

Author: jombart
Date: 2014-03-18 16:41:43 +0100 (Tue, 18 Mar 2014)
New Revision: 1160

Added:
   www/files/tutorial-basics.pdf
Removed:
   www/files/adegenet-basics.pdf
   www/files/adegenet-manual.pdf
   www/files/adegenet.pdf
Modified:
   www/documentation.html
Log:
Added the first new tutorial - basics

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2014-03-14 15:18:54 UTC (rev 1159)
+++ www/documentation.html	2014-03-18 15:41:43 UTC (rev 1160)
@@ -47,6 +47,8 @@
 
 
 
+
+
         engine</a>. <br>
       <br>
       <br>
@@ -56,40 +58,49 @@
 href="http://cran.r-project.org/web/packages/adegenet/adegenet.pdf">pdf</a>),
 
 
+
+
       which compiles all the manpages of the package.<br>
       <br>
       <br>
-      <span style="color: rgb(0, 102, 0); font-weight: bold;">Tutorials
-        vignettes </span><br>
-      - <a
-href="http://cran.r-project.org/web/packages/adegenet/vignettes/adegenet-basics.pdf"><span
-          style="font-style: italic;">adegenet-basics</span></a>:
-      introduction to the package; accessible from R by typing <span
-        style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-basics")</span>.<br>
-      - <a
+      <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>.</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>.<br>
-    </div>
-    <div style="margin-left: 40px;">- <a
+              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-dapc.pdf"><span
-          style="font-style: italic;">adegenet-dapc</span></a>: analysis
-      of the genetic structuring of populations; includes an
-      introduction to Discriminant Analysis of Principal Components
-      (DAPC); accessible from R by typing <span style="font-family:
-        monospace; color: rgb(255, 0, 0);">vignette("adegenet-dapc")</span>.<br>
-      - <a
+              style="font-style: italic;">adegenet-dapc</span></a>:
+          analysis of the genetic structuring of populations; includes
+          an introduction to Discriminant Analysis of Principal
+          Components (DAPC); accessible from R by typing <span
+            style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-dapc")</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>
-      <br>
+              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>
+      </ul>
+    </div>
+    <div style="margin-left: 40px;"> <span style="color: rgb(0, 102,
+        0);"><small>*(note:from adegenet 1.4-0, these tutorials replace
+          the vignettes which used to be part of the package)</small></span><br>
            <br>
-      <span style="font-weight: bold; color: rgb(0, 102, 0);">Lectures
-        and practicals</span><br>
+      <span style="font-weight: bold; color: rgb(0, 102, 0);"><br>
+        Lectures and practicals</span><br>
       - globaldiv summer school 2009, Piacenza, Italie: <a
         href="files/globaldiv-TJ.1.3.pdf">talk</a> - <a
         href="files/globaldiv-PC.1.3.pdf">practical course</a><br>
@@ -119,6 +130,8 @@
 
 
 
+
+
         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
@@ -135,6 +148,8 @@
 
 
 
+
+
         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
@@ -151,6 +166,8 @@
 
 
 
+
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
@@ -183,6 +200,8 @@
 
 
 
+
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to phylogenetics</span>.<br>
       (last updated on the 15/13/2013)<br>
@@ -203,6 +222,8 @@
 
 
 
+
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to multivariate analysis
         / bacterial GWAS</span>.<br>
@@ -221,6 +242,8 @@
 
 
 
+
+
       </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>
@@ -257,6 +280,8 @@
 
 
 
+
+
       <a href="files/hackLib/README">README</a> <br>
       <br>
       <br>

Deleted: www/files/adegenet-basics.pdf
===================================================================
--- www/files/adegenet-basics.pdf	2014-03-14 15:18:54 UTC (rev 1159)
+++ www/files/adegenet-basics.pdf	2014-03-18 15:41:43 UTC (rev 1160)
@@ -1,11439 +0,0 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1160

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