[adegenet-commits] r1082 - in www: . files

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Mar 4 16:09:44 CET 2013 

Author: jombart
Date: 2013-03-04 16:09:44 +0100 (Mon, 04 Mar 2013)
New Revision: 1082

Added:
   www/files/seqTrack-practical.1.3.pdf
Modified:
   www/documentation.html
Log:
New version of the seqTrack tutorial

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2013-03-04 12:10:29 UTC (rev 1081)
+++ www/documentation.html	2013-03-04 15:09:44 UTC (rev 1082)
@@ -1,7 +1,7 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <html>
   <head>
-    <meta content="text/html; charset=ISO-8859-1"
+    <meta content="text/html; charset=windows-1252"
       http-equiv="content-type">
     <title>documentation</title>
     <script type="text/javascript">
@@ -24,19 +24,17 @@
     <div style="margin-left: 40px;">As a <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, each component of adegenet is documented in help pages.
-      As a
-      starting point, one can type <span style="font-family: monospace;
-        font-weight: bold;">?adegenet</span> in
-      R to get an overview of package. Other sources of information
+            30px; height: 23px;"></a></span> package, each component of
+      adegenet is documented in help pages. As a starting point, one can
+      type <span style="font-family: monospace; font-weight: bold;">?adegenet</span>
+      in R to get an overview of package. Other sources of information
       distributed with the package include a manual and vignettes. This
       website also provides other resources such as lectures and
       practicals.<br>
       <br>
       <span style="font-weight: bold;">To search quickly</span> through
-      these
-      resources, use the <a target="_top" href="search.html">search
+      these resources, use the <a target="_top" href="search.html">search
+
         engine</a>. <br>
       <br>
       <br>
@@ -44,51 +42,44 @@
       <span style="font-weight: bold; color: rgb(0, 102, 0);">Manuals</span><br>
       - the adegenet <span style="font-weight: bold;">manual</span> (<a
         href="files/adegenet-manual.pdf">pdf</a>), which compiles all
-      the
-      manpages of the package.<br>
+      the manpages of the package.<br>
       <br>
       <br>
       <span style="color: rgb(0, 102, 0); font-weight: bold;">Tutorials
         vignettes </span><br>
       - <a href="files/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>
+          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
+        href="file:///home/thibaut/dev/adegenet/www/files/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>
-              - <a
-      href="files/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 style="margin-left: 40px;">- <a href="files/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>
+      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 href="files/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>
+          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>
            <br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);">Lectures
-        and
-        practicals</span><br>
+        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>
       <br>
       - Master 2 "Ecology, Evolution, Biometry", Lyon, France: <a
         href="files/talk-E2B.1.0.pdf">talk</a> - <a
-        href="files/TD-E2B.pdf">practical
-        course</a><br>
+        href="files/TD-E2B.pdf">practical course</a><br>
       <br>
       - One-week course on Genetic Data Analysis, Bogota, Colombia: <br>
           > <a href="files/day1.1.2.pdf">lecture 1</a>:
@@ -98,39 +89,39 @@
           > <a href="files/day3.1.2.pdf">lecture 3</a>:
       spatial genetics<br>
           > <a href="files/practical-day1.1.2.pdf">practical
+
         1</a> [<a href="files/practical-day1.1.2-allcmd.pdf">version
-        with all
-        commands</a>]<br>
+        with all commands</a>]<br>
           > <a href="files/practical-day2.1.3.pdf">practical
+
         2</a> [<a href="files/practical-day2.1.3-allcmd.pdf">version
-        with all
-        commands</a>]<br>
+        with all commands</a>]<br>
           > <a href="files/practical-day3.1.2.pdf">practical
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
           > <a href="files/MRCsession2-talk.1.2.pdf">slides</a><br>
           > <a href="files/MRC-session2-tuto.1.3.pdf">practical</a><br>
           > data (<a href="files/usflu.fasta">DNA
-        sequences</a>,
-      <a href="files/usflu.annot.csv">annotations</a>)<br>
+        sequences</a>, <a href="files/usflu.annot.csv">annotations</a>)<br>
       <br>
       - Imperial College - MSc "<span style="font-style: italic;">Modern
         Epidemiology</span>": <span style="font-weight: bold;">Introduction
-        to
-        phylogenetics</span>.<br>
+
+        to phylogenetics</span>.<br>
           > <a href="files/MSc-intro-phylo.1.0.pdf">practical</a><br>
           > data (<a href="files/usflu.fasta">usflu.fasta</a>,
       <a href="files/usflu.annot.csv">usflu.annot.csv</a>)<br>
       <br>
-      - RAPID-NGS workshop, Münster (March 2013) - <span
+      - RAPID-NGS workshop, Münster (March 2013) - <span
         style="font-weight: bold;">Outbreak analysis using <span
           style="font-style: italic;">adegenet </span>and <span
           style="font-style: italic;">ape</span></span> <img
         style="width: 80px; height: 37px;" alt="new"
         src="images/new.png"><br>
           > <a
-        href="files/seqTrack-practical.1.2.pdf">practical</a><br>
+        href="files/seqTrack-practical.1.3.pdf">practical</a><br>
           > data (<a
         href="files/fakeOutbreak/cases.csv">cases.csv</a>, <a
         href="files/fakeOutbreak/alignment.fa">alignment.fa</a>, <a
@@ -138,24 +129,21 @@
       <br>
       <br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);">Mailing
-        lists
-        archives </span><br>
+        lists archives </span><br>
       Use the <a target="_top" href="search.html">search engine</a> to
       browse the <span style="font-weight: bold;">archives</span> of
       the <span style="font-weight: bold;">adegenet forum</span>.<br>
       See the '<a href="contact.html">contact</a>' section of this
-      website
-      for further information on mailing lists.<br>
+      website for further information on mailing lists.<br>
       <br>
       <br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);">Miscellaneous<br>
       </span>- <a href="files/worksOnlyInDiploids.txt">worksOnyInDiploids.txt</a>:
-      the
-      list of <span style="font-weight: bold;">functions</span> working
-      <span style="font-weight: bold;">only for diploid</span> genotypes
+      the list of <span style="font-weight: bold;">functions</span>
+      working <span style="font-weight: bold;">only for diploid</span>
+      genotypes <br>
       <br>
       <br>
-      <br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);"></span><br>
       <span style="text-decoration: underline;"></span><br>
       <span style="color: rgb(255, 0, 0);"></span></div>

Added: www/files/seqTrack-practical.1.3.pdf
===================================================================
--- www/files/seqTrack-practical.1.3.pdf	                        (rev 0)
+++ www/files/seqTrack-practical.1.3.pdf	2013-03-04 15:09:44 UTC (rev 1082)
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+/Annots [ 67 0 R 68 0 R 69 0 R 70 0 R 71 0 R 72 0 R 73 0 R 74 0 R 75 0 R 76 0 R ]
+>> endobj
+77 0 obj <<
+/Type /XObject
+/Subtype /Image
+/Width 300
+/Height 115
+/BitsPerComponent 8
+/ColorSpace /DeviceRGB
+/Length 103641
+/Filter/FlateDecode
+/DecodeParms<</Colors 3/Columns 300/BitsPerComponent 8/Predictor 10>>
+>>
+stream
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1082

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