[adegenet-commits] r992 - in www: . files

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Feb 29 19:44:55 CET 2012 

Author: jombart
Date: 2012-02-29 19:44:55 +0100 (Wed, 29 Feb 2012)
New Revision: 992

Added:
   www/files/MSc-intro-phylo.1.0.pdf
Modified:
   www/documentation.html
Log:
Added material for the MSc practical.


Modified: www/documentation.html
===================================================================
--- www/documentation.html	2012-02-07 11:10:02 UTC (rev 991)
+++ www/documentation.html	2012-02-29 18:44:55 UTC (rev 992)
@@ -1,10 +1,10 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <html>
-<head>
-  <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
-  <title>documentation</title>
-  <script type="text/javascript">
+  <head>
+    <meta content="text/html; charset=ISO-8859-1"
+      http-equiv="content-type">
+    <title>documentation</title>
+    <script type="text/javascript">
 
   var _gaq = _gaq || [];
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@@ -16,114 +16,138 @@
     var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
   })();
   </script>
-</head>
-<body>
-<br>
-<br>
-<br>
-<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
-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; 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>
-<br>
-<span style="color: rgb(0, 102, 0); font-weight: bold;">Tutorials
-vignettes </span><img style="width: 80px; height: 37px;" alt="new"
- src="images/new.png"><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>
-</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>
-- <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>
-<br>
-     <br>
-<span style="font-weight: bold; color: rgb(0, 102, 0);">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>
-- 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>
-- One-week course on Genetic Data Analysis, Bogota, Colombia: <br>
-    > <a href="files/day1.1.2.pdf">lecture 1</a>:
-methodological overview<br>
-    > <a href="files/day2.1.3.pdf">lecture
-2</a>: finding clusters, using cluster information<br>
-    > <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>
-    >
-<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>
-    > <a href="files/practical-day3.1.2.pdf">practical
-3</a><br>
-- MRC methodological session: <span style="font-weight: bold;">Introduction
-to
-phylogenetics</span>:<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>
-<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 <br>
-<br>
-<br>
-Information can also be found from the archives of the <span
- style="font-weight: bold;">adegenet forum</span>; just enter your
-keywords below:<br>
-<center>
-<form method="get" action="http://www.google.com/search">
-  <div style="text-align: left;"><!--<TABLE bgcolor="#FFFFFF"><tr><td>-->
-  <a href="http://www.google.fr/"><img
- src="http://www.google.com/logos/Logo_40wht.gif" alt="Google"
- border="0" align="middle"></a><br>
-  </div>
-  <div style="text-align: left;"><input name="q" size="31"
- maxlength="255" value="Enter keywords here" type="text"><!--<INPUT TYPE=hidden name="domains" value="adegenet.r-forge.r-project.org" />--><input
- name="as_sitesearch"
- value="lists.r-forge.r-project.org/pipermail/adegenet-forum/"
- type="hidden"> <input name="pbil" value="Google search" type="submit"></div>
-</form>
-</center>
-See the '<a href="contact.html">contact</a>' section of this website
-for further information about this mailing list.<br>
-<br>
-<span style="text-decoration: underline;"></span><br>
-<span style="color: rgb(255, 0, 0);"></span></div>
-</body>
+  </head>
+  <body>
+    <br>
+    <br>
+    <br>
+    <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
+      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; 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>
+      <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>
+    </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>
+      - <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>
+      <br>
+           <br>
+      <span style="font-weight: bold; color: rgb(0, 102, 0);">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>
+      <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>
+      <br>
+      - One-week course on Genetic Data Analysis, Bogota, Colombia: <br>
+          > <a href="files/day1.1.2.pdf">lecture 1</a>:
+      methodological overview<br>
+          > <a href="files/day2.1.3.pdf">lecture
+        2</a>: finding clusters, using cluster information<br>
+          > <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>
+          >
+      <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>
+          > <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>
+      - Imperial College - MSc '<span style="font-style: italic;">Modern
+        Epidemiology</span>': <span style="font-weight: bold;">Introduction
+        to phylogenetics</span>.<img style="width: 80px; height: 37px;"
+        alt="new" src="images/new.png"><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>
+      <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
+      <br>
+      <br>
+      <br>
+      Information can also be found from the archives of the <span
+        style="font-weight: bold;">adegenet forum</span>; just enter
+      your
+      keywords below:<br>
+      <center>
+        <form method="get" action="http://www.google.com/search">
+          <div style="text-align: left;"><!--<TABLE bgcolor="#FFFFFF"><tr><td>-->
+            <a href="http://www.google.fr/"><img
+                src="http://www.google.com/logos/Logo_40wht.gif"
+                alt="Google" align="middle" border="0"></a><br>
+          </div>
+          <div style="text-align: left;"><input name="q" size="31"
+              maxlength="255" value="Enter keywords here" type="text"><!--<INPUT TYPE=hidden name="domains" value="adegenet.r-forge.r-project.org" />--><input
+              name="as_sitesearch"
+              value="lists.r-forge.r-project.org/pipermail/adegenet-forum/"
+              type="hidden"> <input name="pbil" value="Google search"
+              type="submit"></div>
+        </form>
+      </center>
+      See the '<a href="contact.html">contact</a>' section of this
+      website
+      for further information about this mailing list.<br>
+      <br>
+      <span style="text-decoration: underline;"></span><br>
+      <span style="color: rgb(255, 0, 0);"></span></div>
+  </body>
 </html>

Added: www/files/MSc-intro-phylo.1.0.pdf
===================================================================
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+F
[TRUNCATED]

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    svnlook diff /svnroot/adegenet -r 992

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