From noreply at r-forge.r-project.org  Sat Mar  2 16:21:54 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat,  2 Mar 2013 16:21:54 +0100 (CET)
Subject: [adegenet-commits] r1076 - in www/files: . fakeOutbreak
Message-ID: <20130302152154.184A9183E14@r-forge.r-project.org>

Author: jombart
Date: 2013-03-02 16:21:53 +0100 (Sat, 02 Mar 2013)
New Revision: 1076

Added:
   www/files/fakeOutbreak/
   www/files/fakeOutbreak/alignment.fa
   www/files/fakeOutbreak/cases.csv
   www/files/fakeOutbreak/truth.csv
Log:
Added data files of fakeOutbreak

Added: www/files/fakeOutbreak/alignment.fa
===================================================================
--- www/files/fakeOutbreak/alignment.fa	                        (rev 0)
+++ www/files/fakeOutbreak/alignment.fa	2013-03-02 15:21:53 UTC (rev 1076)
@@ -0,0 +1,5040 @@
+>1
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+ccccgcaactgagattcatgggcggttaacgcaatgaatccaatacagttaaagagccgt
+acggtcagcctttaaatgaaaggtcggcgttagcgattttctttccttgagcgcagatga
+tcaggcagaggtgtgctccgtgatcaactaaatattacgtaatcatcgacttaactacag
+actctatgcaggtctctcgggtcgcttttcactaccgggccgctacacagtgctgcaccc
+acactaatgcggatggattctttgtctagcttgtgactaaagttttaccagattctagac
+gaccagaaacacctcaaggcttggactgactcttggaacagtgatgtagtgctcacgcat
+gcttgactgctacgcggaaccacaccatggaacgctgagtcacatactggacataaatgt
+ctgttctgatcacgatcctagggagtaaagtgcaatagaggtatgtcctgatattcctct
+gtgattgtttcacgcttatcatactactattggcttacgagtgcacaggagtacataagg
+tgcaaactacacctgtctcgattatgtcgttccgctgagatagagtacacattctaccct
+tgaggcgaactatcaggtacgaatacttatattgaatggatccacacacgatcaagggct
+ctcgtacgatcgttcgccgatccgagtggttcccaactaagacgcatccatttgttatgc
+gcgactaaatgtgtgataatctgtcaaaactagctacgtctgtacccatcagtatttact
+tgacaacctgatggttgtaaaacaggcgagtacagcccgggtccacttatcagatagggg
+agacagcatccagtaaccccactagagggtctcacacgatatggttctattaataattgc
+cggcaaagccactacaatcatggctgcactgcgctagttctggcgcttctgtagataagg
+catctcctcgaaacgttctgttagccactcaccgcttatagcgcttctaacgtcgcagcc
+ggcgactagtgtcatatgttggcaaatatatccaggcaggcttgcataactggttcagag
+gcttaaagcaatttctatggcgagacgctttagcgtagttggcacctggggagggggaga
+tgtctgttctttcatatatcctttacgtcgcaagaaggataccagttgccgcgttaggtg
+ttctgctactgaccattggcaaagggtgcttaacggtcat
+>4
+tcgtttagacaatgaaggtggtagaccgacagttcacctgatgtgtcagaggtcctccac
+ggttatgtccgggagacgaagcgagacgctcagggcaccaagtgccgttgatagtcgatg
+atcggacaccgaaattggtcttagaggatacccataccattttatcctagcgtagggcct
+aagtatctcgcctatatctgacgcttactcagggaccgaggtgctatgagcaactgacta
+acactaattgccataatatgcaggctgcccgcccagcagcctagtctaaccaagcgaatg
+ctctccccggaccaacttacattcgacgacattccccacttaggcggccattaccccgct
+agtacaaaccgtacgccatcgctccctcccgctcacttgtcacttagtgccagttgcttt
+ctctatacctgtctactaacccagaaaaacgttgcaggtgcggctcaagacagcagacac
+gcactgcacgcattctgacccgtggaccaagttaaatcgggctgggaaggctttgggggg
+gactagcgttggcggcattcacagaggtcttgcacgtctaccgagagttgtggcgcctct
+aaggtgactgagagcgacggcggcttacactagtgaaagcatcttccagctccctctcgc
+acgccctcactaaccgtttgttgggcccctaaagacgagtctaaccgagaagccgaaatt
+tacgaagacctcgtagtagcacacacctgttgcagactagctacatacatagtggcgtca
+ggtacgccgtgtcgctcggagaagtcctctttgctagtcattcattatagacggcgtccc
+tatgggcctagcgcatatcggtacaagcaatgtttatcgctcaacttagatcgcacggca
+tggtcttactctaaattatggtgtattcgtagagttagaccgtggtcaacgaaaattatt
+tacctggcaaacacttgccatctgagcctagctatcgtagccccgttcggcaggctgact
+aatgcgtagtctaacagttgccttgatcatacctctgtgtcggtgctcattatgtggcca
+gatggggcagttgactcaacacttaccaggtcgccgtatcgacataagacgggctaacgg
+ctcctctgcacccgctgcgcctggcacatatttaggtgggagtcctgactacttcttaat
+gacgtggaactgcgatatagtcatgctttccactctggtgttgtcctccagaaacagtga
+aattataacgaacacgggccctagcttgagggacttaataccagcggccgtcatagggtc
+ctttcatggaaagcgagcctcgtgtttaggactttagcgggtgaaacgttaattccatta
+ctggtgccggactgttaggtccgtaggagctcgttttgaagcaacctgagctagtcgtta
+acaggtactgtgagagatcagtgaacgtggtgggatcaggtgcgactgggtctatacgtc
+cgtgctttagcacaagctttacaagcgaagccgcgaattgcgacaggtcaataggcgtgc
+aacgctgtacgtaaatgctcaggcattcagtgggcttagtaattcaagtgtatgggtctc
+caatacttccggctcttttgggcgcaaggaaaactgcgagtccgacatctatggttgtga
+tagtgatatttctagtacgttgggtagatcagctgtttgtacacgtgaccgtcgtcgaga
+ggcgcagcataaagagctcagtcggataacgcaacttcgactttactactgtaccgcgtg
+attagtcatacagcttctatcgttaacacgggagagcccgtattgtcaatccagtacgta
+gatggaatctgctttcggtcatctgttagtacgagtacaagggagtagattaccaacagg
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1076

From noreply at r-forge.r-project.org  Sun Mar  3 18:18:24 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  3 Mar 2013 18:18:24 +0100 (CET)
Subject: [adegenet-commits] r1077 - www/files/fakeOutbreak
Message-ID: <20130303171825.0BB4A1842C2@r-forge.r-project.org>

Author: jombart
Date: 2013-03-03 18:18:24 +0100 (Sun, 03 Mar 2013)
New Revision: 1077

Added:
   www/files/fakeOutbreak/update.csv
Removed:
   www/files/fakeOutbreak/truth.csv
Log:
renamed file

Deleted: www/files/fakeOutbreak/truth.csv
===================================================================
--- www/files/fakeOutbreak/truth.csv	2013-03-02 15:21:53 UTC (rev 1076)
+++ www/files/fakeOutbreak/truth.csv	2013-03-03 17:18:24 UTC (rev 1077)
@@ -1,31 +0,0 @@
-"infection.dates","infectors"
-2013-02-15,NA
-2013-02-17,1
-2013-02-19,2
-2013-02-19,NA
-2013-02-21,3
-2013-02-21,4
-2013-02-21,4
-2013-02-22,5
-2013-02-22,6
-2013-02-23,6
-2013-02-23,7
-2013-02-23,8
-2013-02-23,9
-2013-02-24,5
-2013-02-24,5
-2013-02-24,7
-2013-02-24,7
-2013-02-25,8
-2013-02-25,9
-2013-02-25,10
-2013-02-25,11
-2013-02-25,11
-2013-02-25,13
-2013-02-25,13
-2013-02-25,13
-2013-02-25,17
-2013-02-25,17
-2013-02-25,NA
-2013-02-26,10
-2013-02-26,13

Copied: www/files/fakeOutbreak/update.csv (from rev 1076, www/files/fakeOutbreak/truth.csv)
===================================================================
--- www/files/fakeOutbreak/update.csv	                        (rev 0)
+++ www/files/fakeOutbreak/update.csv	2013-03-03 17:18:24 UTC (rev 1077)
@@ -0,0 +1,31 @@
+"infection.dates","infectors"
+2013-02-15,NA
+2013-02-17,1
+2013-02-19,2
+2013-02-19,NA
+2013-02-21,3
+2013-02-21,4
+2013-02-21,4
+2013-02-22,5
+2013-02-22,6
+2013-02-23,6
+2013-02-23,7
+2013-02-23,8
+2013-02-23,9
+2013-02-24,5
+2013-02-24,5
+2013-02-24,7
+2013-02-24,7
+2013-02-25,8
+2013-02-25,9
+2013-02-25,10
+2013-02-25,11
+2013-02-25,11
+2013-02-25,13
+2013-02-25,13
+2013-02-25,13
+2013-02-25,17
+2013-02-25,17
+2013-02-25,NA
+2013-02-26,10
+2013-02-26,13


From noreply at r-forge.r-project.org  Sun Mar  3 18:24:14 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  3 Mar 2013 18:24:14 +0100 (CET)
Subject: [adegenet-commits] r1078 - www/files/fakeOutbreak
Message-ID: <20130303172414.875D11841C8@r-forge.r-project.org>

Author: jombart
Date: 2013-03-03 18:24:14 +0100 (Sun, 03 Mar 2013)
New Revision: 1078

Modified:
   www/files/fakeOutbreak/update.csv
Log:
update.csv now only contains the first 25 cases

Modified: www/files/fakeOutbreak/update.csv
===================================================================
--- www/files/fakeOutbreak/update.csv	2013-03-03 17:18:24 UTC (rev 1077)
+++ www/files/fakeOutbreak/update.csv	2013-03-03 17:24:14 UTC (rev 1078)
@@ -1,4 +1,4 @@
-"infection.dates","infectors"
+infection.dates,infectors
 2013-02-15,NA
 2013-02-17,1
 2013-02-19,2
@@ -23,9 +23,3 @@
 2013-02-25,11
 2013-02-25,13
 2013-02-25,13
-2013-02-25,13
-2013-02-25,17
-2013-02-25,17
-2013-02-25,NA
-2013-02-26,10
-2013-02-26,13


From noreply at r-forge.r-project.org  Sun Mar  3 18:41:58 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  3 Mar 2013 18:41:58 +0100 (CET)
Subject: [adegenet-commits] r1079 - www/files/fakeOutbreak
Message-ID: <20130303174158.66405184EF1@r-forge.r-project.org>

Author: jombart
Date: 2013-03-03 18:41:58 +0100 (Sun, 03 Mar 2013)
New Revision: 1079

Modified:
   www/files/fakeOutbreak/update.csv
Log:
added the 25th case (was missing)

Modified: www/files/fakeOutbreak/update.csv
===================================================================
--- www/files/fakeOutbreak/update.csv	2013-03-03 17:24:14 UTC (rev 1078)
+++ www/files/fakeOutbreak/update.csv	2013-03-03 17:41:58 UTC (rev 1079)
@@ -23,3 +23,4 @@
 2013-02-25,11
 2013-02-25,13
 2013-02-25,13
+2013-02-25,13


From noreply at r-forge.r-project.org  Sun Mar  3 19:43:06 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  3 Mar 2013 19:43:06 +0100 (CET)
Subject: [adegenet-commits] r1080 - in www: . files
Message-ID: <20130303184306.5AA92184D91@r-forge.r-project.org>

Author: jombart
Date: 2013-03-03 19:43:05 +0100 (Sun, 03 Mar 2013)
New Revision: 1080

Added:
   www/files/seqTrack-practical.1.2.pdf
Modified:
   www/documentation.html
Log:
Adding practical for RAPID-NGS in M?\195?\188nster

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2013-03-03 17:41:58 UTC (rev 1079)
+++ www/documentation.html	2013-03-03 18:43:05 UTC (rev 1080)
@@ -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 || [];
   _gaq.push(['_setAccount', 'UA-20083187-1']);
@@ -16,119 +16,148 @@
     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;">To search quickly</span> through these
-resources, use the <a target="_top" href="search.html">search engine</a>.
-<img style="width: 80px; height: 37px;" alt="new" src="images/new.png"><br>
-<br>
-<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>
-<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>
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - <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>
-&nbsp;&nbsp;&nbsp;&nbsp; <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>
-&nbsp;&nbsp;&nbsp; &gt; <a href="files/day1.1.2.pdf">lecture 1</a>:
-methodological overview<br>
-&nbsp;&nbsp;&nbsp; &gt; <a href="files/day2.1.3.pdf">lecture 2</a>:
-finding clusters, using cluster information<br>
-&nbsp;&nbsp;&nbsp; &gt; <a href="files/day3.1.2.pdf">lecture 3</a>:
-spatial genetics<br>
-&nbsp;&nbsp;&nbsp; &gt; <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>
-&nbsp;&nbsp;&nbsp; &gt; <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>
-&nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.2.pdf">practical
-3</a><br>
-<br>
-- MRC methodological session: Introduction to phylogenetics:<br>
-&nbsp;&nbsp;&nbsp; &gt; <a href="files/MRCsession2-talk.1.2.pdf">slides</a><br>
-&nbsp;&nbsp;&nbsp; &gt; <a href="files/MRC-session2-tuto.1.3.pdf">practical</a><br>
-&nbsp;&nbsp;&nbsp; &gt; 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>.<br>
-&nbsp;&nbsp;&nbsp; &gt; <a href="files/MSc-intro-phylo.1.0.pdf">practical</a><br>
-&nbsp;&nbsp;&nbsp; &gt; 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);">Mailing 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>
-<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>
-<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>
-</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;">To search quickly</span> through
+      these
+      resources, use the <a target="_top" href="search.html">search
+        engine</a>. <br>
+      <br>
+      <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>
+      <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>
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; &nbsp; - <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>
+      &nbsp;&nbsp;&nbsp;&nbsp; <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>
+      &nbsp;&nbsp;&nbsp; &gt; <a href="files/day1.1.2.pdf">lecture 1</a>:
+      methodological overview<br>
+      &nbsp;&nbsp;&nbsp; &gt; <a href="files/day2.1.3.pdf">lecture 2</a>:
+      finding clusters, using cluster information<br>
+      &nbsp;&nbsp;&nbsp; &gt; <a href="files/day3.1.2.pdf">lecture 3</a>:
+      spatial genetics<br>
+      &nbsp;&nbsp;&nbsp; &gt; <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>
+      &nbsp;&nbsp;&nbsp; &gt; <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>
+      &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.2.pdf">practical
+        3</a><br>
+      <br>
+      - MRC methodological session: Introduction to phylogenetics:<br>
+      &nbsp;&nbsp;&nbsp; &gt; <a href="files/MRCsession2-talk.1.2.pdf">slides</a><br>
+      &nbsp;&nbsp;&nbsp; &gt; <a href="files/MRC-session2-tuto.1.3.pdf">practical</a><br>
+      &nbsp;&nbsp;&nbsp; &gt; data (<a href="files/usflu.fasta">DNA
+        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>
+      &nbsp;&nbsp;&nbsp; &gt; <a href="files/MSc-intro-phylo.1.0.pdf">practical</a><br>
+      &nbsp;&nbsp;&nbsp; &gt; data (<a href="files/usflu.fasta">usflu.fasta</a>,
+      <a href="files/usflu.annot.csv">usflu.annot.csv</a>)<br>
+      <br>
+      - RAPID-NGS workshop, M&uuml;nster (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>
+      &nbsp;&nbsp;&nbsp; &gt; <a
+        href="files/seqTrack-practical.1.2.pdf">practical</a><br>
+      &nbsp;&nbsp;&nbsp; &gt; data (<a
+        href="files/fakeOutbreak/cases.csv">cases.csv</a>, <a
+        href="files/fakeOutbreak/alignment.fa">alignment.fa</a>, <a
+        href="files/fakeOutbreak/update.csv">update.csv</a>)<br>
+      <br>
+      <br>
+      <span style="font-weight: bold; color: rgb(0, 102, 0);">Mailing
+        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>
+      <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>
+      <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>
+  </body>
 </html>

Added: www/files/seqTrack-practical.1.2.pdf
===================================================================
--- www/files/seqTrack-practical.1.2.pdf	                        (rev 0)
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?R???3??\<{I?|Lt?LS??D?????N?Qg4qNv?-^???W??r-? Eu?:$5=??????????S?:???g???$7??|??,?????6=?M^I{iUgO?:w??jRM?GB?^??b?M?-?oe?!?}??w?9??+??]??????P?A\????????}d???4+&6TO_??0?96<(XdT????????????3??	n???88XP(??? ??	?`^?.?U?\?zE???c?Zj3?Q??,??????).G.w??9zV????^EN9?????(U?????#?A??[Bb??;???Rr:cS[Sr???b?? ?q??.?4??Sq?1%??G??s?QB?????k7????????.Y{????]?3?N??]????	x??UE?0Yc?"`?imtqu06?13???3
? ????
b^^??H:WzZbLtX`?'???yE???{woFG?a?X366???????5?????G?v?(????)??5O???+'7D?M/??H/??U??V??W?]?2????W~??}??a?d????
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??v???kv"
p??58?j?K?<Z?4D???ZTkL???n???|d }??1????@???c*???N????Jn?*?2???ai??]H?ti|???@?w_a??|s.X?????^?,??bc
?7?????-I???????????X?J?>??_??;X??i??k???q?@$w<??
+?
???pp??P??SAA??????k??qv??:f??l?Jf?;X&1???W?h?Q??]??U??Y??,0w??0|a?b??$B?4B?*R?&R?2D?$@Q???G?VuW$?????v| ??}N?-?J?{?Q????l?I????????]:w??9|???=?????????c?}???L&S??U?J?
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t????_?L??,?J??v?yz4??w??"=#hg??d4E8?DC?3??trO!??Bk???%?
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P??tX'%???????P??;X?<??7?z&#???
5iIi?c??Q?g?"????piYF? ??E?%?
\
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???>VSW
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+??????S??S	?
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??GOM??qf"????a7o^?T???????rE???;????3????Fn_w?XP??m??
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56Q??d	KE5K??=??v??????l?|{3f&????%`X?
???GhhhPP?;s????]????#??o??r???????4?A??L?I??gh8?J?pu???"???|?.?;??????ib?p?|?d4????g?
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?.?n??q??@?g???(p??
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h???'???l??????>(????????v~hRT??p??????k??;????6??m???C???<w??57J??M?'????????Q?4??1??V?N?F}??x?F.??????????? ???B?yx??}\?????Z??zO??o???{a??e????????I????eh???yW(u6n??.?R?%>U???5a
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1{?<????P??B?H?HV?,2*???n*@??p8?#???exx???S?????`??w?<<?444???7m??}??]???U-X????d??R??B?}??
+p??+$??"??]???????#?/^??????X?~
+?|??
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+m????%a(?.+\?w?+HS?]?V???T`??A??b:?]?????o?s???u?m???}??U?6???
+x?a??m?
+?,??S?2>v????????????cE{
+k?4{?c?{?
+?*gJ-??K??k6?\?k?@???}????h?? ??L?kZ?9??e????i#?????/zK7P???
+???56?d?U??rm	???g?K^;?TsB?G@???%t[e?!?'?\???????lfaRS[14?????e8?1?&
TH??~"k ??$?????????{????
+b??r3\&?R?@??? ,?#)m ?D???1d??????????D+w,?????S??b??c?'0??9???????@???B??l=???M
1?a	]???n???????u??+7??&S???)??!??,??
+}??(??G4?????????T??{???*umS?]??*j?[bh?-???y8r????=Q?'?w?B?fZ?x59= ?o????L3g???Kp??Z scaG??x?u??$??>?'uF(U??????2??j??U???O^~????m?uv?????M?z??L?9lP`t?*I?*?Q?W?y??
+3rH?h??y???V1??A???????I????j>SUR???????????;?pf^??-3???
??%?????eb?Hj???h?%?tW???@????^??q" ?J??"???[w??rw
E?Yl?>??????s9???0???^&?(??<}n/??$&?`??i????R????C>? ????ZF\?{jh??%MDLKTL]??rXh???M?Nl???????L???????V???N)??j0jqplcny^??????????V|?5????????]q6?Bx??W^?5???F2??H?J?I?9<zf?N)?
+45?SVI_a?pq?Pv????F??b?3e??O4o??(?s?????B%?o?????????????/??'??&\Y??P?RX?TN??@?DT?D\?\B2"??w????e??-?	^gq&?c??????y?:??50?m??L???c}qit???S?'&?&?Q???ciQI}aq?;??o?W?zW??????*?~P???0g?????????w?;|???S%W?rr??CK?Z????u?????|???????e???7?8?{????TO???i?~?????ds??????G?RrF?/?m?y?????Y????5????l?n????W????????
+K??~"?:?B>3??a??S?~??????8?<S4=}Qt??G??i?7????f9???|?V??[?7w?????_???UKV???e??gL?&????XM7? Smr\??????????W??????|?????b?'??}???????]???Wn?u????n?y$?I	???????\???????q??7????t5???????g??_?/??`??KW/\?f??5KW?[?f?????8}???Y?Vc???L?[l1l.?;9???/???/]?s?????^?z?O??_?f????W???/]	??z???K?nX???????:x??????????>?O?5%?_y???2\?6???????4??=?H	????D??!?? _:??$?
+F
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1080

From noreply at r-forge.r-project.org  Mon Mar  4 13:10:30 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  4 Mar 2013 13:10:30 +0100 (CET)
Subject: [adegenet-commits] r1081 - www
Message-ID: <20130304121030.461B11848C9@r-forge.r-project.org>

Author: jombart
Date: 2013-03-04 13:10:29 +0100 (Mon, 04 Mar 2013)
New Revision: 1081

Modified:
   www/literature.html
Log:
+1ref

Modified: www/literature.html
===================================================================
--- www/literature.html	2013-03-03 18:43:05 UTC (rev 1080)
+++ www/literature.html	2013-03-04 12:10:29 UTC (rev 1081)
@@ -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">
@@ -54,6 +54,7 @@
 
 
 
+
         the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
       <br style="color: rgb(0, 153, 0);">
       <br>
@@ -77,6 +78,7 @@
 
 
 
+
         abstract</a>]<br>
       <br>
       - the paper presenting the <span style="font-style: italic;">spatial
@@ -85,6 +87,7 @@
 
 
 
+
         principal component analysis</span> (<span style="font-style:
         italic;">sPCA</span>, function <span style="font-family:
         monospace; color: rgb(255, 0, 0);">spca</span>), global and
@@ -96,6 +99,7 @@
 
 
 
+
       cryptic spatial patterns in genetic variability by a new
       multivariate method.&nbsp; <span style="font-style: italic;">Heredity</span>
       <span style="font-weight: bold;">101</span>: 92-103. doi:
@@ -108,6 +112,7 @@
 
 
 
+
         abstract</a>]<br>
     </div>
     <br>
@@ -122,6 +127,7 @@
 
 
 
+
       simulations of genealoies of haplotypes (<span style="font-family:
         monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
       <b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010)
@@ -136,6 +142,7 @@
 
 
 
+
         of Principal Components</span> (<span style="font-style:
         italic;">DAPC</span>, functions <span style="font-family:
         monospace;"><span style="color: rgb(255, 0, 0);">find.clusters</span>
@@ -156,11 +163,11 @@
         adegenet:</span><br style="text-decoration: underline;">
       <br>
       [1] Cohas A, Yoccoz NG, Bonenfant C, Goossens B, Genton C, Galan
-      M, Kempenaers B, Allain&eacute; D (2007) The<span style="color:
-        rgb(0, 0, 0);">genetic similarity between pair members
-        influences the frequency of extrapair paternity in alpine
-        marmots</span>. <i>Animal Behaviour</i><i></i><span
-        style="font-weight: bold;">76</span>: 87-95.<br>
+      M, Kempenaers B, Allain? D (2007) The<span style="color: rgb(0, 0,
+        0);">genetic similarity between pair members influences the
+        frequency of extrapair paternity in alpine marmots</span>. <i>Animal
+        Behaviour</i><i></i><span style="font-weight: bold;">76</span>:
+      87-95.<br>
       <br>
       [2] Satkoski JA,&nbsp; Malhi RS, Kanthaswamy S, Tito RY, Malladi
       VS, Smith DG (2008) Pyrosequencing as a method for SNP
@@ -170,6 +177,7 @@
 
 
 
+
           Genomics</span></span><span class="citation-publication-date"></span><span
         style="font-weight: bold;" class="citation-volume">9</span><span
         class="citation-issue"></span>: 256.<br>
@@ -183,33 +191,31 @@
           style="font-style: italic;">Int J Primatol</span> <span
           style="font-weight: bold;">29</span>: 1295-1311.<br>
         <br>
-        [4] Kidd, AG, Bowman J, Lesbarr&egrave;res D, Schulte-Hostedde
-        AI (2009). Hybridization between escaped domestic and wild
-        American mink (<span style="font-style: italic;">Neovison vison</span>).
-
-
-
-
+        [4] Kidd, AG, Bowman J, Lesbarr?res D, Schulte-Hostedde AI
+        (2009). Hybridization between escaped domestic and wild American
+        mink (<span style="font-style: italic;">Neovison vison</span>).
         <span style="font-style: italic;">Molecular Ecology</span> <span
           style="font-weight: bold;">18</span>: 1175-1186.<br>
         <br>
-        [5] Cohas E, Bonenfant C, Kempaners B, Allain&eacute; D (2009).
+        [5] Cohas E, Bonenfant C, Kempaners B, Allain? D (2009).
         Age-specific effect of heterozygosity on survival in alpine
         marmots, <span class="i"><span style="font-style: italic;">Marmota
 
 
 
 
+
             marmota</span>.</span><span style="font-style: italic;">Molecular
 
 
 
 
+
           Ecology</span> <span style="font-weight: bold;">18</span>:
         1491-1503.<br>
         <br>
-        [6] O'Brien J, Devillard S, Say L, Vanthomme A, L&eacute;ger F,
-        Ruette S, Pontier D (2009). Preserving genetic integrity in a
+        [6] O'Brien J, Devillard S, Say L, Vanthomme A, L?ger F, Ruette
+        S, Pontier D (2009). Preserving genetic integrity in a
         hybridising world:<br>
         are European Wildcats (<span style="font-style: italic;">Felis
           silvestris silvestris</span>) in eastern France distinct from
@@ -249,16 +255,17 @@
 
 
 
+
           australis</i> in North America. <span style="font-style:
           italic;">Biological Invasions</span>. doi:
         10.1007/s10530-010-9699-6.<br>
         <br>
-        [12] C. BERTHOULY, D. DO NGOC, S. TH&Eacute;VENON, D. BOUCHEL,
-        T. NHU VAN, C. DANES, V. GROSBOIS, H. HOANG THANH, C. VU CHI,
-        J.-C. MAILLARD (2009) How does farmer connectivity influence
-        livestock genetic structure? A case-study in a Vietnamese goat
-        population. <span style="font-style: italic;">Molecular Ecology</span>
-        <span style="font-weight: bold;">18</span>: 3980-3991<br>
+        [12] C. BERTHOULY, D. DO NGOC, S. TH?VENON, D. BOUCHEL, T. NHU
+        VAN, C. DANES, V. GROSBOIS, H. HOANG THANH, C. VU CHI, J.-C.
+        MAILLARD (2009) How does farmer connectivity influence livestock
+        genetic structure? A case-study in a Vietnamese goat population.
+        <span style="font-style: italic;">Molecular Ecology</span> <span
+          style="font-weight: bold;">18</span>: 3980-3991<br>
         <br>
         [13] <span class="name"><span class="forenames">COLIN J.</span>
           <span class="surname">GARROWAY</span><sup><nobr></nobr></sup></span>,
@@ -298,10 +305,10 @@
             style="text-decoration: underline;"></span></span>1965-1977<br>
         <br>
         [15] Gwenaelle&nbsp;Comont, Marie-France&nbsp;Corio-Costet,
-        Philippe&nbsp;Larignon and Fran&ccedil;ois&nbsp;Delmotte (2010)
-        AFLP markers reveal two genetic groups in the French population
-        of the grapevine fungal pathogen <i>Phaeomoniella
-          chlamydospora. European Journal of Plant Pathology</i> Doi:
+        Philippe&nbsp;Larignon and Fran?ois&nbsp;Delmotte (2010) AFLP
+        markers reveal two genetic groups in the French population of
+        the grapevine fungal pathogen <i>Phaeomoniella chlamydospora.
+          European Journal of Plant Pathology</i> Doi:
         10.1007/s10658-010-9611-3<br>
         <br>
         [16] <span class="name"><span class="forenames">Michelle F.</span>
@@ -342,16 +349,16 @@
             style="font-style: italic;">Animal Genetics </span><span
             style="font-weight: bold;">41</span>: 47-63.<br>
           &nbsp;</span><span class="authors"><span style="white-space:
-            nowrap;">[20] Denis Lalo&euml;</span>, <span
-            style="white-space: nowrap;">Katayoun Moazami-Goudarzi</span>,
-          <span style="white-space: nowrap;">Johannes A. Lenstra</span>,
-          <span style="white-space: nowrap;">Paolo Ajmone Marsan</span>,
-          <span style="white-space: nowrap;">Pedro Azor</span>, <span
+            nowrap;">[20] Denis Lalo?</span>, <span style="white-space:
+            nowrap;">Katayoun Moazami-Goudarzi</span>, <span
+            style="white-space: nowrap;">Johannes A. Lenstra</span>, <span
+            style="white-space: nowrap;">Paolo Ajmone Marsan</span>, <span
+            style="white-space: nowrap;">Pedro Azor</span>, <span
             style="white-space: nowrap;">Roswitha Baumung</span>, <span
             style="white-space: nowrap;">Daniel G. Bradley</span>, <span
             style="white-space: nowrap;">Michael W. Bruford</span>, <span
-            style="white-space: nowrap;">Javier Ca&ntilde;&oacute;n</span>,
-          <span style="white-space: nowrap;">Gaudenz Dolf</span>, <span
+            style="white-space: nowrap;">Javier Ca??n</span>, <span
+            style="white-space: nowrap;">Gaudenz Dolf</span>, <span
             style="white-space: nowrap;">Susana Dunner</span>, <span
             style="white-space: nowrap;">Georg Erhardt</span>, <span
             style="white-space: nowrap;">Godfrey Hewitt</span>, <span
@@ -368,7 +375,7 @@
           <b>2010</b>, <em>2</em>(6), 932-945; doi:10.3390/d2060932</span><br>
         <span style="display: block;" id="records_chunks"><br>
         </span><span class="citation_author">[21] Gautier M, </span> <span
-          class="citation_author">Lalo&euml; D, </span> <span
+          class="citation_author">Lalo? D, </span> <span
           class="citation_author">Moazami-Goudarzi K, </span> <span
           class="citation_date">2010</span> <span
           class="citation_article_title">Insights into the Genetic
@@ -397,15 +404,17 @@
 
 
 
+
           Oct 6. [Epub ahead of print]<br>
         </p>
         <p class="auth_list">[24] SANTOS, H., BURBAN, C., ROUSSELET, J.,
-          ROSSI, J.-P., BRANCO, M. and KERDELHU&Eacute;, C. , Incipient
+          ROSSI, J.-P., BRANCO, M. and KERDELHU?, C. , Incipient
           allochronic speciation in the pine processionary moth (<em>Thaumetopoea
 
 
 
 
+
             pityocampa</em>, Lepidoptera, Notodontidae). <span
             style="font-style: italic;">Journal of Evolutionary Biology</span>,
           no. doi:&nbsp;10.1111/j.1420-9101.2010.02147.x<br>
@@ -420,6 +429,7 @@
 
 
 
+
             Vol. Sci. Pap. ICCAT</span>, 65(3): 988-995</p>
         <p class="intro">[26] <span class="citation_author">Vandewoestijne
 
@@ -427,6 +437,7 @@
 
 
 
+
             S, </span> <span class="citation_author">Van Dyck H, </span>
           <span class="citation_date">2010</span> <span
             class="citation_article_title">Population Genetic
@@ -437,6 +448,7 @@
 
 
 
+
             ONE</span><span class="citation_issue">5(11):</span> <span
             class="citation_start_page">e13810.</span> <span
             class="citation_doi">doi:10.1371/journal.pone.0013810<br>
@@ -458,6 +470,7 @@
 
 
 
+
           </span><span class="doi"><span class="label">DOI:</span> <span
               class="value">10.1007/s10329-010-0232-4<br>
             </span></span></p>
@@ -516,6 +529,7 @@
 
 
 
+
             tetradactylum</em>: Polynemidae). Molecular Ecology,
           20:&nbsp;no. doi:&nbsp;10.1111/j.1365-294X.2011.05097.x<br>
         </p>
@@ -532,6 +546,7 @@
 
 
 
+
               neoformans</i> Variety <i>grubii</i> Multilocus Sequence
             Types from Thailand Are Consistent with an Ancestral African
             Origin.</span> <span class="citation_journal_title">PLoS
@@ -549,14 +564,10 @@
         <p class="intro">[38] A. Mercier, D. Ajzenberg, S.<span
             class="hit">Devillard</span>, M.P. Demar, B. de Thoisy, H.
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1081

From noreply at r-forge.r-project.org  Mon Mar  4 16:09:44 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  4 Mar 2013 16:09:44 +0100 (CET)
Subject: [adegenet-commits] r1082 - in www: . files
Message-ID: <20130304150944.C4C4A184C5A@r-forge.r-project.org>

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>
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp; &nbsp; - <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>
       &nbsp;&nbsp;&nbsp;&nbsp; <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>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/day1.1.2.pdf">lecture 1</a>:
@@ -98,39 +89,39 @@
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/day3.1.2.pdf">lecture 3</a>:
       spatial genetics<br>
       &nbsp;&nbsp;&nbsp; &gt; <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>
       &nbsp;&nbsp;&nbsp; &gt; <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>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.2.pdf">practical
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/MRCsession2-talk.1.2.pdf">slides</a><br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/MRC-session2-tuto.1.3.pdf">practical</a><br>
       &nbsp;&nbsp;&nbsp; &gt; 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>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/MSc-intro-phylo.1.0.pdf">practical</a><br>
       &nbsp;&nbsp;&nbsp; &gt; data (<a href="files/usflu.fasta">usflu.fasta</a>,
       <a href="files/usflu.annot.csv">usflu.annot.csv</a>)<br>
       <br>
-      - RAPID-NGS workshop, M&uuml;nster (March 2013) - <span
+      - RAPID-NGS workshop, M?nster (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>
       &nbsp;&nbsp;&nbsp; &gt; <a
-        href="files/seqTrack-practical.1.2.pdf">practical</a><br>
+        href="files/seqTrack-practical.1.3.pdf">practical</a><br>
       &nbsp;&nbsp;&nbsp; &gt; 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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[TRUNCATED]

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

From noreply at r-forge.r-project.org  Mon Mar 11 17:37:04 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 11 Mar 2013 17:37:04 +0100 (CET)
Subject: [adegenet-commits] r1083 - www
Message-ID: <20130311163704.57343184DA2@r-forge.r-project.org>

Author: jombart
Date: 2013-03-11 17:37:04 +0100 (Mon, 11 Mar 2013)
New Revision: 1083

Modified:
   www/download.html
Log:
fixed broken links

Modified: www/download.html
===================================================================
--- www/download.html	2013-03-04 15:09:44 UTC (rev 1082)
+++ www/download.html	2013-03-11 16:37:04 UTC (rev 1083)
@@ -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>download</title>
     <script type="text/javascript">
@@ -23,18 +23,16 @@
     <br>
     <br>
     <div style="margin-left: 40px;"><img alt="" src="images/bullet.png"
-        style="width: 10px; height: 10px;"> The package adegenet is
-      available from <a href="http://cran.r-project.org/mirrors.html">CRAN</a>
-      (stable version).<br>
+        style="width: 10px; height: 10px;"> The package <b>adegenet is
+        available from</b> <a
+        href="http://cran.r-project.org/mirrors.html">CRAN</a> (stable
+      version).<br>
       <br>
       <img alt="" src="images/bullet.png" style="width: 10px; height:
         10px;"> The <span style="font-weight: bold;">current stable
         version</span> (adegenet_1.3-6) is available as:<br>
       - <a href="files/adegenet_1.3-6.tar.gz">linux sources</a><br>
-      - <a
-        href="file:///home/thibaut/dev/adegenet/www/files/adegenet_1.3-6.tgz">MacOS
-
-        X binary</a><br>
+      - <a href="files/adegenet_1.3-6.tgz">MacOS X binary</a><br>
       - <a href="files/adegenet_1.3-6.zip">Windows binary</a><br>
       <br>
       <img alt="" src="images/bullet.png" style="width: 10px; height:
@@ -48,6 +46,7 @@
       </span><img alt="" src="images/bullet.png" style="width: 10px;
         height: 10px;"> <span style="font-weight: bold;">Patches</span>&nbsp;
 
+
       <br>
       Patches correct minor bugs or implement new functionnalities, and
       will be included into the next CRAN release. It is recommended to
@@ -58,6 +57,7 @@
 to
 use
 
+
       a patch.<br>
       <a href="files/patches/addedFeatures.R"><span style="font-family:
           monospace;">addedFeatures.R</span></a>: (for adegenet
@@ -70,18 +70,9 @@
       <img alt="" src="images/bullet.png" style="width: 10px; height:
         10px;"> <span style="font-weight: bold;">Older versions</span>:<br>
       adegenet _1.3-5<br>
-      - <a
-        href="file:///home/thibaut/dev/adegenet/www/files/adegenet_1.3-5.tar.gz">linux
-
-        sources</a><br>
-      - <a
-        href="file:///home/thibaut/dev/adegenet/www/files/adegenet_1.3-5.tgz">MacOS
-
-        X binary</a><br>
-      - <a
-        href="file:///home/thibaut/dev/adegenet/www/files/adegenet_1.3-5.zip">Windows
-
-        binary</a><br>
+      - <a href="files/adegenet_1.3-5.tar.gz">linux sources</a><br>
+      - <a href="files/adegenet_1.3-5.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.3-5.zip">Windows binary</a><br>
       <br>
       &nbsp;adegenet _1.3-4<br>
       - <a href="files/adegenet_1.3-4.tar.gz">linux sources</a><br>


From noreply at r-forge.r-project.org  Tue Mar 12 18:26:46 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 12 Mar 2013 18:26:46 +0100 (CET)
Subject: [adegenet-commits] r1084 - www
Message-ID: <20130312172646.EA3A7184F3A@r-forge.r-project.org>

Author: jombart
Date: 2013-03-12 18:26:46 +0100 (Tue, 12 Mar 2013)
New Revision: 1084

Modified:
   www/literature.html
Log:
+3 ref

Modified: www/literature.html
===================================================================
--- www/literature.html	2013-03-11 16:37:04 UTC (rev 1083)
+++ www/literature.html	2013-03-12 17:26:46 UTC (rev 1084)
@@ -55,6 +55,7 @@
 
 
 
+
         the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
       <br style="color: rgb(0, 153, 0);">
       <br>
@@ -79,6 +80,7 @@
 
 
 
+
         abstract</a>]<br>
       <br>
       - the paper presenting the <span style="font-style: italic;">spatial
@@ -88,6 +90,7 @@
 
 
 
+
         principal component analysis</span> (<span style="font-style:
         italic;">sPCA</span>, function <span style="font-family:
         monospace; color: rgb(255, 0, 0);">spca</span>), global and
@@ -100,6 +103,7 @@
 
 
 
+
       cryptic spatial patterns in genetic variability by a new
       multivariate method.&nbsp; <span style="font-style: italic;">Heredity</span>
       <span style="font-weight: bold;">101</span>: 92-103. doi:
@@ -113,6 +117,7 @@
 
 
 
+
         abstract</a>]<br>
     </div>
     <br>
@@ -128,6 +133,7 @@
 
 
 
+
       simulations of genealoies of haplotypes (<span style="font-family:
         monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
       <b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010)
@@ -143,6 +149,7 @@
 
 
 
+
         of Principal Components</span> (<span style="font-style:
         italic;">DAPC</span>, functions <span style="font-family:
         monospace;"><span style="color: rgb(255, 0, 0);">find.clusters</span>
@@ -166,6 +173,7 @@
       M, Kempenaers B, Allain? D (2007) The<span style="color: rgb(0, 0,
         0);">genetic similarity between pair members influences the
         frequency of extrapair paternity in alpine marmots</span>. <i>Animal
+
         Behaviour</i><i></i><span style="font-weight: bold;">76</span>:
       87-95.<br>
       <br>
@@ -178,6 +186,7 @@
 
 
 
+
           Genomics</span></span><span class="citation-publication-date"></span><span
         style="font-weight: bold;" class="citation-volume">9</span><span
         class="citation-issue"></span>: 256.<br>
@@ -205,12 +214,14 @@
 
 
 
+
             marmota</span>.</span><span style="font-style: italic;">Molecular
 
 
 
 
 
+
           Ecology</span> <span style="font-weight: bold;">18</span>:
         1491-1503.<br>
         <br>
@@ -256,6 +267,7 @@
 
 
 
+
           australis</i> in North America. <span style="font-style:
           italic;">Biological Invasions</span>. doi:
         10.1007/s10530-010-9699-6.<br>
@@ -405,6 +417,7 @@
 
 
 
+
           Oct 6. [Epub ahead of print]<br>
         </p>
         <p class="auth_list">[24] SANTOS, H., BURBAN, C., ROUSSELET, J.,
@@ -415,6 +428,7 @@
 
 
 
+
             pityocampa</em>, Lepidoptera, Notodontidae). <span
             style="font-style: italic;">Journal of Evolutionary Biology</span>,
           no. doi:&nbsp;10.1111/j.1420-9101.2010.02147.x<br>
@@ -430,6 +444,7 @@
 
 
 
+
             Vol. Sci. Pap. ICCAT</span>, 65(3): 988-995</p>
         <p class="intro">[26] <span class="citation_author">Vandewoestijne
 
@@ -438,6 +453,7 @@
 
 
 
+
             S, </span> <span class="citation_author">Van Dyck H, </span>
           <span class="citation_date">2010</span> <span
             class="citation_article_title">Population Genetic
@@ -449,6 +465,7 @@
 
 
 
+
             ONE</span><span class="citation_issue">5(11):</span> <span
             class="citation_start_page">e13810.</span> <span
             class="citation_doi">doi:10.1371/journal.pone.0013810<br>
@@ -471,6 +488,7 @@
 
 
 
+
           </span><span class="doi"><span class="label">DOI:</span> <span
               class="value">10.1007/s10329-010-0232-4<br>
             </span></span></p>
@@ -530,6 +548,7 @@
 
 
 
+
             tetradactylum</em>: Polynemidae). Molecular Ecology,
           20:&nbsp;no. doi:&nbsp;10.1111/j.1365-294X.2011.05097.x<br>
         </p>
@@ -547,6 +566,7 @@
 
 
 
+
               neoformans</i> Variety <i>grubii</i> Multilocus Sequence
             Types from Thailand Are Consistent with an Ancestral African
             Origin.</span> <span class="citation_journal_title">PLoS
@@ -796,6 +816,7 @@
 
 
 
+
         10.1007/s10709-012-9640-2<br>
         <br>
         [76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright,
@@ -1281,9 +1302,29 @@
         archive them in the Demiurge information system. Molecular
         Ecology Resources. doi: 10.1111/1755-0998.12084<br>
         <br>
+        [158]* Kato-Maeda M, Ho C, Passarelli B, Banaei N, Grinsdale J,
+        et al. (2013) Use of Whole Genome Sequencing to Determine the
+        Microevolution of Mycobacterium tuberculosis during an Outbreak.
+        PLoS ONE 8(3): e58235. doi:10.1371/journal.pone.0058235<br>
         <br>
+        [159]* Florent Tivet, Joao Carlos de Moraes S, Rattan Lal,
+        Clever Briedis, Paulo Rogerio Borszowskei, et al. (2013)
+        Aggregate C depletion by plowing and its restoration by diverse
+        biomass-C inputs under no-till in sub-tropical and tropical
+        regions of Brazil. Soil &amp; Tillage Research 126 (2013)
+        203?218<br>
         <br>
+        [160] Fontaine et al. (2013) Genetic signature of a range
+        expansion and leap-frog event after the recent invasion of
+        Europe by the grapevine downy mildew pathogen <i>Plasmopara
+          viticola</i>. Molecular Ecology. doi: 10.1111/mec.12293<br>
         <br>
+        <br>
+        <br>
+        <br>
+        <br>
+        <br>
+        <br>
         <p></p>
         <p class="intro">* adegenet not or wrongly cited, but actually
           used in the paper. <br>


From noreply at r-forge.r-project.org  Thu Mar 14 11:37:13 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 14 Mar 2013 11:37:13 +0100 (CET)
Subject: [adegenet-commits] r1085 - www
Message-ID: <20130314103713.99DD0184E61@r-forge.r-project.org>

Author: jombart
Date: 2013-03-14 11:37:13 +0100 (Thu, 14 Mar 2013)
New Revision: 1085

Modified:
   www/literature.html
Log:
+1ref

Modified: www/literature.html
===================================================================
--- www/literature.html	2013-03-12 17:26:46 UTC (rev 1084)
+++ www/literature.html	2013-03-14 10:37:13 UTC (rev 1085)
@@ -56,6 +56,7 @@
 
 
 
+
         the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
       <br style="color: rgb(0, 153, 0);">
       <br>
@@ -81,6 +82,7 @@
 
 
 
+
         abstract</a>]<br>
       <br>
       - the paper presenting the <span style="font-style: italic;">spatial
@@ -91,6 +93,7 @@
 
 
 
+
         principal component analysis</span> (<span style="font-style:
         italic;">sPCA</span>, function <span style="font-family:
         monospace; color: rgb(255, 0, 0);">spca</span>), global and
@@ -104,6 +107,7 @@
 
 
 
+
       cryptic spatial patterns in genetic variability by a new
       multivariate method.&nbsp; <span style="font-style: italic;">Heredity</span>
       <span style="font-weight: bold;">101</span>: 92-103. doi:
@@ -118,6 +122,7 @@
 
 
 
+
         abstract</a>]<br>
     </div>
     <br>
@@ -134,6 +139,7 @@
 
 
 
+
       simulations of genealoies of haplotypes (<span style="font-family:
         monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
       <b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010)
@@ -150,6 +156,7 @@
 
 
 
+
         of Principal Components</span> (<span style="font-style:
         italic;">DAPC</span>, functions <span style="font-family:
         monospace;"><span style="color: rgb(255, 0, 0);">find.clusters</span>
@@ -174,6 +181,7 @@
         0);">genetic similarity between pair members influences the
         frequency of extrapair paternity in alpine marmots</span>. <i>Animal
 
+
         Behaviour</i><i></i><span style="font-weight: bold;">76</span>:
       87-95.<br>
       <br>
@@ -187,6 +195,7 @@
 
 
 
+
           Genomics</span></span><span class="citation-publication-date"></span><span
         style="font-weight: bold;" class="citation-volume">9</span><span
         class="citation-issue"></span>: 256.<br>
@@ -215,6 +224,7 @@
 
 
 
+
             marmota</span>.</span><span style="font-style: italic;">Molecular
 
 
@@ -222,6 +232,7 @@
 
 
 
+
           Ecology</span> <span style="font-weight: bold;">18</span>:
         1491-1503.<br>
         <br>
@@ -268,6 +279,7 @@
 
 
 
+
           australis</i> in North America. <span style="font-style:
           italic;">Biological Invasions</span>. doi:
         10.1007/s10530-010-9699-6.<br>
@@ -418,6 +430,7 @@
 
 
 
+
           Oct 6. [Epub ahead of print]<br>
         </p>
         <p class="auth_list">[24] SANTOS, H., BURBAN, C., ROUSSELET, J.,
@@ -429,6 +442,7 @@
 
 
 
+
             pityocampa</em>, Lepidoptera, Notodontidae). <span
             style="font-style: italic;">Journal of Evolutionary Biology</span>,
           no. doi:&nbsp;10.1111/j.1420-9101.2010.02147.x<br>
@@ -445,6 +459,7 @@
 
 
 
+
             Vol. Sci. Pap. ICCAT</span>, 65(3): 988-995</p>
         <p class="intro">[26] <span class="citation_author">Vandewoestijne
 
@@ -454,6 +469,7 @@
 
 
 
+
             S, </span> <span class="citation_author">Van Dyck H, </span>
           <span class="citation_date">2010</span> <span
             class="citation_article_title">Population Genetic
@@ -466,6 +482,7 @@
 
 
 
+
             ONE</span><span class="citation_issue">5(11):</span> <span
             class="citation_start_page">e13810.</span> <span
             class="citation_doi">doi:10.1371/journal.pone.0013810<br>
@@ -489,6 +506,7 @@
 
 
 
+
           </span><span class="doi"><span class="label">DOI:</span> <span
               class="value">10.1007/s10329-010-0232-4<br>
             </span></span></p>
@@ -549,6 +567,7 @@
 
 
 
+
             tetradactylum</em>: Polynemidae). Molecular Ecology,
           20:&nbsp;no. doi:&nbsp;10.1111/j.1365-294X.2011.05097.x<br>
         </p>
@@ -567,6 +586,7 @@
 
 
 
+
               neoformans</i> Variety <i>grubii</i> Multilocus Sequence
             Types from Thailand Are Consistent with an Ancestral African
             Origin.</span> <span class="citation_journal_title">PLoS
@@ -817,6 +837,7 @@
 
 
 
+
         10.1007/s10709-012-9640-2<br>
         <br>
         [76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright,
@@ -1319,12 +1340,17 @@
         Europe by the grapevine downy mildew pathogen <i>Plasmopara
           viticola</i>. Molecular Ecology. doi: 10.1111/mec.12293<br>
         <br>
+        [161] Hagen, I. J., Billing, A. M., R?nning, B., Pedersen, S.
+        A., P?rn, H., Slate, J. and Jensen, H. (2013), The easy road to
+        genome-wide medium density SNP screening in a non-model species:
+        development and application of a 10 K SNP-chip for the house
+        sparrow (Passer domesticus). Molecular Ecology Resources. doi:
+        10.1111/1755-0998.12088<br>
         <br>
         <br>
         <br>
         <br>
         <br>
-        <br>
         <p></p>
         <p class="intro">* adegenet not or wrongly cited, but actually
           used in the paper. <br>


From noreply at r-forge.r-project.org  Thu Mar 14 18:58:03 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 14 Mar 2013 18:58:03 +0100 (CET)
Subject: [adegenet-commits] r1086 - www/files
Message-ID: <20130314175803.DE802183D5D@r-forge.r-project.org>

Author: jombart
Date: 2013-03-14 18:58:03 +0100 (Thu, 14 Mar 2013)
New Revision: 1086

Modified:
   www/files/MSc-intro-phylo.1.0.pdf
Log:
new version of the practical for Monday

Modified: www/files/MSc-intro-phylo.1.0.pdf
===================================================================
--- www/files/MSc-intro-phylo.1.0.pdf	2013-03-14 10:37:13 UTC (rev 1085)
+++ www/files/MSc-intro-phylo.1.0.pdf	2013-03-14 17:58:03 UTC (rev 1086)
@@ -106,25 +106,21 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1086

From noreply at r-forge.r-project.org  Fri Mar 15 12:33:20 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 15 Mar 2013 12:33:20 +0100 (CET)
Subject: [adegenet-commits] r1087 - in www: . files
Message-ID: <20130315113320.5A2B71806AD@r-forge.r-project.org>

Author: jombart
Date: 2013-03-15 12:33:19 +0100 (Fri, 15 Mar 2013)
New Revision: 1087

Added:
   www/files/MSc-intro-phylo.1.1.pdf
Modified:
   www/documentation.html
Log:
Last update for the phylo tuto - MSc students 2013

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2013-03-14 17:58:03 UTC (rev 1086)
+++ www/documentation.html	2013-03-15 11:33:19 UTC (rev 1087)
@@ -35,6 +35,7 @@
       <span style="font-weight: bold;">To search quickly</span> through
       these resources, use the <a target="_top" href="search.html">search
 
+
         engine</a>. <br>
       <br>
       <br>
@@ -90,14 +91,17 @@
       spatial genetics<br>
       &nbsp;&nbsp;&nbsp; &gt; <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>
       &nbsp;&nbsp;&nbsp; &gt; <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>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.2.pdf">practical
 
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
@@ -105,15 +109,6 @@
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/MRC-session2-tuto.1.3.pdf">practical</a><br>
       &nbsp;&nbsp;&nbsp; &gt; data (<a href="files/usflu.fasta">DNA
         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>
-      &nbsp;&nbsp;&nbsp; &gt; <a href="files/MSc-intro-phylo.1.0.pdf">practical</a><br>
-      &nbsp;&nbsp;&nbsp; &gt; data (<a href="files/usflu.fasta">usflu.fasta</a>,
-      <a href="files/usflu.annot.csv">usflu.annot.csv</a>)<br>
-      <br>
       - RAPID-NGS workshop, M?nster (March 2013) - <span
         style="font-weight: bold;">Outbreak analysis using <span
           style="font-style: italic;">adegenet </span>and <span
@@ -126,6 +121,16 @@
         href="files/fakeOutbreak/cases.csv">cases.csv</a>, <a
         href="files/fakeOutbreak/alignment.fa">alignment.fa</a>, <a
         href="files/fakeOutbreak/update.csv">update.csv</a>)<br>
+      - Imperial College - Master <span style="font-style: italic;">Modern
+
+        Epidemiology</span> / <i>Public Health</i>: <span
+        style="font-weight: bold;">Introduction to phylogenetics</span>.<img
+        style="width: 80px; height: 37px;" alt="new"
+        src="file:///home/thibaut/dev/adegenet/www/images/new.png"><br>
+      (last updated on the 15/13/2013)<br>
+      &nbsp;&nbsp;&nbsp; &gt; <a href="files/MSc-intro-phylo.1.1.pdf">practical</a><br>
+      &nbsp;&nbsp;&nbsp; &gt; 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);">Mailing

Added: www/files/MSc-intro-phylo.1.1.pdf
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1087

From noreply at r-forge.r-project.org  Sun Mar 17 23:59:24 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun, 17 Mar 2013 23:59:24 +0100 (CET)
Subject: [adegenet-commits] r1088 - www
Message-ID: <20130317225924.1B6ED184D67@r-forge.r-project.org>

Author: jombart
Date: 2013-03-17 23:59:23 +0100 (Sun, 17 Mar 2013)
New Revision: 1088

Modified:
   www/documentation.html
   www/news.html
Log:
Fixed some absolute path file://home/thibaut... 

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2013-03-15 11:33:19 UTC (rev 1087)
+++ www/documentation.html	2013-03-17 22:59:23 UTC (rev 1088)
@@ -36,6 +36,7 @@
       these resources, use the <a target="_top" href="search.html">search
 
 
+
         engine</a>. <br>
       <br>
       <br>
@@ -53,7 +54,7 @@
       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
+        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
@@ -92,16 +93,19 @@
       &nbsp;&nbsp;&nbsp; &gt; <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>
       &nbsp;&nbsp;&nbsp; &gt; <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>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.2.pdf">practical
 
 
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
@@ -123,10 +127,11 @@
         href="files/fakeOutbreak/update.csv">update.csv</a>)<br>
       - Imperial College - Master <span style="font-style: italic;">Modern
 
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to phylogenetics</span>.<img
-        style="width: 80px; height: 37px;" alt="new"
-        src="file:///home/thibaut/dev/adegenet/www/images/new.png"><br>
+        style=" width: 80px; height: 37px;" alt="new"
+        src="images/new.png"><br>
       (last updated on the 15/13/2013)<br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/MSc-intro-phylo.1.1.pdf">practical</a><br>
       &nbsp;&nbsp;&nbsp; &gt; data (<a href="files/usflu.fasta">usflu.fasta</a>,

Modified: www/news.html
===================================================================
--- www/news.html	2013-03-15 11:33:19 UTC (rev 1087)
+++ www/news.html	2013-03-17 22:59:23 UTC (rev 1088)
@@ -47,7 +47,7 @@
       <span style="font-weight: bold;">30/01/2013 </span><span
         style="font-weight: bold;"></span><img style="width: 80px;
         height: 37px;" alt=""
-        src="file:///home/thibaut/dev/adegenet/www/images/new.png"><br>
+        src="images/new.png"><br>
       <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-6</span>)
         has
         been


From noreply at r-forge.r-project.org  Mon Mar 18 10:52:23 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 18 Mar 2013 10:52:23 +0100 (CET)
Subject: [adegenet-commits] r1089 - www
Message-ID: <20130318095223.87306184AA7@r-forge.r-project.org>

Author: jombart
Date: 2013-03-18 10:52:23 +0100 (Mon, 18 Mar 2013)
New Revision: 1089

Modified:
   www/literature.html
Log:
+2ref

Modified: www/literature.html
===================================================================
--- www/literature.html	2013-03-17 22:59:23 UTC (rev 1088)
+++ www/literature.html	2013-03-18 09:52:23 UTC (rev 1089)
@@ -57,6 +57,7 @@
 
 
 
+
         the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
       <br style="color: rgb(0, 153, 0);">
       <br>
@@ -83,6 +84,7 @@
 
 
 
+
         abstract</a>]<br>
       <br>
       - the paper presenting the <span style="font-style: italic;">spatial
@@ -94,6 +96,7 @@
 
 
 
+
         principal component analysis</span> (<span style="font-style:
         italic;">sPCA</span>, function <span style="font-family:
         monospace; color: rgb(255, 0, 0);">spca</span>), global and
@@ -108,6 +111,7 @@
 
 
 
+
       cryptic spatial patterns in genetic variability by a new
       multivariate method.&nbsp; <span style="font-style: italic;">Heredity</span>
       <span style="font-weight: bold;">101</span>: 92-103. doi:
@@ -123,6 +127,7 @@
 
 
 
+
         abstract</a>]<br>
     </div>
     <br>
@@ -140,6 +145,7 @@
 
 
 
+
       simulations of genealoies of haplotypes (<span style="font-family:
         monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
       <b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010)
@@ -157,6 +163,7 @@
 
 
 
+
         of Principal Components</span> (<span style="font-style:
         italic;">DAPC</span>, functions <span style="font-family:
         monospace;"><span style="color: rgb(255, 0, 0);">find.clusters</span>
@@ -182,6 +189,7 @@
         frequency of extrapair paternity in alpine marmots</span>. <i>Animal
 
 
+
         Behaviour</i><i></i><span style="font-weight: bold;">76</span>:
       87-95.<br>
       <br>
@@ -196,6 +204,7 @@
 
 
 
+
           Genomics</span></span><span class="citation-publication-date"></span><span
         style="font-weight: bold;" class="citation-volume">9</span><span
         class="citation-issue"></span>: 256.<br>
@@ -225,6 +234,7 @@
 
 
 
+
             marmota</span>.</span><span style="font-style: italic;">Molecular
 
 
@@ -233,6 +243,7 @@
 
 
 
+
           Ecology</span> <span style="font-weight: bold;">18</span>:
         1491-1503.<br>
         <br>
@@ -280,6 +291,7 @@
 
 
 
+
           australis</i> in North America. <span style="font-style:
           italic;">Biological Invasions</span>. doi:
         10.1007/s10530-010-9699-6.<br>
@@ -431,6 +443,7 @@
 
 
 
+
           Oct 6. [Epub ahead of print]<br>
         </p>
         <p class="auth_list">[24] SANTOS, H., BURBAN, C., ROUSSELET, J.,
@@ -443,6 +456,7 @@
 
 
 
+
             pityocampa</em>, Lepidoptera, Notodontidae). <span
             style="font-style: italic;">Journal of Evolutionary Biology</span>,
           no. doi:&nbsp;10.1111/j.1420-9101.2010.02147.x<br>
@@ -460,6 +474,7 @@
 
 
 
+
             Vol. Sci. Pap. ICCAT</span>, 65(3): 988-995</p>
         <p class="intro">[26] <span class="citation_author">Vandewoestijne
 
@@ -470,6 +485,7 @@
 
 
 
+
             S, </span> <span class="citation_author">Van Dyck H, </span>
           <span class="citation_date">2010</span> <span
             class="citation_article_title">Population Genetic
@@ -483,6 +499,7 @@
 
 
 
+
             ONE</span><span class="citation_issue">5(11):</span> <span
             class="citation_start_page">e13810.</span> <span
             class="citation_doi">doi:10.1371/journal.pone.0013810<br>
@@ -507,6 +524,7 @@
 
 
 
+
           </span><span class="doi"><span class="label">DOI:</span> <span
               class="value">10.1007/s10329-010-0232-4<br>
             </span></span></p>
@@ -568,6 +586,7 @@
 
 
 
+
             tetradactylum</em>: Polynemidae). Molecular Ecology,
           20:&nbsp;no. doi:&nbsp;10.1111/j.1365-294X.2011.05097.x<br>
         </p>
@@ -587,6 +606,7 @@
 
 
 
+
               neoformans</i> Variety <i>grubii</i> Multilocus Sequence
             Types from Thailand Are Consistent with an Ancestral African
             Origin.</span> <span class="citation_journal_title">PLoS
@@ -838,6 +858,7 @@
 
 
 
+
         10.1007/s10709-012-9640-2<br>
         <br>
         [76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright,
@@ -1347,7 +1368,18 @@
         sparrow (Passer domesticus). Molecular Ecology Resources. doi:
         10.1111/1755-0998.12088<br>
         <br>
+        [162] Therkildsen, N. O., Hemmer-Hansen, J., Hedeholm, R. B.,
+        Wisz, M. S., Pampoulie, C., Meldrup, D., Bonanomi, S., Retzel,
+        A., Olsen, S. M. and Nielsen, E. E. (2013), Spatiotemporal SNP
+        analysis reveals pronounced biocomplexity at the northern range
+        margin of Atlantic cod Gadus morhua. Evolutionary Applications.
+        doi: 10.1111/eva.12055<br>
         <br>
+        [163] Kanthaswamy, S., Ng, J., Trask, J. S., George, D.A., Kou,
+        A.J., Hoffman, L.N., Doherty, T.B., Houghton, P. and Smith, D.G.
+        (2013), The genetic composition of populations of cynomolgus
+        macaques (Macaca fascicularis) used in biomedical research.
+        Journal of Medical Primatology. doi: 10.1111/jmp.12043<br>
         <br>
         <br>
         <br>


From noreply at r-forge.r-project.org  Tue Mar 19 20:21:59 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 19 Mar 2013 20:21:59 +0100 (CET)
Subject: [adegenet-commits] r1090 - www
Message-ID: <20130319192159.BC6D2184C7F@r-forge.r-project.org>

Author: jombart
Date: 2013-03-19 20:21:59 +0100 (Tue, 19 Mar 2013)
New Revision: 1090

Modified:
   www/literature.html
Log:
+1ref

Modified: www/literature.html
===================================================================
--- www/literature.html	2013-03-18 09:52:23 UTC (rev 1089)
+++ www/literature.html	2013-03-19 19:21:59 UTC (rev 1090)
@@ -58,6 +58,7 @@
 
 
 
+
         the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
       <br style="color: rgb(0, 153, 0);">
       <br>
@@ -85,6 +86,7 @@
 
 
 
+
         abstract</a>]<br>
       <br>
       - the paper presenting the <span style="font-style: italic;">spatial
@@ -97,6 +99,7 @@
 
 
 
+
         principal component analysis</span> (<span style="font-style:
         italic;">sPCA</span>, function <span style="font-family:
         monospace; color: rgb(255, 0, 0);">spca</span>), global and
@@ -112,6 +115,7 @@
 
 
 
+
       cryptic spatial patterns in genetic variability by a new
       multivariate method.&nbsp; <span style="font-style: italic;">Heredity</span>
       <span style="font-weight: bold;">101</span>: 92-103. doi:
@@ -128,6 +132,7 @@
 
 
 
+
         abstract</a>]<br>
     </div>
     <br>
@@ -146,6 +151,7 @@
 
 
 
+
       simulations of genealoies of haplotypes (<span style="font-family:
         monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
       <b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010)
@@ -164,6 +170,7 @@
 
 
 
+
         of Principal Components</span> (<span style="font-style:
         italic;">DAPC</span>, functions <span style="font-family:
         monospace;"><span style="color: rgb(255, 0, 0);">find.clusters</span>
@@ -190,6 +197,7 @@
 
 
 
+
         Behaviour</i><i></i><span style="font-weight: bold;">76</span>:
       87-95.<br>
       <br>
@@ -205,6 +213,7 @@
 
 
 
+
           Genomics</span></span><span class="citation-publication-date"></span><span
         style="font-weight: bold;" class="citation-volume">9</span><span
         class="citation-issue"></span>: 256.<br>
@@ -235,6 +244,7 @@
 
 
 
+
             marmota</span>.</span><span style="font-style: italic;">Molecular
 
 
@@ -244,6 +254,7 @@
 
 
 
+
           Ecology</span> <span style="font-weight: bold;">18</span>:
         1491-1503.<br>
         <br>
@@ -292,6 +303,7 @@
 
 
 
+
           australis</i> in North America. <span style="font-style:
           italic;">Biological Invasions</span>. doi:
         10.1007/s10530-010-9699-6.<br>
@@ -444,6 +456,7 @@
 
 
 
+
           Oct 6. [Epub ahead of print]<br>
         </p>
         <p class="auth_list">[24] SANTOS, H., BURBAN, C., ROUSSELET, J.,
@@ -457,6 +470,7 @@
 
 
 
+
             pityocampa</em>, Lepidoptera, Notodontidae). <span
             style="font-style: italic;">Journal of Evolutionary Biology</span>,
           no. doi:&nbsp;10.1111/j.1420-9101.2010.02147.x<br>
@@ -475,6 +489,7 @@
 
 
 
+
             Vol. Sci. Pap. ICCAT</span>, 65(3): 988-995</p>
         <p class="intro">[26] <span class="citation_author">Vandewoestijne
 
@@ -486,6 +501,7 @@
 
 
 
+
             S, </span> <span class="citation_author">Van Dyck H, </span>
           <span class="citation_date">2010</span> <span
             class="citation_article_title">Population Genetic
@@ -500,6 +516,7 @@
 
 
 
+
             ONE</span><span class="citation_issue">5(11):</span> <span
             class="citation_start_page">e13810.</span> <span
             class="citation_doi">doi:10.1371/journal.pone.0013810<br>
@@ -525,6 +542,7 @@
 
 
 
+
           </span><span class="doi"><span class="label">DOI:</span> <span
               class="value">10.1007/s10329-010-0232-4<br>
             </span></span></p>
@@ -587,6 +605,7 @@
 
 
 
+
             tetradactylum</em>: Polynemidae). Molecular Ecology,
           20:&nbsp;no. doi:&nbsp;10.1111/j.1365-294X.2011.05097.x<br>
         </p>
@@ -607,6 +626,7 @@
 
 
 
+
               neoformans</i> Variety <i>grubii</i> Multilocus Sequence
             Types from Thailand Are Consistent with an Ancestral African
             Origin.</span> <span class="citation_journal_title">PLoS
@@ -859,6 +879,7 @@
 
 
 
+
         10.1007/s10709-012-9640-2<br>
         <br>
         [76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright,
@@ -1381,8 +1402,14 @@
         macaques (Macaca fascicularis) used in biomedical research.
         Journal of Medical Primatology. doi: 10.1111/jmp.12043<br>
         <br>
+        [164] Molfetti ?, Torres Vila?a S, Georges J-Y, Plot V, Delcroix
+        E, et al. (2013) Recent Demographic History and Present
+        Fine-Scale Structure in the Northwest Atlantic Leatherback
+        (Dermochelys coriacea) Turtle Population. PLoS ONE 8(3): e58061.
+        doi:10.1371/journal.pone.0058061<br>
         <br>
         <br>
+        <br>
         <p></p>
         <p class="intro">* adegenet not or wrongly cited, but actually
           used in the paper. <br>


From noreply at r-forge.r-project.org  Wed Mar 20 13:24:47 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 20 Mar 2013 13:24:47 +0100 (CET)
Subject: [adegenet-commits] r1091 - www/files
Message-ID: <20130320122448.103EA1811FD@r-forge.r-project.org>

Author: jombart
Date: 2013-03-20 13:24:47 +0100 (Wed, 20 Mar 2013)
New Revision: 1091

Added:
   www/files/hackLib.R
Log:
added script to install libraries without admin rights

Added: www/files/hackLib.R
===================================================================
--- www/files/hackLib.R	                        (rev 0)
+++ www/files/hackLib.R	2013-03-20 12:24:47 UTC (rev 1091)
@@ -0,0 +1,24 @@
+
+##
+## HACK TO INSTALL R PACKAGES ON WINDOWS SYSTEMS
+## WITHOUT ADMIN RIGHTS
+##
+## Thibaut Jombart, March 2013
+## tjombart at imperial.ac.uk
+##
+## usage:
+## hackLib()
+## install.packages("foo")
+##
+hackLib <- function(myPath="C:/Users/Public/Rlibs"){
+    if(file.exists(myPath)) myPath <- paste(myPath,"Rlibs", sep="/")
+    myPath <- gsub("/+", "/", myPath)
+    if(!file.exists(myPath)){
+        if(!dir.create(myPath)) stop(paste(myPath, "could not be created."))
+    }
+
+    .libPaths(myPath)
+    cat(paste("\nR library set to:",myPath,"\n"))
+    if(as.numeric(file.info(myPath)$mode)<500) warning(paste(myPath, "may not be 'writable'."))
+    return(invisible())
+}


From noreply at r-forge.r-project.org  Wed Mar 20 17:04:36 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 20 Mar 2013 17:04:36 +0100 (CET)
Subject: [adegenet-commits] r1092 - in www: . files files/hackLib
Message-ID: <20130320160436.376B2184FB6@r-forge.r-project.org>

Author: jombart
Date: 2013-03-20 17:04:35 +0100 (Wed, 20 Mar 2013)
New Revision: 1092

Added:
   www/files/hackLib/
   www/files/hackLib/README
   www/files/hackLib/hackLib.R
Removed:
   www/files/hackLib.R
Modified:
   www/documentation.html
Log:
hack for lib install

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2013-03-20 12:24:47 UTC (rev 1091)
+++ www/documentation.html	2013-03-20 16:04:35 UTC (rev 1092)
@@ -37,6 +37,7 @@
 
 
 
+
         engine</a>. <br>
       <br>
       <br>
@@ -53,12 +54,11 @@
           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="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>
+      - <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>
     <div style="margin-left: 40px;">- <a href="files/adegenet-dapc.pdf"><span
           style="font-style: italic;">adegenet-dapc</span></a>: analysis
@@ -94,18 +94,21 @@
 
 
 
+
         1</a> [<a href="files/practical-day1.1.2-allcmd.pdf">version
         with all commands</a>]<br>
       &nbsp;&nbsp;&nbsp; &gt; <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>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.2.pdf">practical
 
 
 
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
@@ -128,6 +131,7 @@
       - Imperial College - Master <span style="font-style: italic;">Modern
 
 
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to phylogenetics</span>.<img
         style=" width: 80px; height: 37px;" alt="new"
@@ -138,6 +142,15 @@
       <a href="files/usflu.annot.csv">usflu.annot.csv</a>)<br>
       <br>
       <br>
+      <span style="font-weight: bold; color: rgb(0, 102, 0);">Dirty
+        hacks useful for teaching</span><br>
+      - a small hack for installing R packages on computers without
+      administrative rights: <a href="files/hackLib/hackLib.R">hackLib.R</a>&nbsp;
+      <a href="files/hackLib/README">README</a> <img style=" width:
+        80px; height: 37px;" alt="new" src="images/new.png" height="37"
+        width="80"><br>
+      <br>
+      <br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);">Mailing
         lists archives </span><br>
       Use the <a target="_top" href="search.html">search engine</a> to

Added: www/files/hackLib/README
===================================================================
--- www/files/hackLib/README	                        (rev 0)
+++ www/files/hackLib/README	2013-03-20 16:04:35 UTC (rev 1092)
@@ -0,0 +1,23 @@
+
+=================================================
+ HACK TO INSTALL R PACKAGES WITHOUT ADMIN RIGHTS
+=================================================
+== AUTHOR ==
+ Thibaut Jombart, March 2013
+ tjombart at imperial.ac.uk
+
+
+
+== USAGE ==
+The function hackLib has to be loaded in R, either by copy-pasting the code of libHack.R into the R console, or by using the R command 'source' to load the file, e.g.:
+source("libHack.R")
+
+The hack is made active by typing:
+hackLib()
+
+By default, libraries will be installed in "C:/Users/Public/Rlibs" (windows systems). Other locations can be specified by the user, as an argument of the function. For instance, linux users might use:
+hackLib("~/Rlibs")
+to create a library in their home directory.
+
+Once the hack is activated, install packages normally. For instance, to install a package 'foo', simply use:
+install.packages("foo")

Added: www/files/hackLib/hackLib.R
===================================================================
--- www/files/hackLib/hackLib.R	                        (rev 0)
+++ www/files/hackLib/hackLib.R	2013-03-20 16:04:35 UTC (rev 1092)
@@ -0,0 +1,24 @@
+
+##
+## HACK TO INSTALL R PACKAGES ON WINDOWS SYSTEMS
+## WITHOUT ADMIN RIGHTS
+##
+## Thibaut Jombart, March 2013
+## tjombart at imperial.ac.uk
+##
+## usage:
+## hackLib()
+## install.packages("foo")
+##
+hackLib <- function(myPath="C:/Users/Public/Rlibs"){
+    if(file.exists(myPath)) myPath <- paste(myPath,"Rlibs", sep="/")
+    myPath <- gsub("/+", "/", myPath)
+    if(!file.exists(myPath)){
+        if(!dir.create(myPath)) stop(paste(myPath, "could not be created."))
+    }
+
+    .libPaths(myPath)
+    cat(paste("\nR library set to:",myPath,"\n"))
+    if(as.numeric(file.info(myPath)$mode)<500) warning(paste(myPath, "may not be 'writable'."))
+    return(invisible())
+}

Deleted: www/files/hackLib.R
===================================================================
--- www/files/hackLib.R	2013-03-20 12:24:47 UTC (rev 1091)
+++ www/files/hackLib.R	2013-03-20 16:04:35 UTC (rev 1092)
@@ -1,24 +0,0 @@
-
-##
-## HACK TO INSTALL R PACKAGES ON WINDOWS SYSTEMS
-## WITHOUT ADMIN RIGHTS
-##
-## Thibaut Jombart, March 2013
-## tjombart at imperial.ac.uk
-##
-## usage:
-## hackLib()
-## install.packages("foo")
-##
-hackLib <- function(myPath="C:/Users/Public/Rlibs"){
-    if(file.exists(myPath)) myPath <- paste(myPath,"Rlibs", sep="/")
-    myPath <- gsub("/+", "/", myPath)
-    if(!file.exists(myPath)){
-        if(!dir.create(myPath)) stop(paste(myPath, "could not be created."))
-    }
-
-    .libPaths(myPath)
-    cat(paste("\nR library set to:",myPath,"\n"))
-    if(as.numeric(file.info(myPath)$mode)<500) warning(paste(myPath, "may not be 'writable'."))
-    return(invisible())
-}


From noreply at r-forge.r-project.org  Wed Mar 20 20:21:01 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 20 Mar 2013 20:21:01 +0100 (CET)
Subject: [adegenet-commits] r1093 - in www/files: . simGWAS
Message-ID: <20130320192101.38B9E1845F0@r-forge.r-project.org>

Author: jombart
Date: 2013-03-20 20:21:00 +0100 (Wed, 20 Mar 2013)
New Revision: 1093

Added:
   www/files/simGWAS/
   www/files/simGWAS/simGWAS.csv.zip
Log:
adding simulated GWAS data

Added: www/files/simGWAS/simGWAS.csv.zip
===================================================================
(Binary files differ)


Property changes on: www/files/simGWAS/simGWAS.csv.zip
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream


From noreply at r-forge.r-project.org  Wed Mar 20 20:46:05 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 20 Mar 2013 20:46:05 +0100 (CET)
Subject: [adegenet-commits] r1094 - www/files/simGWAS
Message-ID: <20130320194605.7FBE3184CAD@r-forge.r-project.org>

Author: jombart
Date: 2013-03-20 20:46:05 +0100 (Wed, 20 Mar 2013)
New Revision: 1094

Added:
   www/files/simGWAS/simGWAS.csv
Removed:
   www/files/simGWAS/simGWAS.csv.zip
Log:
replacing data with unzipped version

Added: www/files/simGWAS/simGWAS.csv
===================================================================
--- www/files/simGWAS/simGWAS.csv	                        (rev 0)
+++ www/files/simGWAS/simGWAS.csv	2013-03-20 19:46:05 UTC (rev 1094)
@@ -0,0 +1,96 @@
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1094

From noreply at r-forge.r-project.org  Wed Mar 20 20:47:10 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 20 Mar 2013 20:47:10 +0100 (CET)
Subject: [adegenet-commits] r1095 - www/files/simGWAS
Message-ID: <20130320194710.9A376183E4A@r-forge.r-project.org>

Author: jombart
Date: 2013-03-20 20:47:10 +0100 (Wed, 20 Mar 2013)
New Revision: 1095

Added:
   www/files/simGWAS/simGWAS.RData
Removed:
   www/files/simGWAS/simGWAS.csv
Log:
replacing raw data with RData

Added: www/files/simGWAS/simGWAS.RData
===================================================================
(Binary files differ)


Property changes on: www/files/simGWAS/simGWAS.RData
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Deleted: www/files/simGWAS/simGWAS.csv
===================================================================
--- www/files/simGWAS/simGWAS.csv	2013-03-20 19:46:05 UTC (rev 1094)
+++ www/files/simGWAS/simGWAS.csv	2013-03-20 19:47:10 UTC (rev 1095)
@@ -1,96 +0,0 @@
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1095

From noreply at r-forge.r-project.org  Thu Mar 21 17:27:00 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 21 Mar 2013 17:27:00 +0100 (CET)
Subject: [adegenet-commits] r1096 - www/files/simGWAS
Message-ID: <20130321162701.08D09183E73@r-forge.r-project.org>

Author: jombart
Date: 2013-03-21 17:27:00 +0100 (Thu, 21 Mar 2013)
New Revision: 1096

Modified:
   www/files/simGWAS/simGWAS.RData
Log:
renamed the rows of the snps matrix

Modified: www/files/simGWAS/simGWAS.RData
===================================================================
(Binary files differ)


From noreply at r-forge.r-project.org  Thu Mar 21 18:03:43 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 21 Mar 2013 18:03:43 +0100 (CET)
Subject: [adegenet-commits] r1097 - pkg/R
Message-ID: <20130321170343.22BD3184ED0@r-forge.r-project.org>

Author: jombart
Date: 2013-03-21 18:03:42 +0100 (Thu, 21 Mar 2013)
New Revision: 1097

Modified:
   pkg/R/dapc.R
Log:
Fixed glitch in printing of DAPC - adding #####

Modified: pkg/R/dapc.R
===================================================================
--- pkg/R/dapc.R	2013-03-21 16:27:00 UTC (rev 1096)
+++ pkg/R/dapc.R	2013-03-21 17:03:42 UTC (rev 1097)
@@ -380,9 +380,9 @@
 # Function print.dapc
 ######################
 print.dapc <- function(x, ...){
-    cat("\t#########################################\n")
+    cat("\t#################################################\n")
     cat("\t# Discriminant Analysis of Principal Components #\n")
-    cat("\t#########################################\n")
+    cat("\t#################################################\n")
     cat("class: ")
     cat(class(x))
     cat("\n$call: ")


From noreply at r-forge.r-project.org  Thu Mar 21 18:15:31 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 21 Mar 2013 18:15:31 +0100 (CET)
Subject: [adegenet-commits] r1098 - www/files/simGWAS
Message-ID: <20130321171531.9156F184ED0@r-forge.r-project.org>

Author: jombart
Date: 2013-03-21 18:15:31 +0100 (Thu, 21 Mar 2013)
New Revision: 1098

Added:
   www/files/simGWAS/MSc-GWAS-1.1.pdf
   www/files/simGWAS/lecture-MSc-MVA.1.2.pdf
Log:
adding slides and pdf of GWAS lecture/tutorial

Added: www/files/simGWAS/MSc-GWAS-1.1.pdf
===================================================================
(Binary files differ)


Property changes on: www/files/simGWAS/MSc-GWAS-1.1.pdf
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: www/files/simGWAS/lecture-MSc-MVA.1.2.pdf
===================================================================
(Binary files differ)


Property changes on: www/files/simGWAS/lecture-MSc-MVA.1.2.pdf
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream


From noreply at r-forge.r-project.org  Thu Mar 21 18:20:43 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 21 Mar 2013 18:20:43 +0100 (CET)
Subject: [adegenet-commits] r1099 - www
Message-ID: <20130321172043.E4F371847FE@r-forge.r-project.org>

Author: jombart
Date: 2013-03-21 18:20:43 +0100 (Thu, 21 Mar 2013)
New Revision: 1099

Modified:
   www/documentation.html
Log:
added lecture + practical for MA/GWAS

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2013-03-21 17:15:31 UTC (rev 1098)
+++ www/documentation.html	2013-03-21 17:20:43 UTC (rev 1099)
@@ -38,6 +38,7 @@
 
 
 
+
         engine</a>. <br>
       <br>
       <br>
@@ -95,6 +96,7 @@
 
 
 
+
         1</a> [<a href="files/practical-day1.1.2-allcmd.pdf">version
         with all commands</a>]<br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day2.1.3.pdf">practical
@@ -102,6 +104,7 @@
 
 
 
+
         2</a> [<a href="files/practical-day2.1.3-allcmd.pdf">version
         with all commands</a>]<br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.2.pdf">practical
@@ -109,6 +112,7 @@
 
 
 
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
@@ -132,6 +136,7 @@
 
 
 
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to phylogenetics</span>.<img
         style=" width: 80px; height: 37px;" alt="new"
@@ -140,12 +145,28 @@
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/MSc-intro-phylo.1.1.pdf">practical</a><br>
       &nbsp;&nbsp;&nbsp; &gt; data (<a href="files/usflu.fasta">usflu.fasta</a>,
       <a href="files/usflu.annot.csv">usflu.annot.csv</a>)<br>
+      - Imperial College - Master <span style="font-style: italic;">Modern
+
+
+
+
+        Epidemiology</span> / <i>Public Health</i>: <span
+        style="font-weight: bold;">Introduction to multivariate analysis</span>.<img
+        style=" width: 80px; height: 37px;" alt="new"
+        src="file:///home/thibaut/dev/adegenet/www/images/new.png"><br>
+      (last updated on the 21/13/2013)<br>
+      &nbsp;&nbsp;&nbsp; &gt; <a
+        href="files/simGWAS/lecture-MSc-MVA.1.2.pdf">lecture</a><br>
+      &nbsp;&nbsp;&nbsp; &gt; <a href="files/simGWAS/MSc-GWAS-1.1.pdf">practical</a><br>
+      &nbsp;&nbsp;&nbsp; &gt; data (<a
+        href="files/simGWAS/simGWAS.RData">simGWAS.RData</a>)<br>
       <br>
       <br>
       <span style="font-weight: bold; color: rgb(0, 102, 0);">Dirty
         hacks useful for teaching</span><br>
       - a small hack for installing R packages on computers without
       administrative rights: <a href="files/hackLib/hackLib.R">hackLib.R</a>&nbsp;
+
       <a href="files/hackLib/README">README</a> <img style=" width:
         80px; height: 37px;" alt="new" src="images/new.png" height="37"
         width="80"><br>


From noreply at r-forge.r-project.org  Thu Mar 21 18:26:30 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 21 Mar 2013 18:26:30 +0100 (CET)
Subject: [adegenet-commits] r1100 - www
Message-ID: <20130321172630.C9E7A18467E@r-forge.r-project.org>

Author: jombart
Date: 2013-03-21 18:26:30 +0100 (Thu, 21 Mar 2013)
New Revision: 1100

Modified:
   www/documentation.html
Log:
relative link restored

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2013-03-21 17:20:43 UTC (rev 1099)
+++ www/documentation.html	2013-03-21 17:26:30 UTC (rev 1100)
@@ -39,6 +39,7 @@
 
 
 
+
         engine</a>. <br>
       <br>
       <br>
@@ -97,6 +98,7 @@
 
 
 
+
         1</a> [<a href="files/practical-day1.1.2-allcmd.pdf">version
         with all commands</a>]<br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day2.1.3.pdf">practical
@@ -105,6 +107,7 @@
 
 
 
+
         2</a> [<a href="files/practical-day2.1.3-allcmd.pdf">version
         with all commands</a>]<br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.2.pdf">practical
@@ -113,6 +116,7 @@
 
 
 
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
@@ -137,10 +141,11 @@
 
 
 
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to phylogenetics</span>.<img
         style=" width: 80px; height: 37px;" alt="new"
-        src="images/new.png"><br>
+        src="images/new.png" height="37" width="80"><br>
       (last updated on the 15/13/2013)<br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/MSc-intro-phylo.1.1.pdf">practical</a><br>
       &nbsp;&nbsp;&nbsp; &gt; data (<a href="files/usflu.fasta">usflu.fasta</a>,
@@ -150,10 +155,11 @@
 
 
 
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to multivariate analysis</span>.<img
         style=" width: 80px; height: 37px;" alt="new"
-        src="file:///home/thibaut/dev/adegenet/www/images/new.png"><br>
+        src="images/new.png" height="37" width="80"><br>
       (last updated on the 21/13/2013)<br>
       &nbsp;&nbsp;&nbsp; &gt; <a
         href="files/simGWAS/lecture-MSc-MVA.1.2.pdf">lecture</a><br>
@@ -167,6 +173,7 @@
       - a small hack for installing R packages on computers without
       administrative rights: <a href="files/hackLib/hackLib.R">hackLib.R</a>&nbsp;
 
+
       <a href="files/hackLib/README">README</a> <img style=" width:
         80px; height: 37px;" alt="new" src="images/new.png" height="37"
         width="80"><br>


From noreply at r-forge.r-project.org  Thu Mar 21 18:36:25 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 21 Mar 2013 18:36:25 +0100 (CET)
Subject: [adegenet-commits] r1101 - www
Message-ID: <20130321173625.5FBED18467E@r-forge.r-project.org>

Author: jombart
Date: 2013-03-21 18:36:25 +0100 (Thu, 21 Mar 2013)
New Revision: 1101

Modified:
   www/documentation.html
Log:
better description of the content

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2013-03-21 17:26:30 UTC (rev 1100)
+++ www/documentation.html	2013-03-21 17:36:25 UTC (rev 1101)
@@ -40,6 +40,7 @@
 
 
 
+
         engine</a>. <br>
       <br>
       <br>
@@ -99,6 +100,7 @@
 
 
 
+
         1</a> [<a href="files/practical-day1.1.2-allcmd.pdf">version
         with all commands</a>]<br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day2.1.3.pdf">practical
@@ -108,6 +110,7 @@
 
 
 
+
         2</a> [<a href="files/practical-day2.1.3-allcmd.pdf">version
         with all commands</a>]<br>
       &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.2.pdf">practical
@@ -117,6 +120,7 @@
 
 
 
+
         3</a><br>
       <br>
       - MRC methodological session: Introduction to phylogenetics:<br>
@@ -142,6 +146,7 @@
 
 
 
+
         Epidemiology</span> / <i>Public Health</i>: <span
         style="font-weight: bold;">Introduction to phylogenetics</span>.<img
         style=" width: 80px; height: 37px;" alt="new"
@@ -156,10 +161,11 @@
 
 
 
+
         Epidemiology</span> / <i>Public Health</i>: <span
-        style="font-weight: bold;">Introduction to multivariate analysis</span>.<img
-        style=" width: 80px; height: 37px;" alt="new"
-        src="images/new.png" height="37" width="80"><br>
+        style="font-weight: bold;">Introduction to multivariate analysis
+        / bacterial GWAS</span>.<img style=" width: 80px; height: 37px;"
+        alt="new" src="images/new.png" height="37" width="80"><br>
       (last updated on the 21/13/2013)<br>
       &nbsp;&nbsp;&nbsp; &gt; <a
         href="files/simGWAS/lecture-MSc-MVA.1.2.pdf">lecture</a><br>
@@ -174,6 +180,7 @@
       administrative rights: <a href="files/hackLib/hackLib.R">hackLib.R</a>&nbsp;
 
 
+
       <a href="files/hackLib/README">README</a> <img style=" width:
         80px; height: 37px;" alt="new" src="images/new.png" height="37"
         width="80"><br>