[adegenet-commits] r985 - pkg pkg/R www www/images www/images/gimp

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Dec 23 14:10:59 CET 2011 

Author: jombart
Date: 2011-12-23 14:10:59 +0100 (Fri, 23 Dec 2011)
New Revision: 985

Modified:
   pkg/DESCRIPTION
   pkg/R/zzz.R
   www/download.html
   www/images/acceuil.png
   www/images/gimp/acceuil.xcf
   www/news.html
Log:
New release on website; changed devel to 1.3-4


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2011-12-23 12:59:21 UTC (rev 984)
+++ pkg/DESCRIPTION	2011-12-23 13:10:59 UTC (rev 985)
@@ -1,5 +1,5 @@
 Package: adegenet
-Version: 1.3-3
+Version: 1.3-4
 Date: 2011/12/22
 Title: adegenet: an R package for the exploratory analysis of genetic and genomic data.
 Author:  Thibaut Jombart <t.jombart at imperial.ac.uk>

Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R	2011-12-23 12:59:21 UTC (rev 984)
+++ pkg/R/zzz.R	2011-12-23 13:10:59 UTC (rev 985)
@@ -2,7 +2,7 @@
 #.initAdegenetClasses()
 #.initAdegenetUtils()
     library.dynam("adegenet", pkg, lib)
-    startup.txt <- "   ==========================\n    adegenet 1.3-3 is loaded\n   ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n"
+    startup.txt <- "   ==========================\n    adegenet 1.3-4 is loaded\n   ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n"
 
     packageStartupMessage(startup.txt)
 }

Modified: www/download.html
===================================================================
--- www/download.html	2011-12-23 12:59:21 UTC (rev 984)
+++ www/download.html	2011-12-23 13:10:59 UTC (rev 985)
@@ -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>download</title>
-  <script type="text/javascript">
+  <head>
+    <meta content="text/html; charset=ISO-8859-1"
+      http-equiv="content-type">
+    <title>download</title>
+    <script type="text/javascript">
 
   var _gaq = _gaq || [];
   _gaq.push(['_setAccount', 'UA-20083187-1']);
@@ -17,142 +17,159 @@
   })();
 
   </script>
-</head>
-<body>
-<br>
-<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>
-<br>
-<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
-The <span style="font-weight: bold;">current stable version</span>
-(adegenet_1.3-2) is available as:<br>
-- <a href="files/adegenet_1.3-2.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.3-2.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.3-2.zip">Windows binary</a><br>
-<br>
-<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
-The <span style="font-weight: bold;">devel version</span>
-(adegenet_1.3-3) is also available from <a
- href="https://r-forge.r-project.org/scm/?group_id=120" target="_top">R-Forge's
-daily
-snapshots</a>.<br>
-It can be installed directly from R console using: <br>
-<span style="font-family: monospace;">install.packages("adegenet",repos="http://r-forge.r-project.org")<br>
-<br>
-</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 use these
-versions instead of the current (CRAN) ones. Simply download the file
-(right click -&gt; 'Save link as') in your working directory and type <span
- style="font-family: monospace;">source("[your-patch-file.R]")</span>&nbsp;
-
-to
-use
-a
-patch.<br>
-<a href="files/patches/addedFeatures.R"><span
- style="font-family: monospace;">addedFeatures.R</span></a>: (for
-adegenet &gt;=1.3-1) added features not included in the CRAN version of
-the
-package; includes conversion from <span style="font-family: monospace;">seqTrack
-</span>outputs to <span style="font-family: monospace;">graphNEL </span>objects.<br>
-<a href="files/patches/export.R"><span style="font-family: monospace;"></span></a><br>
-<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
-<span style="font-weight: bold;">Older versions</span>:<br>
-adegenet_1.3-1<br>
-- <a href="files/adegenet_1.3-1.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.3-1.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.3-1.zip">Windows binary</a><br>
-<br>
-adegenet_1.3-0<br>
-- <a href="files/adegenet_1.3-0.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.3-0.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.3-0.zip">Windows binary<br>
-</a><a href="files/adegenet_1.3-0.zip"></a><br>
-adegenet_1.2-9: there is no adegenet_1.2-9...<br>
-<br>
-adegenet_1.2-8<br>
-- <a href="files/adegenet_1.2-8.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-8.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-8.zip">Windows binary</a><br>
-<br>
-adegenet_1.2-7<br>
-- <a href="files/adegenet_1.2-7.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-7.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-7.zip">Windows binary</a><br>
-<br>
-adegenet_1.2-6<br>
-- <a href="files/adegenet_1.2-6.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-6.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-6.zip">Windows binary</a><br>
-<br>
-adegenet_1.2-5<br>
-- <a href="files/adegenet_1.2-5.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-5.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-5.zip">Windows binary</a><br>
-<br>
-adegenet_1.2-4<br>
-- <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-4.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-4.zip">Windows binary</a><br>
-<br>
-adegenet_1.3-3<br>
-- <a href="files/adegenet_1.2-3.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-3.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-3.zip">Windows binary</a><br>
-<br>
-adegenet_1.2-2<br>
-- <a href="files/adegenet_1.2-2.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-2.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-2.zip">Windows binary</a><br>
-<br>
-adegenet_1.2-1<br>
-- <a href="files/adegenet_1.2-1.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-1.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-1.zip">Windows binary</a><br>
-<br>
-adegenet_1.2-0<br>
-- <a href="files/adegenet_1.2-0.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-0.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-0.zip">Windows binary</a><br>
-<br>
-adegenet_1.1-2<br>
-- <a href="files/adegenet_1.1-2.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.1-2.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.1-2.zip">Windows binary</a><br>
-<br>
-adegenet_1.1-1<br>
-- <a href="files/adegenet_1.1-1.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.1-1.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.1-1.zip">Windows binary</a><br>
-<br>
-adegenet_1.1-0<br>
-- <a href="files/adegenet_1.1-0.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.1-0.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.1-0.zip">Windows binary</a><br>
-<br>
-adegenet_1.0-2<br>
-- <a href="files/adegenet_1.0-2.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.0-2.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.0-2.zip">Windows binary</a><br>
-<br>
-adegenet_1.0-1<br>
-- <a href="files/adegenet_1.0-1.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.0-1.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.0-1.zip">Windows binary</a><span
- style="text-decoration: underline;"><br>
-<br>
-</span>adegenet_1.0-0<br>
-- <a href="files/adegenet_1.0-0.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.0-0.tgz">MacOS X binary</a> <br>
-- <a href="files/adegenet_1.0-0.zip">Windows binary</a><br>
-<span style="font-weight: bold;"></span><br>
-</div>
-</body>
+  </head>
+  <body>
+    <br>
+    <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>
+      <br>
+      <img alt="" src="images/bullet.png" style="width: 10px; height:
+        10px;">
+      The <span style="font-weight: bold;">current stable version</span>
+      (adegenet_1.3-3) is available as:<br>
+      - <a href="files/adegenet_1.3-3.tar.gz">linux/unix sources</a><br>
+      - MacOS X binary<br>
+      - Windows binary<br>
+      <br>
+      <img alt="" src="images/bullet.png" style="width: 10px; height:
+        10px;">
+      The <span style="font-weight: bold;">devel version</span>
+      (adegenet_1.3-4) is also available from <a
+        href="https://r-forge.r-project.org/scm/?group_id=120"
+        target="_top">R-Forge's
+        daily
+        snapshots</a>.<br>
+      It can be installed directly from R console using: <br>
+      <span style="font-family: monospace;">install.packages("adegenet",repos="http://r-forge.r-project.org")<br>
+        <br>
+      </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 use
+      these
+      versions instead of the current (CRAN) ones. Simply download the
+      file
+      (right click -&gt; 'Save link as') in your working directory and
+      type <span style="font-family: monospace;">source("[your-patch-file.R]")</span>&nbsp;
+      to
+      use
+      a
+      patch.<br>
+      <a href="files/patches/addedFeatures.R"><span style="font-family:
+          monospace;">addedFeatures.R</span></a>: (for
+      adegenet &gt;=1.3-1) added features not included in the CRAN
+      version of
+      the
+      package; includes conversion from <span style="font-family:
+        monospace;">seqTrack
+      </span>outputs to <span style="font-family: monospace;">graphNEL
+      </span>objects.<br>
+      <a href="files/patches/export.R"><span style="font-family:
+          monospace;"></span></a><br>
+      <img alt="" src="images/bullet.png" style="width: 10px; height:
+        10px;">
+      <span style="font-weight: bold;">Older versions</span>:<br>
+      adegenet _1.3-2<br>
+      - <a href="files/adegenet_1.3-2.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.3-2.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.3-2.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.3-1<br>
+      - <a href="files/adegenet_1.3-1.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.3-1.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.3-1.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.3-0<br>
+      - <a href="files/adegenet_1.3-0.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.3-0.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.3-0.zip">Windows binary<br>
+      </a><a href="files/adegenet_1.3-0.zip"></a><br>
+      adegenet_1.2-9: there is no adegenet_1.2-9...<br>
+      <br>
+      adegenet_1.2-8<br>
+      - <a href="files/adegenet_1.2-8.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.2-8.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.2-8.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.2-7<br>
+      - <a href="files/adegenet_1.2-7.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.2-7.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.2-7.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.2-6<br>
+      - <a href="files/adegenet_1.2-6.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.2-6.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.2-6.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.2-5<br>
+      - <a href="files/adegenet_1.2-5.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.2-5.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.2-5.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.2-4<br>
+      - <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.2-4.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.2-4.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.3-3<br>
+      - <a href="files/adegenet_1.2-3.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.2-3.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.2-3.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.2-2<br>
+      - <a href="files/adegenet_1.2-2.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.2-2.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.2-2.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.2-1<br>
+      - <a href="files/adegenet_1.2-1.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.2-1.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.2-1.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.2-0<br>
+      - <a href="files/adegenet_1.2-0.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.2-0.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.2-0.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.1-2<br>
+      - <a href="files/adegenet_1.1-2.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.1-2.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.1-2.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.1-1<br>
+      - <a href="files/adegenet_1.1-1.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.1-1.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.1-1.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.1-0<br>
+      - <a href="files/adegenet_1.1-0.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.1-0.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.1-0.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.0-2<br>
+      - <a href="files/adegenet_1.0-2.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.0-2.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.0-2.zip">Windows binary</a><br>
+      <br>
+      adegenet_1.0-1<br>
+      - <a href="files/adegenet_1.0-1.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.0-1.tgz">MacOS X binary</a><br>
+      - <a href="files/adegenet_1.0-1.zip">Windows binary</a><span
+        style="text-decoration: underline;"><br>
+        <br>
+      </span>adegenet_1.0-0<br>
+      - <a href="files/adegenet_1.0-0.tar.gz">linux/unix sources</a><br>
+      - <a href="files/adegenet_1.0-0.tgz">MacOS X binary</a> <br>
+      - <a href="files/adegenet_1.0-0.zip">Windows binary</a><br>
+      <span style="font-weight: bold;"></span><br>
+    </div>
+  </body>
 </html>

Modified: www/images/acceuil.png
===================================================================
(Binary files differ)

Modified: www/images/gimp/acceuil.xcf
===================================================================
(Binary files differ)

Modified: www/news.html
===================================================================
--- www/news.html	2011-12-23 12:59:21 UTC (rev 984)
+++ www/news.html	2011-12-23 13:10:59 UTC (rev 985)
@@ -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>news</title>
-  <script type="text/javascript">
+  <head>
+    <meta content="text/html; charset=ISO-8859-1"
+      http-equiv="content-type">
+    <title>news</title>
+    <script type="text/javascript">
 
   var _gaq = _gaq || [];
   _gaq.push(['_setAccount', 'UA-20083187-1']);
@@ -17,717 +17,858 @@
   })();
 
   </script>
-</head>
-<body>
-<span style="font-weight: bold;"></span><span style="font-weight: bold;"></span><br>
-<br>
-<div style="margin-left: 40px;"><big><big><span
- style="font-weight: bold;"></span></big></big><span
- style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span
- style="color: rgb(255, 0, 0);"></span><br>
-<br>
-<span style="font-weight: bold;"><big><br>
-</big></span><span style="font-weight: bold;"><big>Coming soon</big></span><br>
-Next release (1.3-3) is under development.<br>
-<br>
-<br>
-<span style="font-weight: bold;"><big>Today</big> </span><span
- style="font-weight: bold;"></span><span style="font-weight: bold;"></span><br>
-<span style="font-weight: bold;"></span>Current
-stable version of <span style="color: rgb(255, 0, 0);">adegenet is
-1.3-2 </span>for R.2.14.0.<br>
-You can install the devel version from <a
- href="https://r-forge.r-project.org/scm/?group_id=120">R-Forge</a>.<br>
-See the current <a
- href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a>
-for a list of
-all modifications.<br>
-<br>
-<span style="font-weight: bold;">11/11/2011 </span><span
- style="font-weight: bold;"></span><img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-2</span>)
-has
-been
-released
-for
-R-2.14.0!</big> This minor release fixes some issues in the detection
-of the number of cores occuring on some platforms, as well as a few
-fixes in manpages. Function <span
- style="font-family: monospace; color: rgb(255, 0, 0);">fstat</span> is
-now gone for good as <span style="font-style: italic;">hierfstat </span>package
-seems to be gone for good from CRAN, but the documentation shows how to
-use <span style="color: rgb(255, 0, 0); font-family: monospace;">Fst</span>
-from the <span style="font-style: italic;">pegas </span>package
-instead. <span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">See
-the </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><a
- href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file for more details.</span></span><br>
-<br>
-<br>
-<span style="font-weight: bold;">02/09/2011 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-1</span>)
-has
-been
-released
-for
-R-2.13.1!</big> Less is more: this new release is much smaller in size
-than 1.3-0, while containing the same material. It also fixes a few
-minor issues in documentation and in the legend of dapc scatterplots. <span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">See
-the </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><a
- href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file for more details.</span></span><br>
-<br>
-<br>
-<span style="font-weight: bold;">27/06/2011 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-0</span>)
-has
-been
-released
-for
-R-2.13.0!</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">
-This new major release implements new classes and methods for the
-handling and analysis of genome-wide SNP data, along with several
-improvements to previous tools (especially new graphics for DAPC) </span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">and
-a few bug fixes. It also include 4 new tutorial distributed as
-vignettes. See the </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><a
- href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file for details of the release.</span></span> Given this is a major
-release, version number switched directly from 1.2-8 to 1.3-0.<br>
-<br>
-<br>
-<span style="font-weight: bold;">02/06/2011</span><br>
-A new tutorial dedicated to DAPC has been uploaded on the website (see
-section "documents").<br>
-<br>
-<br>
-<span style="font-weight: bold;">14/12/2010 </span><br>
-<span style="font-weight: bold;">The DAPC paper has been nicely
-reviewed by Laurent Excoffier on Faculty of 1000</span> [<a
- href="reviewDAPC.html">see evaluation</a>].<br>
-<br>
-<br>
-<span style="font-weight: bold;">08/11/2010 </span><span
- style="font-weight: bold;"></span><br>
-<big>A 'Frequently Asked Question' section has been added in the
-'contact' section of adegenet website.</big><br>
-<br>
-<br>
-<span style="font-weight: bold;">05/11/2010 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-8</span>)
-has
-been
-released
-for
-R-2.12.0!</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">
-This release </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">fixes a bug in exports from adegenet to
-hierfstat (function <span
- style="color: rgb(255, 0, 0); font-family: monospace;">genind2hierfstat</span>),
-which
-lead
-to
-wrong
-<span style="font-family: monospace; color: rgb(255, 0, 0);">fstat</span>
-computations in some cases. See the </span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><a
- href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file for details.</span></span><br>
-<br>
-<br>
-<span style="font-weight: bold;">29/10/2010 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-7</span>)
-has
-been
-released
-for
-R-2.12.0!</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">
-This release includes the stable implementation of the <span
- style="font-style: italic;">Discriminant Analysis of Principal
-Components</span> (<span style="font-style: italic;">DAPC</span>, <span
- style="color: rgb(255, 0, 0); font-family: monospace;">?dapc</span>, <span
- style="color: rgb(255, 0, 0); font-family: monospace;">?find.clusters</span>)</span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">,
-and fixes a bug from the ape package which impacted adegenet and
-prevented windows binaries to be generated with R-2.12.0. See the </span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><a
- href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file for more information.</span></span><br>
-<br>
-<br>
-<span style="font-weight: bold;">22/09/2010 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-6</span>)
-has
-been
-released
-for
-R-2.11.1!</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">
-This release adds the computation of pairwise Fst (</span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
- style="color: rgb(255, 0, 0);"></span><span
- style="font-family: monospace; color: rgb(255, 0, 0);">?pairwise.fst</span></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">) </span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">and
-a new function for extracting the polymorphism of aligned proteic
-sequences (class </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"><span
- style="font-family: monospace; color: rgb(255, 0, 0);">alignment </span></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">in
-the seqinr package) into genind objects (</span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
- style="font-family: monospace; color: rgb(255, 0, 0);">?alignment2genind</span></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">).
-See the </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><a
- href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file for more information, and check out new updates of the tutorial.</span></span><br>
-<br>
-<span style="font-weight: bold;"><br>
-30/07/2010 </span><span style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-5</span>)
-has
-been
-released
-for
-R-2.11.1!</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">
-This release includes a stable implementation of the <span
- style="font-style: italic;">SeqTrack </span>algorithm&nbsp;</span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-(see literature section for a reference) for reconstructing genealogies
-of haplotypes; see<span style="color: rgb(255, 0, 0);"> </span><span
- style="font-family: monospace; color: rgb(255, 0, 0);">?seqTrack</span>
-</span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"> for more information. A new tool for
-simulating genealogies of haplotypes has also been implemented (see </span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
- style="color: rgb(255, 0, 0);"></span><span
- style="font-family: monospace; color: rgb(255, 0, 0);">?haploGen</span></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">).
-Minor issues pertaining to the definition of summary methods for genind
-and genpop objects have been fixed. See the </span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><a
- href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file for more information.</span></span><br>
-<br>
-<br>
-<span style="font-weight: bold;">19/04/2010 </span><span
- style="font-weight: bold;"></span><br>
-<big>New version of the adegenet tutorial online.</big><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-This new version of the tutorial is compatible with the latest release
-of adegenet (version 1.2-4). It incorporates a new section on importing
-data into adegenet which is more explicit and detailed than the
-previous one.</span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"><br>
-</span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><br>
-<br>
-<span style="font-weight: bold;">19/04/2010 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-4</span>)
-has
-been
-released
-for
-R-2.10.1
-!</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">
-This release corrects a few issues and bugs from previous version, and
-includes new material currently under review in scientific journals.
-Once 'stable', these new functionalities will give rise to the major
-release 1.3-0. Look at </span></span><a
- href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"> for
-more information about this new version.<br>
-</span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><br>
-<br>
-<span style="font-weight: bold;">15/04/2010 </span><span
- style="font-weight: bold;"></span><span style="font-weight: bold;"></span><br>
-<big>The adegenet forum's archives can now be searched from this
-website.</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"> Look at the 'contact' section for more
-information. The next major adegenet release is on its way. It will
-include new methods of genetic data analysis, as well as new simulation
-systems. Pending work under review, the release of 1.3-0 should be done
-within the next two months. Intermediate release correcting minor bugs
-may occur meanwhile.<br>
-</span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><br>
-<br>
-<span style="font-weight: bold;">02/04/2009 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-3</span>)
-has
-been
-released
-for
-R.2.8.1
-!</big><br>
-This is a important<span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"> release, including some significant
-improvements
-(see </span></span><a href="files/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file). The most important new feature is that <span
- style="color: rgb(255, 0, 0);">presence/absence </span>data like AFLP
-are now handled. A new slot 'type' now distinguishes, in genind and
-genpop objects, codominant markers (type="codom") from presence/absence
-(type="PA"). Also, <span
- style="color: rgb(255, 0, 0); font-family: monospace;">hybridize</span>
-can now perform hybridization between genotypes with any even degree of
-ploidy. Another noticeable feature is that SNPs can be obtained from
-aligned DNA sequences using <span
- style="color: rgb(255, 0, 0); font-family: monospace;">DNAbin2genind</span>.This
-time,
-the
-tutorial
-has
-been
-updated
-at
-the
-same
-time
-as
-the
-package
-release!<br>
-<br>
-<br>
-</span></span><span style="font-weight: bold;">19/12/2008 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-2</span>)
-has
-been
-released
-for
-R.2.8.0
-!</big><br>
-<span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
-new,
-big
-release
-implements
-many
-new
-things
-and
-corrects
-a
-few
-bugs
-(see
-</span></span><a href="files/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file). Amongst the biggest news, <span style="font-weight: bold;">several
-levels
-of
-ploidy</span> are now handled throughout the package, apart
-from a few exceptions. New graphics are available for multivariate
-methods: the <span
- style="font-family: monospace; color: rgb(255, 0, 0);">colorplot</span>,
-which
-can
-represent
-genetic
-diversity
-using
-RGB
-scale,
-and
-a
-<span style="font-family: monospace; color: rgb(255, 0, 0);">loadingplot</span>,
-which
-can
-be
-used
-to
-assess
-the
-most
-structuring
-alleles
-and
-loci
-in
-an
-analysis.&nbsp;
-A
-new georeferenced genetic dataset is also available
-(dataset <span style="color: rgb(255, 0, 0); font-family: monospace;">rupica</span>).
-And...
-<a href="files/ChangeLog">several other things</a>!<br>
-</span></span><br>
-<br>
-<span style="font-weight: bold;">03/08/2008 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-1</span>)
-has
-been
-released
-for
-R.2.7.1
-!</big><br>
-<span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
-new
-release
-corrects
-a
-few
-bugs
-arising
-in
-version
-1.2-0
-(see
-</span></span><a href="files/ChangeLog">ChangeLog</a><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
-file), especially an issue with the detection of NAs. Documentation was
-also improved (have a look at <span
- style="font-family: monospace; color: rgb(255, 0, 0);">?scaleGen</span>).<br>
-</span></span><br>
-<br>
-<span style="font-weight: bold;">09/07/2008 </span><span
- style="font-weight: bold;"></span><br>
-<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-0</span>)
-has
-been
-released
-for
-R.2.7.1
-!</big><br>
[TRUNCATED]

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    svnlook diff /svnroot/adegenet -r 985

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