[adegenet-commits] r1237 - in www: . images images/gimp
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Oct 13 12:19:30 CEST 2017
Author: jombart
Date: 2017-10-13 12:19:30 +0200 (Fri, 13 Oct 2017)
New Revision: 1237
Modified:
www/acceuil.html
www/download.html
www/images/acceuil.png
www/images/gimp/acceuil.xcf
www/news.html
Log:
new release
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2016-11-02 09:55:28 UTC (rev 1236)
+++ www/acceuil.html 2017-10-13 10:19:30 UTC (rev 1237)
@@ -96,7 +96,7 @@
<br>
</small></div>
<small><br>
- </small><span style="text-decoration: underline;">Main
+ </small><span style="text-decoration: underline;">The main
features of adegenet are:</span><br>
<ul>
<li>data representation (<span style="font-weight: bold;">classes</span>)
@@ -105,24 +105,9 @@
from GENETIX, STRUCTURE, Genepop, Fstat, Easypop, or any
dataframe of genotypes</li>
<li>data import from <span style="font-weight: bold;">aligned
-
-
-
-
-
-
-
DNA sequences</span> to <span style="font-weight:
bold;">SNPs</span></li>
<li> data import from <span style="font-weight: bold;">aligned
-
-
-
-
-
-
-
-
protein sequences</span> to polymorphic sites </li>
<li> data <span style="font-weight: bold;">export</span> to
the R packages genetics, hierfstat, LDheatmap</li>
@@ -133,19 +118,6 @@
</span>markers and<span style="font-weight: bold;">
presence/absence</span> data</li>
<li>basic and advanced <span style="font-weight: bold;">data
-
-
-
-
-
-
-
-
-
-
-
-
-
manipulation</span></li>
<li> basic <span style="font-weight: bold;">data
information </span>(heterozygosity, numbers of alleles,
@@ -155,13 +127,6 @@
<li>simulation of <span style="font-weight: bold;">hybridization</span></li>
<li>methods for <span style="font-weight: bold;">spatial
genetics: sPCA, </span><span style="font-weight: bold;">tests
-
-
-
-
-
-
-
for global and local structuring, </span><span
style="font-weight: bold;">Monmonier algorithm</span></li>
<li>the <span style="font-style: italic; font-weight:
@@ -169,19 +134,6 @@
algorithm </span>for reconstructing genealogies of
haplotypes</li>
<li>simulation of <span style="font-weight: bold;">genealogies
-
-
-
-
-
-
-
-
-
-
-
-
-
of haplotypes</span></li>
<li> Discriminant Analysis of Principal Components (<span
style="font-weight: bold;">DAPC</span>)</li>
@@ -195,8 +147,9 @@
randomness of their distribution</li>
<li><b>web interface for DAPC</b>, including feature
selection and cross validation </li>
- <li>and more...<br>
- </li>
+ <li><b>fast maximum-likelihood clustering</b> and identification of hybrids using <b>snapclust</b></li>
+ <li>export multivariate analysis results for geographic mapping using <b>mvmapper</b></li>
+ <li>and more...</li>
</ul>
</div>
<span style="font-weight: bold;"><br>
Modified: www/download.html
===================================================================
--- www/download.html 2016-11-02 09:55:28 UTC (rev 1236)
+++ www/download.html 2017-10-13 10:19:30 UTC (rev 1237)
@@ -2,217 +2,45 @@
<html>
<head>
<meta content="text/html; charset=windows-1252"
- http-equiv="content-type">
+ http-equiv="content-type">
<title>download</title>
<script type="text/javascript">
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', 'UA-20083187-1']);
- _gaq.push(['_trackPageview']);
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-20083187-1']);
+ _gaq.push(['_trackPageview']);
- (function() {
- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
- })();
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
- </script>
+ </script>
</head>
<body>
+ <br>
<br style="font-family: Helvetica,Arial,sans-serif;">
- <br style="font-family: Helvetica,Arial,sans-serif;">
- <br style="font-family: Helvetica,Arial,sans-serif;">
- <div style="margin-left: 40px; font-family:
- Helvetica,Arial,sans-serif;"><img alt="" src="images/bullet.png"
- style="width: 10px; height: 10px;"> The <span
- style="font-weight: bold;">current stable version</span>
- (adegenet_1.4-2) <b>is available from</b> <a
- href="http://cran.r-project.org/web/packages/adegenet/index.html">CRAN</a>.
- <br>
- You can also install adegenet from R by simply typing:<br>
- <big style="font-family: monospace;">install.packages("adegenet",
- dep=TRUE)</big><br>
- <br>
- <br>
- <img alt="" src="images/bullet.png" style="width: 10px; height:
- 10px;"> <span style="font-weight: bold;">Patches</span> <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 -> 'Save link as') in your
- working directory and type source("[your-patch-file.R]")
- to
- use a patch.<br>
- <a href="files/patches/addedFeatures.R">addedFeatures.R</a>: (for
- adegenet >=1.3-1) added features not included in the CRAN
- version of the package; includes conversion from seqTrack outputs
- to graphNEL objects. If you have a choice though, consider using
- current igraph implementation, which is probably better and still
- maintained.<br>
- <br>
- <br>
- <img alt="" src="images/bullet.png" style="width: 10px; height:
- 10px;"> <span style="font-weight: bold;">Older versions</span>:<br>
- adegenet_1.4-1<br>
- - <a
- href="http://cran.r-project.org/src/contrib/adegenet_1.4-1.tar.gz">linux
+ <br>
+ <br>
- sources</a><br>
- - <a
-href="http://cran.r-project.org/bin/macosx/contrib/r-release/adegenet_1.4-0.tgz">MacOS
+ <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;"> The current version of <b>adegenet</b> can be installed from CRAN, by simply typing:<br>
+ <pre>install.packages("adegenet")</pre>
- X binary</a><br>
- - <a
-href="http://cran.r-project.org/bin/windows/contrib/r-release/adegenet_1.4-1.zip">Windows
+ <br>
+ <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
+ The development version of the package is hosted on <a href="https://github.com/thibautjombart/adegenet">github</a>. See installation guidelines for the devel version <a href="https://github.com/thibautjombart/adegenet/wiki/Installing-adegenet-devel">here</a>.
- binary</a><br>
- <br>
- <br>
- adegenet_1.3-9<br>
- - <a
- href="http://cran.at.r-project.org/src/contrib/adegenet_1.3-9.tar.gz">linux
-
-
- sources</a><br>
- - MacOS X binary<br>
- - Windows binary<br>
- <br>
- adegenet _1.3-8<br>
- - <a
- href="file:///home/thibaut/dev/adegenet/www/files/adegenet_1.3-8.tar.gz">linux
-
-
- sources</a><br>
- - <a
- href="file:///home/thibaut/dev/adegenet/www/files/adegenet_1.3-8.tgz">MacOS
-
-
- X binary</a><br>
- - <a
- href="file:///home/thibaut/dev/adegenet/www/files/adegenet_1.3-8.zip">Windows
-
-
- binary</a><br>
- <br>
- adegenet _1.3-7<br>
- - <a href="files/adegenet_1.3-7.tar.gz">linux sources</a><br>
- - <a href="files/adegenet_1.3-7.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.3-7.zip">Windows binary</a><br>
- <br>
- adegenet _1.3-6<br>
- - <a href="files/adegenet_1.3-6.tar.gz">linux sources</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>
- adegenet _1.3-5<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>
- adegenet _1.3-4<br>
- - <a href="files/adegenet_1.3-4.tar.gz">linux sources</a><br>
- - <a href="files/adegenet_1.3-4.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.3-4.zip">Windows binary</a><br>
- <br>
- adegenet _1.3-3<br>
- - <a href="files/adegenet_1.3-3.tar.gz">linux sources</a><br>
- - MacOS X binary<br>
- - Windows binary<br>
- <br>
- adegenet _1.3-2<br>
- - <a href="files/adegenet_1.3-2.tar.gz">linux 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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>
+ <br>
+ <br>
+ <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
+ <b>adegenet</b> is also available as a Docker container; see <a href="https://github.com/thibautjombart/adegenet_docker">this page</a> for more details.
+ <br>
+ <br>
+ <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
+ This website no longer distributes old sources of <b>adegenet</b>. These are
+ available on <a href="https://cran.r-project.org/src/contrib/Archive/adegenet/">CRAN</a>.
+
</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 2016-11-02 09:55:28 UTC (rev 1236)
+++ www/news.html 2017-10-13 10:19:30 UTC (rev 1237)
@@ -30,22 +30,38 @@
0, 0);"></span><br>
<br>
<big><span style="font-weight: bold;">What's next</span>?</big><br>
- Next release (1.4-3) is under development.<br>
+ Next release (2.1.1) 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 2.0.0 </span>for
- R.3.2.1.<br>
+ <span style="color: rgb(255, 0, 0);">adegenet is 2.1.0 </span>for
+ R.3.4.2.<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>
<br>
- 07/07/2015 <img style=" width: 80px; height: 37px;" alt=""
+ 13/10/2017 <img style=" width: 80px; height: 37px;" alt=""
src="images/new.png" height="37" width="80"><br>
+
+ <big>New adegenet version (<span style="color: rgb(255, 0,
+ 0);">2.1.0</span>) has been released for R-3.4.2!</big>While semantic
+ says it is a minor release, it is a substantial one, after more than a
+ year of implementing new tools and fixing issues since the last patch. A
+ new fast-ML clustering method, exports to mvmapper, a bunch of fixes,
+ and more.
+ <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>
+ 07/07/2015 <br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">2.0.0</span>)
has been released for R-3.2.1!</big> <span style="color:
rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
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