[adegenet-commits] r1201 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jul 8 18:11:32 CEST 2015
Author: jombart
Date: 2015-07-08 18:11:32 +0200 (Wed, 08 Jul 2015)
New Revision: 1201
Modified:
www/acceuil.html
www/news.html
Log:
updated website
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2015-07-08 15:55:44 UTC (rev 1200)
+++ www/acceuil.html 2015-07-08 16:11:32 UTC (rev 1201)
@@ -24,16 +24,22 @@
<br>
<br>
<br>
- <div style="text-align: left;"> <span style="font-weight: bold;">adegenet</span>
- is an <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 dedicated to the
- exploratory analysis of genetic data. It implements a set of
- tools ranging from multivariate methods to spatial genetics and
- genome-wise SNP data analysis. <br>
+ <div style="text-align: left;"> <span style="font-weight: bold;">NOTE:
+ this website will soon be replaced by a new github page.
+ Meanwhile, up-to-date information on adegenet can be found on
+ github:<br>
+ <a href="https://github.com/thibautjombart/adegenet/wiki">https://github.com/thibautjombart/adegenet/wiki</a><br>
+ <br>
+ adegenet</span> is an <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 dedicated
+ to the exploratory analysis of genetic data. It implements a set
+ of tools ranging from multivariate methods to spatial genetics
+ and genome-wise SNP data analysis. <br>
<br>
- It is developed on <a href="http://sourceforge.net/p/adegenet">Sourceforge</a>
+ It is developed on <a
+ href="https://github.com/thibautjombart/adegenet">Github</a>
by <a href="http://sites.google.com/site/thibautjombart/">Thibaut
@@ -41,17 +47,12 @@
- Jombart</a>, <a
- href="https://sites.google.com/site/caitlincollinswebpage/home">Caitlin
- Collins</a>, Ismail Ahmed, <a
- href="http://www.federicocalboli.com/">Federico Calboli</a>, <a
- href="http://www1.imperial.ac.uk/medicine/people/a.cori/">Anne
- Cori</a>, Tobias Erik Reiners, and <a
- href="https://sites.google.com/site/psolymos/">Péter Sólymos</a>,
- and officially released on <a href="http://cran.r-project.org">CRAN</a>
- periodically. <br>
+ Jombart</a>, Caitlin Collins, Zhian N Kamvar, Roman Lustrik,
+ Ismail Ahmed, Federico Calboli, Anne Cori, Tobias Erik Reiners,
+ and Péter Sólymos, and officially released on CRAN periodically.
<br>
+ <br>
adegenet is described in the following publications:<br>
<ul>
<li> Jombart T. (2008) adegenet: a R package for the
@@ -78,6 +79,7 @@
+
the bublisher's website</a>]<br>
</li>
</ul>
@@ -106,6 +108,7 @@
+
DNA sequences</span> to <span style="font-weight:
bold;">SNPs</span></li>
<li> data import from <span style="font-weight: bold;">aligned
@@ -113,6 +116,7 @@
+
protein sequences</span> to polymorphic sites </li>
<li> data <span style="font-weight: bold;">export</span> to
the R packages genetics, hierfstat, LDheatmap</li>
@@ -131,6 +135,7 @@
+
manipulation</span></li>
<li> basic <span style="font-weight: bold;">data
information </span>(heterozygosity, numbers of alleles,
@@ -151,6 +156,7 @@
+
Fst </span></li>
<li> simulation of <span style="font-weight: bold;">hybridization</span></li>
<li>methods for <span style="font-weight: bold;">spatial
@@ -158,6 +164,7 @@
+
for global and local structuring, </span><span
style="font-weight: bold;">Monmonier algorithm</span></li>
<li>the <span style="font-style: italic; font-weight:
@@ -171,6 +178,7 @@
+
</span>for reconstructing genealogies of haplotypes</li>
<li>simulation of <span style="font-weight: bold;">genealogies
@@ -182,6 +190,7 @@
+
of haplotypes</span></li>
<li> Discriminant Analysis of Principal Components (<span
style="font-weight: bold;">DAPC</span>)</li>
@@ -214,6 +223,7 @@
+
Collins (<a href="mailto:caitiecollins17 at gmail.com">caitiecollins at gmail.com</a>),
@@ -224,11 +234,13 @@
+
Ismaïl Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
+
Federico Calboli (<a href="mailto:f.calboli at imperial.ac.uk">f.calboli at imperial.ac.uk</a>),
@@ -237,6 +249,7 @@
+
Anne Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>),
Tobias
@@ -248,6 +261,7 @@
+
Erik Reiners (<a href="mailto:Tobias.Reiners at Senckenberg.de">Tobias.Reiners at Senckenberg.de</a>),
@@ -258,6 +272,7 @@
+
Péter Sólymos (<a href="mailto:solymos at ualberta.ca">solymos at ualberta.ca</a>)<br>
<span style="text-decoration: underline;">Contributors
(datasets/ideas):</span> Christophe Fraser, Katayoun
Modified: www/news.html
===================================================================
--- www/news.html 2015-07-08 15:55:44 UTC (rev 1200)
+++ www/news.html 2015-07-08 16:11:32 UTC (rev 1201)
@@ -37,15 +37,32 @@
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 1.4-2 </span>for
- R.3.1.0.<br>
+ <span style="color: rgb(255, 0, 0);">adegenet is 2.0.0 </span>for
+ R.3.2.1.<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>
- 13/05/2014 <img style=" width: 80px; height: 37px;" alt=""
- src="images/new.png"><br>
+ 07/07/2015 <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);">2.0.0</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
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
+ 0);">This is a new major release, which implements a lot of
+ improvements over previous versions, including support for
+ varying ploidy in a single dataset, simplified data
+ structures, hierarchical stucture storage and manipulation,
+ and more. </span><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>
+ 13/05/2014 <br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.4-2</span>)
has been released for R-3.1.0!</big> <span style="color:
rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
@@ -101,6 +118,7 @@
+
and DAPC-based feature selection (</span></span><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
0);"><span style="color: rgb(255, 0, 0); font-family:
@@ -111,6 +129,7 @@
+
</span><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
@@ -238,10 +257,10 @@
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
0);">download and installed size (respectively 4-5MB and
6-7MB). Many examples have been 'inactivated' to comply with
- CRAN check runtime policy, meaning these won't be run by 'example(myFunction)'
- anymore, but will still be available in the documentation. See
- the </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><a
+ CRAN check runtime policy, meaning these won't be run by
+ 'example(myFunction)' anymore, but will still be available in
+ the documentation. 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
@@ -524,6 +543,7 @@
loci in an analysis. A new georeferenced genetic dataset
is also available (dataset <span style="color: rgb(255, 0,
0);">rupica</span>). And... <a href="files/ChangeLog">several
+
other things</a>!<br>
</span></span><br>
<br>
@@ -674,6 +694,7 @@
+
Principal Component Analysis (Jombart et al, submitted to
Heredity), two multivariate spatial tests, and new functionalities
for Monmonier's algorithm.<br>
@@ -698,6 +719,7 @@
+
manipulation:</span> new function to separate data by
population. Accessors to genind and genpop object like with
matrices using 'foo[ chosenGenotypes, chosenAlleles]'.<br>
@@ -752,6 +774,7 @@
+
using <span style="color: rgb(255, 0, 0);">sim2pop</span><span
style="color: rgb(255, 0, 0);"> </span>data.<br>
<span style="font-weight: bold;"><br>
More information about the adegenet-commits
mailing list