[adegenet-commits] r1140 - www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 5 15:03:34 CEST 2013
Author: jombart
Date: 2013-06-05 15:03:34 +0200 (Wed, 05 Jun 2013)
New Revision: 1140
Modified:
www/download.html
www/literature.html
www/news.html
Log:
changes to the website to reflect new version
Modified: www/download.html
===================================================================
--- www/download.html 2013-06-05 12:54:43 UTC (rev 1139)
+++ www/download.html 2013-06-05 13:03:34 UTC (rev 1140)
@@ -30,14 +30,16 @@
<br>
<img alt="" src="images/bullet.png" style="width: 10px; height:
10px;"> The <span style="font-weight: bold;">current stable
- version</span> (adegenet_1.3-8) is available as:<br>
- - <a href="files/adegenet_1.3-8.tar.gz">linux sources</a><br>
- - <a href="files/adegenet_1.3-8.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.3-8.zip">Windows binary</a><br>
+ version</span> (adegenet_1.3-9) is available as:<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>
<img alt="" src="images/bullet.png" style="width: 10px; height:
10px;"> The <span style="font-weight: bold;">devel version</span>
- (adegenet_1.3-9) is also available from <a
+ (adegenet_1.4-0) 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>
@@ -50,6 +52,7 @@
+
<br>
Patches correct minor bugs or implement new functionnalities, and
will be included into the next CRAN release. It is recommended to
@@ -64,6 +67,7 @@
+
a patch.<br>
<a href="files/patches/addedFeatures.R"><span style="font-family:
monospace;">addedFeatures.R</span></a>: (for adegenet
@@ -77,6 +81,17 @@
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 _1.3-8<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>
Modified: www/literature.html
===================================================================
--- www/literature.html 2013-06-05 12:54:43 UTC (rev 1139)
+++ www/literature.html 2013-06-05 13:03:34 UTC (rev 1140)
@@ -67,6 +67,7 @@
+
the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
<br style="color: rgb(0, 153, 0);">
<br>
@@ -103,6 +104,7 @@
+
abstract</a>]<br>
<br>
- the paper presenting the <span style="font-style: italic;">spatial
@@ -124,6 +126,7 @@
+
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
@@ -148,6 +151,7 @@
+
cryptic spatial patterns in genetic variability by a new
multivariate method. <span style="font-style: italic;">Heredity</span>
<span style="font-weight: bold;">101</span>: 92-103. doi:
@@ -173,6 +177,7 @@
+
abstract</a>]<br>
</div>
<br>
@@ -200,6 +205,7 @@
+
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)
@@ -227,6 +233,7 @@
+
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>
@@ -262,6 +269,7 @@
+
Behaviour</i><i></i><span style="font-weight: bold;">76</span>:
87-95.<br>
<br>
@@ -286,6 +294,7 @@
+
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>
@@ -325,6 +334,7 @@
+
marmota</span>.</span><span style="font-style: italic;">Molecular
@@ -343,6 +353,7 @@
+
Ecology</span> <span style="font-weight: bold;">18</span>:
1491-1503.<br>
<br>
@@ -400,6 +411,7 @@
+
australis</i> in North America. <span style="font-style:
italic;">Biological Invasions</span>. doi:
10.1007/s10530-010-9699-6.<br>
@@ -561,6 +573,7 @@
+
Oct 6. [Epub ahead of print]<br>
</p>
<p class="auth_list">[24] SANTOS, H., BURBAN, C., ROUSSELET, J.,
@@ -583,6 +596,7 @@
+
pityocampa</em>, Lepidoptera, Notodontidae). <span
style="font-style: italic;">Journal of Evolutionary Biology</span>,
no. doi: 10.1111/j.1420-9101.2010.02147.x<br>
@@ -610,6 +624,7 @@
+
Vol. Sci. Pap. ICCAT</span>, 65(3): 988-995</p>
<p class="intro">[26] <span class="citation_author">Vandewoestijne
@@ -630,6 +645,7 @@
+
S, </span> <span class="citation_author">Van Dyck H, </span>
<span class="citation_date">2010</span> <span
class="citation_article_title">Population Genetic
@@ -653,6 +669,7 @@
+
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>
@@ -687,6 +704,7 @@
+
</span><span class="doi"><span class="label">DOI:</span> <span
class="value">10.1007/s10329-010-0232-4<br>
</span></span></p>
@@ -758,6 +776,7 @@
+
tetradactylum</em>: Polynemidae). Molecular Ecology,
20: no. doi: 10.1111/j.1365-294X.2011.05097.x<br>
</p>
@@ -787,6 +806,7 @@
+
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
@@ -1048,6 +1068,7 @@
+
10.1007/s10709-012-9640-2<br>
<br>
[76] Samantha Baldwin, Meeghan Pither-Joyce, Kathryn Wright,
@@ -1726,10 +1747,22 @@
Amietophrynus mauritanicus (Schlegel, 1841). Conservation
Genetics Resources. DOI: 10.1007/s12686-013-9963-z<br>
<br>
+ [193] Roullier C, Duputié A, Wennekes P, Benoit L, Fernández
+ Bringas VM, et al. (2013) Disentangling the Origins of
+ Cultivated Sweet Potato (Ipomoea batatas (L.) Lam.). PLoS ONE
+ 8(5): e62707. doi:10.1371/journal.pone.0062707<br>
<br>
+ [194] Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A,
+ et al. (2013) Uniparental Markers in Italy Reveal a Sex-Biased
+ Genetic Structure and Different Historical Strata. PLoS ONE
+ 8(5): e65441. doi:10.1371/journal.pone.0065441<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>
Modified: www/news.html
===================================================================
--- www/news.html 2013-06-05 12:54:43 UTC (rev 1139)
+++ www/news.html 2013-06-05 13:03:34 UTC (rev 1140)
@@ -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>news</title>
<script type="text/javascript">
@@ -28,15 +28,15 @@
0, 0);"></span><br>
<br>
<span style="font-weight: bold;">What's next<big></big></span>?<br>
- Next release (1.3-9) is under development.<br>
+ Next release (1.4-0) 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 1.3-8 </span>for
- R.3.0.0.<br>
+ <span style="color: rgb(255, 0, 0);">adegenet is 1.3-9 </span>for
+ R.3.0.1.<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
@@ -44,8 +44,29 @@
for a list of all modifications.<br>
<br>
<br>
- 15/05/2013 <img style="width: 80px; height: 37px;" alt=""
- src="images/new.png"><br>
+ 05/06/2013 <img style="width: 80px; height: 37px;" alt=""
+ src="file:///home/thibaut/dev/adegenet/www/images/new.png"><br>
+ <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-9</span>)
+ has been released for R-3.0.1!</big> <span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">New features
+ include some improvements on and the separate documentation of
+ the cross-validation procedure for DAPC (</span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
+ 0);"><span style="color: rgb(255, 0, 0);"><span style="color:
+ rgb(0, 0, 0);"><span style="font-family: monospace; color:
+ rgb(255, 0, 0);">xvalDapc</span></span><span
+ style="font-family: monospace;"></span><span style="color:
+ rgb(0, 0, 0);"></span></span>), and improvement of color
+ palettes alongside new ones. </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>
+ <br>
+ 15/05/2013 <br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-8</span>)
has been released for R-3.0.0!</big> <span style="color:
rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">New features
@@ -88,6 +109,7 @@
include a function for identifying mutations (position and
nature) between pairs of DNA sequences (<span style="color:
rgb(255, 0, 0); font-family: monospace;">findMutations</span>),
+
with a possibility of visualization using graphs (</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:
@@ -175,6 +197,7 @@
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
@@ -410,6 +433,7 @@
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>
@@ -547,6 +571,7 @@
possible to ask for a given length of boundary (argument <span
style="font-family: monospace; color: rgb(255, 0, 0);">bd.length</span>).
+
The function <span style="font-family: monospace; color: rgb(255,
0, 0);">chooseCN</span> has a new option to return a list of
spatial weights defined as the inverse of spatial distances, at a
@@ -584,6 +609,7 @@
0);">S3 classes.<br>
- <span style="text-decoration:
underline;">Spatial genetics:</span> the </span></span>spatial
+
Principal Component Analysis (Jombart et al, submitted to
Heredity), two multivariate spatial tests, and new functionalities
for Monmonier's algorithm.<br>
@@ -599,6 +625,7 @@
datasets. Can output to STRUCTURE format.<br>
- <span style="text-decoration: underline;">Data
+
manipulation:</span> new function to separate data by
population. Accessors to genind and genpop object like with
matrices using 'foo[ chosenGenotypes, chosenAlleles]'.<br>
@@ -644,6 +671,7 @@
genetic
example,
+
using <span style="font-family: monospace; color: rgb(255, 0,
0);">sim2pop</span><span style="color: rgb(255, 0, 0);"> </span>data.<br>
<span style="font-weight: bold;"><br>
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