[adegenet-commits] r1047 - pkg/vignettes www www/files www/images www/images/gimp

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Nov 8 12:57:18 CET 2012 

Author: jombart
Date: 2012-11-08 12:57:17 +0100 (Thu, 08 Nov 2012)
New Revision: 1047

Added:
   pkg/vignettes/genomics-055.pdf
   pkg/vignettes/genomics-070.pdf
   pkg/vignettes/loadingplotGLzoom.png
   www/files/adegenet_1.3-5.tar.gz
   www/files/adegenet_1.3-5.tgz
   www/files/adegenet_1.3-5.zip
Modified:
   www/acceuil.html
   www/download.html
   www/files/adegenet-basics.pdf
   www/files/adegenet-dapc.pdf
   www/files/adegenet-genomics.pdf
   www/files/adegenet-manual.pdf
   www/files/adegenet-spca.pdf
   www/images/acceuil.png
   www/images/gimp/acceuil.xcf
   www/news.html
Log:
update website for release 1.3-5

Added: pkg/vignettes/genomics-055.pdf
===================================================================
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Property changes on: pkg/vignettes/genomics-055.pdf
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Added: svn:mime-type
   + application/octet-stream

Added: pkg/vignettes/genomics-070.pdf
===================================================================
(Binary files differ)


Property changes on: pkg/vignettes/genomics-070.pdf
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: pkg/vignettes/loadingplotGLzoom.png
===================================================================
(Binary files differ)


Property changes on: pkg/vignettes/loadingplotGLzoom.png
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Modified: www/acceuil.html
===================================================================
--- www/acceuil.html	2012-11-05 16:21:48 UTC (rev 1046)
+++ www/acceuil.html	2012-11-08 11:57:17 UTC (rev 1047)
@@ -56,7 +56,8 @@
 10.1093/bioinformatics/btr521 [<a
  href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
 
-to the bublisher's website</a>]<br>
+to
+the bublisher's website</a>]<br>
 <br>
 <br>
 <div style="text-align: center;"><img
@@ -92,7 +93,8 @@
 manipulation</span><br>
 - basic <span style="font-weight: bold;">data information </span>(heterozygosity,
 
-numbers of alleles, sample sizes, ...)<br>
+numbers
+of alleles, sample sizes, ...)<br>
 - <span style="font-weight: bold;">HWE</span> and <span
  style="font-weight: bold;">G-statistic</span> <span
  style="font-weight: bold;">tests</span>, F statistics implemented for
@@ -113,10 +115,11 @@
 - Discriminant Analysis of Principal Components (<span
  style="font-weight: bold;">DAPC</span>)<span style="font-weight: bold;">
 </span><br>
-- efficient genome-wise SNP data handling and analysis <img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
-- extraction of SNP data from genomic alignments <img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+- efficient genome-wise SNP data handling and analysis <br>
+- extraction of SNP data from genomic alignments <br>
+- <span style="font-weight: bold;">graph-based clustering</span> of
+genomic data <img style="width: 80px; height: 37px;" alt=""
+ src="images/new.png"><br>
 <span style="font-weight: bold;"><br>
 <span style="text-decoration: underline; font-weight: bold;">Maintainer</span></span><span
  style="text-decoration: underline; font-weight: bold;">:</span>
@@ -125,10 +128,13 @@
 <span style="text-decoration: underline;">Developers:</span> Thibaut
 Jombart (<a href="mailto:tjombart at imperial.ac.uk">tjombart at imperial.ac.uk</a>),
 
-Ismaïl Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
-Anne Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>)<br>
+Ismaïl
+Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
+Anne
+Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>)<br>
 <span style="text-decoration: underline;">Contributors
-(functions/datasets):</span> Péter Sólymos, Christophe
+(functions/datasets/ideas):</span> Péter Sólymos,
+Christophe
 Fraser, Katayoun Moazami-Goudarzi, Denis Laloë, Francois Balloux,
 Dominique Pontier, Daniel Maillard<span style="font-weight: bold;"><br>
 <br>

Modified: www/download.html
===================================================================
--- www/download.html	2012-11-05 16:21:48 UTC (rev 1046)
+++ www/download.html	2012-11-08 11:57:17 UTC (rev 1047)
@@ -29,23 +29,23 @@
 <br>
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 The <span style="font-weight: bold;">current stable version</span>
-(adegenet_1.3-4) is available as:<br>
-- <a href="files/adegenet_1.3-4.tar.gz">linux/unix 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>
+(adegenet_1.3-5) is available as:<br>
+- <a href="files/adegenet_1.3-5.tar.gz">linux/unix 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>
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 The <span style="font-weight: bold;">devel version</span>
-(adegenet_1.3-5) is also available from <a
+(adegenet_1.3-6) 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>
+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> 
-
 <br>
 Patches correct minor bugs or implement new functionnalities, and will
 be included into the next CRAN release. It is recommended to use these
@@ -53,7 +53,8 @@
 (right click -> 'Save link as') in your working directory and type <span
  style="font-family: monospace;">source("[your-patch-file.R]")</span> 
 
-to use a patch.<br>
+to
+use a patch.<br>
 <a href="files/patches/addedFeatures.R"><span
  style="font-family: monospace;">addedFeatures.R</span></a>: (for
 adegenet >=1.3-1) added features not included in the CRAN version of
@@ -63,6 +64,11 @@
 <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 _1.3-4<br>
+- <a href="files/adegenet_1.3-4.tar.gz">linux/unix 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/unix sources</a><br>
 - MacOS X binary<br>

Modified: www/files/adegenet-basics.pdf
===================================================================
--- www/files/adegenet-basics.pdf	2012-11-05 16:21:48 UTC (rev 1046)
+++ www/files/adegenet-basics.pdf	2012-11-08 11:57:17 UTC (rev 1047)
@@ -1,71 +1,135 @@
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 1047

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