[adegenet-commits] r926 - pkg/inst/files www www/files

Wed Jun 22 18:48:50 CEST 2011

Author: jombart
Date: 2011-06-22 18:48:34 +0200 (Wed, 22 Jun 2011)
New Revision: 926

Added:
   pkg/inst/files/AFLP.txt
   www/files/adegenet-basics.pdf
   www/files/adegenet-genomics.pdf
   www/files/adegenet-spca.pdf
   www/files/adegenet_1.3-0.tar.gz
Modified:
   www/documentation.html
   www/download.html
   www/files/adegenet-dapc.pdf
   www/files/adegenet-manual.pdf
   www/news.html
Log:
Updated the webpage for the new release.


Added: pkg/inst/files/AFLP.txt
===================================================================

--- pkg/inst/files/AFLP.txt	                        (rev 0)
+++ pkg/inst/files/AFLP.txt	2011-06-22 16:48:34 UTC (rev 926)
@@ -0,0 +1,8 @@
+	loc1	loc2	loc3	loc4
+indA	1	0	1	1
+indB	0	1	1	1
+indC	1	1	0	1
+indD	0	NA	1	NA
+indE	1	1	0	0
+indF	1	0	1	1
+indG	0	1	1	0

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2011-06-22 15:05:40 UTC (rev 925)
+++ www/documentation.html	2011-06-22 16:48:34 UTC (rev 926)
@@ -37,52 +37,35 @@
  href="files/adegenet-manual.pdf">pdf</a>), which compiles all the
 manpages of the package.<br>
 <br>
-<br>
-<span style="color: rgb(0, 102, 0); font-weight: bold;">Tutorials</span><br>
-</div>
-&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; - anaylis of genetic markers
-using adegenet: an introduction (<a href="files/tutorial.pdf">pdf</a>);
+<span style="color: rgb(0, 102, 0); font-weight: bold;">Tutorials
+vignettes </span><img style="width: 80px; height: 37px;" alt="new"
+ src="images/new.png"><br>
+- <a href="files/adegenet-basics.pdf"><span style="font-style: italic;">adegenet-basics</span></a>:
+introduction to the package;
 accessible from R by typing <span
  style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-basics")</span>.<br>
-<div style="margin-left: 40px;">- <span style="font-weight: bold;">files</span>
-<span style="font-weight: bold;">required</span> for some parts of the
-tutorial<br>
-&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &gt; <a href="files/AFLP.txt">AFLP.txt</a>:
-a
-toy
-dataset
-reproducing
-AFLP
-data
+</div>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - <a
+ href="files/adegenet-spca.pdf"><span style="font-style: italic;">adegenet-spca</span></a>:
+spatial multivariate analysis using adegenet; includes an introduction
+to spatial PCA (sPCA);
+accessible from R by typing <span
+ style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-spca")</span>.<br>
+<div style="margin-left: 40px;">- <a href="files/adegenet-dapc.pdf"><span
+ style="font-style: italic;">adegenet-dapc</span></a>: analysis of the
+genetic structuring of populations;
+includes an introduction to Discriminant Analysis of Principal
+Components (DAPC); accessible from R by typing <span
+ style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-dapc")</span>.<br>
+- <a href="files/adegenet-genomics.pdf"><span
+ style="font-style: italic;">adegenet-genomics</span></a>: introduction
+to the handling of genome-wide SNP data using adegenet;
+accessible from R by typing <span
+ style="font-family: monospace; color: rgb(255, 0, 0);">vignette("adegenet-genomics")</span>.<br>
 <br>
-&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &gt; <a href="files/haplo.txt">haplo.txt</a>:
-a
-toy
-dataset
-reproducing
-haploid
-data
-<br>
-&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &gt; <a href="files/triplo.txt">triplo.txt</a>:
-a
-toy
-dataset
-reproducing
-triploid
-data
-<br>
-<br>
-- a <span style="font-weight: bold;">tutorial for Discriminant
-Analysis of Principal Components</span> (DAPC) (<a
- href="files/adegenet-dapc.pdf">pdf</a>) <img
- style="width: 80px; height: 37px;" alt="new" src="images/new.png"><br>
-<br>
-- <a href="files/worksOnlyInDiploids.txt">worksOnyInDiploids.txt</a>:
-the list of <span style="font-weight: bold;">functions</span> working <span
- style="font-weight: bold;">only for diploid</span> genotypes <br>
-- a <span style="font-weight: bold;">sPCA tutorial</span> (<a
- href="files/tutorial-spca.pdf">pdf</a>), showing how to use the
-spatial Principal Component Analysis (Jombart et al. 2008)<br>
+&nbsp;&nbsp;&nbsp;&nbsp; <br>
+<span style="font-weight: bold; color: rgb(0, 102, 0);">Lectures and
+practicals</span><br>
 - globaldiv summer school 2009, Piacenza, Italie: <a
  href="files/globaldiv-TJ.1.3.pdf">talk</a>
 - <a href="files/globaldiv-PC.1.3.pdf">practical course</a><br>
@@ -112,7 +95,15 @@
 &nbsp;&nbsp;&nbsp; &gt; data (<a href="files/usflu.fasta">DNA sequences</a>,
 <a href="files/usflu.annot.csv">annotations</a>)<br>
 <br>
-Some information can also be found from the archives of the <span
+<br>
+<span style="font-weight: bold; color: rgb(0, 102, 0);">Miscellaneous<br>
+</span>- <a href="files/worksOnlyInDiploids.txt">worksOnyInDiploids.txt</a>:
+the
+list of <span style="font-weight: bold;">functions</span> working <span
+ style="font-weight: bold;">only for diploid</span> genotypes <br>
+<br>
+<br>
+Information can also be found from the archives of the <span
  style="font-weight: bold;">adegenet forum</span>; just enter your
 keywords below:<br>
 <center>

Modified: www/download.html
===================================================================
--- www/download.html	2011-06-22 15:05:40 UTC (rev 925)
+++ www/download.html	2011-06-22 16:48:34 UTC (rev 926)
@@ -31,15 +31,15 @@
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 The
 <span style="font-weight: bold;">current stable version</span>
-(adegenet_1.2-8)
+(adegenet_1.3-0)
 is available as:<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>
+- <a href="files/adegenet_1.3-0.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_1.2-9)
+<span style="font-weight: bold;">devel version</span> (adegenet_1.3-1)
 is also available
 from <a href="https://r-forge.r-project.org/scm/?group_id=120"
  target="_top">R-Forge's
@@ -49,7 +49,8 @@
 <br>
 </span><img alt="" src="images/bullet.png"
  style="width: 10px; height: 10px;">
-<span style="font-weight: bold;">Patches</span> to current version <br>
+<span style="font-weight: bold;">Patches</span> to versions &lt;
+1.3-0&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
@@ -65,14 +66,16 @@
 adegenet_1.2-8
 or
 lower)
-fixes a an issue occuring when trying to
+fixes
+a an issue occuring when trying to
 compute frequences in data consisting in a single monomorphic locus.<br>
 <a href="files/patches/export.R"><span style="font-family: monospace;">export.R</span></a>:
 (for
 adegenet_1.2-7
 or
 lower)
-fixes issues in data conversion from adegenet
+fixes
+issues in data conversion from adegenet
 to hierfstat
 (genind2hierfstat); also fixes <span style="font-family: monospace;">fstat</span>
 function.<br>
@@ -81,7 +84,8 @@
 adegenet_1.2-8
 or
 lower)
-implements new plotting options for dapc scatterplots<span
+implements
+new plotting options for dapc scatterplots<span
  style="font-family: monospace;"> (scatter</span> on <span
  style="font-family: monospace;">dapc</span> objects).<br>
 <a href="files/patches/auxil.R"><span style="font-family: monospace;">auxil.R</span></a>:
@@ -89,7 +93,8 @@
 adegenet_1.2-8
 or
 lower)
-implements useful auxiliary functions for plotting data such as <span
+implements
+useful auxiliary functions for plotting data such as <span
  style="font-family: monospace;">transp</span> or <span
  style="font-family: monospace;">num2col</span>.<br>
 <br>
@@ -97,6 +102,11 @@
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 <span style="font-weight: bold;">Older
 versions</span>:<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>

Added: www/files/adegenet-basics.pdf
===================================================================
--- www/files/adegenet-basics.pdf	                        (rev 0)
+++ www/files/adegenet-basics.pdf	2011-06-22 16:48:34 UTC (rev 926)
@@ -0,0 +1,63762 @@
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+endobj
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+endobj
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+(Object classes)
+endobj
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 926
