[adegenet-commits] r91 - pkg/inst pkg/man www

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Apr 10 14:20:22 CEST 2008 

Author: jombart
Date: 2008-04-10 14:20:22 +0200 (Thu, 10 Apr 2008)
New Revision: 91

Modified:
   pkg/inst/CITATION
   pkg/man/adegenet.package.Rd
   www/acceuil.html
   www/documentation.html
Log:
Update the reference to adegenet.


Modified: pkg/inst/CITATION
===================================================================
--- pkg/inst/CITATION	2008-04-07 14:20:58 UTC (rev 90)
+++ pkg/inst/CITATION	2008-04-10 12:20:22 UTC (rev 91)
@@ -4,7 +4,7 @@
 entry="Article",
 title = "adegenet: a R package for the multivariate analysis of genetic markers",
 journal= "Bioinformatics",
-year = "in press",
+year = "2008",
 author = "T. Jombart",
-textVersion = "Jombart, T. (in press) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics"
+textVersion = "Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. doi: 10.1093/bioinformatics/btn129"
 )

Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2008-04-07 14:20:58 UTC (rev 90)
+++ pkg/man/adegenet.package.Rd	2008-04-10 12:20:22 UTC (rev 91)
@@ -92,7 +92,7 @@
    For more information, visit the adegenet website by typing
    \code{adegenetWeb()}.\cr
 
-   To cite adegenet, please use \code{citation("adegenet")}.
+   To cite adegenet, please use the reference given by \code{citation("adegenet")}.
  }
 \details{
   \tabular{ll}{
@@ -105,6 +105,9 @@
 }
 \author{Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>}
 \references{
+Jombart T. (2008) adegenet: a R package for the multivariate analysis of genetic markers
+\emph{Bioinformatics}. doi: 10.1093/bioinformatics/btn129\cr
+  
   See adegenet website: \url{http://adegenet.r-forge.r-project.org/}
 }
 \keyword{manip}

Modified: www/acceuil.html
===================================================================
--- www/acceuil.html	2008-04-07 14:20:58 UTC (rev 90)
+++ www/acceuil.html	2008-04-10 12:20:22 UTC (rev 91)
@@ -24,9 +24,14 @@
 analysis. It is currently hosted by <a
  href="https://r-forge.r-project.org/projects/adegenet/" target="_top">R-Forge</a>.
 adegenet is described in the following application note:<br>
-Jombart, T. (<span style="font-style: italic;">in press</span>)
-adegenet: a R package for the multivariate analysis of genetic markers.
-<span style="font-style: italic;">Bioinformatics</span><br>
+<span style="font-style: italic;"></span>Jombart T. (<span
+ style="font-style: italic;"></span>2008)<span
+ style="font-weight: bold;"> </span>adegenet: a R
+package for the multivariate analysis of genetic markers. <span
+ style="font-style: italic;">Bioinformatics</span>. doi:
+10.1093/bioinformatics/btn129
+[<a href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129">link</a>
+to a free pdf]<br>
 <br>
 <div style="text-align: left;">
 <table style="width: 95%; text-align: left;" border="0" cellpadding="2"
@@ -43,22 +48,23 @@
     </tr>
   </tbody>
 </table>
-adegenet main features are:<br>
+<span style="text-decoration: underline;">Main features of adegenet are:</span><br>
 </div>
 <br>
 - definition of new object <span style="font-weight: bold;">classes</span>
 to facilitate multivariate analysis<br>
 - data <span style="font-weight: bold;">import</span> from GENETIX,
-Genepop, Fstat, Easypop, or any dataframe of genotypes<br>
+STRUCTURE, Genepop, Fstat, Easypop, or any dataframe of genotypes<br>
 - data <span style="font-weight: bold;">export</span> to the R
 packages genetics, hierfstat, LDheatmap<br>
 - <span style="font-weight: bold;">HWE</span> and <span
  style="font-weight: bold;">G-statistic</span> <span
- style="font-weight: bold;">tests</span> implemented for adegenet
+ style="font-weight: bold;">tests</span>, F statistics implemented for
+adegenet
 objects<br>
 - computation of <span style="font-weight: bold;">genetic</span> <span
  style="font-weight: bold;">distances<br>
-</span>- basic data information and functions for <span
+</span>- basic data information and advanced functions for <span
  style="font-weight: bold;">data handling<br>
 </span>- methods for <span style="font-weight: bold;">spatial
 genetics: Monmonier algorithm, spatial PCA, tests for global and local

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2008-04-07 14:20:58 UTC (rev 90)
+++ www/documentation.html	2008-04-10 12:20:22 UTC (rev 91)
@@ -31,17 +31,22 @@
 functionalities of the package.<br>
 <br>
 <span style="text-decoration: underline;">Related publications:</span><br>
-- a paper presenting the sPCA, global and local tests [<b>Jombart T, </b>Devillard
-S, Dufour AB, Pontier D<b> </b>(in
-press)<b> </b>Revealing
+- a paper presenting the sPCA, global and local tests:<br>
+&nbsp;&nbsp;&nbsp; <b>Jombart T, </b>Devillard
+S, Dufour AB, Pontier D<b> </b>(<span style="font-style: italic;">in
+press</span>)<b> </b>Revealing
 cryptic spatial patterns in genetic variability by a new multivariate
-method. <span style="font-style: italic;">Heredity</span>.]<br>
-- an application note presenting the adegenet package [<span
- style="font-weight: bold;">Jombart T</span>.<span
- style="font-weight: bold;"> </span>(<span style="font-style: italic;">in
-press</span>)<span style="font-weight: bold;"> </span>adegenet: a R
+method. <span style="font-style: italic;">Heredity</span>.<br>
+- an application note presenting the adegenet package:<br>
+&nbsp;&nbsp;&nbsp; <span style="font-style: italic; font-weight: bold;"></span><span
+ style="font-weight: bold;">Jombart T.</span> (<span
+ style="font-style: italic;"></span>2008)<span
+ style="font-weight: bold;"> </span>adegenet: a R
 package for the multivariate analysis of genetic markers. <span
- style="font-style: italic;">Bioinformatics</span>.]<br>
+ style="font-style: italic;">Bioinformatics</span>. doi:
+10.1093/bioinformatics/btn129
+[<a href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129">link</a>
+to a free pdf]<br>
 <span style="color: rgb(255, 0, 0);"></span></div>
 </body>
 </html>

More information about the adegenet-commits mailing list