[adegenet-commits] r690 - pkg/man www

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2010-10-18 17:20:58 +0200 (Mon, 18 Oct 2010)
New Revision: 690

Modified:
   pkg/man/adegenet.package.Rd
   pkg/man/dapc.Rd
   pkg/man/find.clusters.Rd
   www/literature.html
Log:
updating the references
- added dapc paper - 


Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2010-10-18 14:50:03 UTC (rev 689)
+++ pkg/man/adegenet.package.Rd	2010-10-18 15:20:58 UTC (rev 690)
@@ -177,19 +177,25 @@
   Dominique Pontier, Daniel Maillard, Francois Balloux
 }
 \references{
-  Jombart T. (2008) adegenet: a R package for the multivariate analysis of
-  genetic markers \emph{Bioinformatics} 24: 1403-1405. doi: 10.1093/bioinformatics/btn129\cr
+  Jombart T. (2008) adegenet: a R package for the multivariate analysis
+  of genetic markers \emph{Bioinformatics} 24: 1403-1405. doi:
+  10.1093/bioinformatics/btn129\cr
 
+  Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
+  principal components: a new method for the analysis of genetically
+  structured populations. BMC Genetics 11:94.
+  doi:10.1186/1471-2156-11-94\cr
+
   Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease
   outbreaks from genetic data: a graph approach. \emph{Heredity}. doi:
   10.1038/hdy.2010.78.\cr
+  
+  Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D.  Revealing
+  cryptic spatial patterns in genetic variability by a new multivariate
+  method. \emph{Heredity}, \bold{101}, 92--103.\cr
 
-  Jombart, T., Devillard, S. and Balloux, F.
-  Discriminant analysis of principal components: a new method for the analysis of
-  genetically structured populations. Submitted to \emph{BMC genetics}.\cr
-
   See adegenet website: \url{http://adegenet.r-forge.r-project.org/}\cr
-
+  
   Please post your questions on 'the adegenet forum': adegenet-forum at lists.r-forge.r-project.org
 
 }

Modified: pkg/man/dapc.Rd
===================================================================
--- pkg/man/dapc.Rd	2010-10-18 14:50:03 UTC (rev 689)
+++ pkg/man/dapc.Rd	2010-10-18 15:20:58 UTC (rev 690)
@@ -168,9 +168,10 @@
   - \code{scatter.dapc, assignplot} return the matched call.\cr
 }
 \references{
-Jombart, T., Devillard, S. and Balloux, F.
-Discriminant analysis of principal components: a new method for the analysis of
-genetically structured populations. Submitted to \emph{BMC genetics}.
+  Jombart T, Devillard S and Balloux F  (2010) Discriminant analysis of
+  principal components: a new method for the analysis of genetically
+  structured populations. BMC Genetics
+  11:94. doi:10.1186/1471-2156-11-94
 }
 \seealso{
   - \code{\link{find.clusters}}: to identify clusters without prior.

Modified: pkg/man/find.clusters.Rd
===================================================================
--- pkg/man/find.clusters.Rd	2010-10-18 14:50:03 UTC (rev 689)
+++ pkg/man/find.clusters.Rd	2010-10-18 15:20:58 UTC (rev 690)
@@ -152,9 +152,10 @@
   \item{size}{an \code{integer} vector giving the size of the different clusters.}
 }
 \references{
-Jombart, T., Devillard, S. and Balloux, F.
-Discriminant analysis of principal components: a new method for the analysis of
-genetically structured populations. Submitted to \emph{Genetics}.
+  Jombart T, Devillard S and Balloux F  (2010) Discriminant analysis of
+  principal components: a new method for the analysis of genetically
+  structured populations. BMC Genetics
+  11:94. doi:10.1186/1471-2156-11-94
 }
 \seealso{
   - \code{\link{dapc}}: implements the DAPC.

Modified: www/literature.html
===================================================================
--- www/literature.html	2010-10-18 14:50:03 UTC (rev 689)
+++ www/literature.html	2010-10-18 15:20:58 UTC (rev 690)
@@ -45,9 +45,10 @@
 abstract</a>]<br>
 <br>
 - the paper presenting the <span style="font-style: italic;">spatial
-principal component analysis</span> (<span
- style="font-family: monospace; color: rgb(255, 0, 0);">spca</span>),
-global and local tests (<span
+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 local tests (<span
  style="font-family: monospace; color: rgb(255, 0, 0);">global.rtest</span>
 and <span style="font-family: monospace; color: rgb(255, 0, 0);">local.rtest</span>):<br>
 <b>Jombart T, </b>Devillard
@@ -70,13 +71,24 @@
 and
 simulations
 of
-genealoies of haplotypes (<span
+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) Reconstructing
 disease outbreaks from genetic data: a graph approach. <span
  style="font-style: italic;">Heredity</span>. Doi: 10.1038/hdy.2010.78<br>
 <br>
+- the paper introducing the <span style="font-style: italic;">Discriminant
+Analysis 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>
+</span>and <span style="font-family: monospace; color: rgb(255, 0, 0);">dapc</span>):<br>
+<b>Jombart T</b>, Devillard S and Balloux F <b> </b>(2010)
+Discriminant analysis of principal components: a new method for the
+analysis of genetically structured populations. <i>BMC Genetics</i> <strong>11</strong><strong>:</strong>94.
+<span>doi:10.1186/1471-2156-11-94</span><br>
 <br>
+<br>
 <span style="text-decoration: underline;">Publications citing
 adegenet:</span><br style="text-decoration: underline;">
 <br>