[adegenet-commits] r657 - pkg pkg/R pkg/man www www/files www/images

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Jul 31 11:30:05 CEST 2010 

Author: jombart
Date: 2010-07-31 11:30:05 +0200 (Sat, 31 Jul 2010)
New Revision: 657

Modified:
   pkg/DESCRIPTION
   pkg/R/zzz.R
   pkg/man/adegenet.package.Rd
   pkg/man/haploGen.Rd
   pkg/man/seqTrack.Rd
   www/acceuil.html
   www/download.html
   www/files/ChangeLog
   www/images/sshotstart.png
   www/literature.html
   www/news.html
Log:
Updated stuff for new release.


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2010-07-21 15:14:58 UTC (rev 656)
+++ pkg/DESCRIPTION	2010-07-31 09:30:05 UTC (rev 657)
@@ -1,5 +1,5 @@
 Package: adegenet
-Version: 1.2-5
+Version: 1.2-6
 Date: 2010/07/14
 Title: adegenet: a R package for the multivariate analysis of genetic markers.
 Author:  Thibaut Jombart <t.jombart at imperial.ac.uk>

Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R	2010-07-21 15:14:58 UTC (rev 656)
+++ pkg/R/zzz.R	2010-07-31 09:30:05 UTC (rev 657)
@@ -2,7 +2,7 @@
 #.initAdegenetClasses()
 #.initAdegenetUtils()
     library.dynam("adegenet", pkg, lib)
-    startup.txt <- "   ==========================\n    adegenet 1.2-5 is loaded\n   ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n"
+    startup.txt <- "   ==========================\n    adegenet 1.2-6 is loaded\n   ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n"
 
     packageStartupMessage(startup.txt)
 

Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2010-07-21 15:14:58 UTC (rev 656)
+++ pkg/man/adegenet.package.Rd	2010-07-31 09:30:05 UTC (rev 657)
@@ -158,7 +158,7 @@
   \tabular{ll}{
     Package: \tab adegenet\cr
     Type: \tab Package\cr
-    Version: \tab 1.2-5\cr
+    Version: \tab 1.2-6\cr
     Date: \tab 2010-07-14 \cr
     License: \tab GPL (>=2)
   }  

Modified: pkg/man/haploGen.Rd
===================================================================
--- pkg/man/haploGen.Rd	2010-07-21 15:14:58 UTC (rev 656)
+++ pkg/man/haploGen.Rd	2010-07-31 09:30:05 UTC (rev 657)
@@ -101,7 +101,7 @@
   \item{n}{an integer indicating the number of haplotypes to be retained
     in the sample}
   \item{from, to}{arguments of the conversion function, for converting a
-    \code{haploGen} object into a \linkS4class{graphNEL}.}
+    \code{haploGen} object into a \code{\link[graph]{graphNEL-class}}.}
   \item{tz, origin}{ aguments to be passed to \code{\link{as.POSIXct}}
     (see ?as.POSIXct)}
   \item{\dots}{further arguments to be passed to other methods}
@@ -142,7 +142,7 @@
   \code{install.packages("ape")}
 
   - for various purposes including plotting, converting genealogies to
-  graphs (\linkS4class{graphNEL} class) can be useful. This requires the
+  graphs (\code{\link[graph]{graphNEL-class}} class) can be useful. This requires the
   packages graph, and possibly Rgraphviz for plotting. These packages are
   not on CRAN, but on Bioconductor. To install them, use:\cr
   source("http://bioconductor.org/biocLite.R")\cr
@@ -153,7 +153,7 @@
 
 
   === Converting haploGen objects to graphs ===\cr
-  \code{haploGen} objects can be converted to \linkS4class{graphNEL}
+  \code{haploGen} objects can be converted to \code{\link[graph]{graphNEL-class}}
   objects, which can in turn be plotted and manipulated using classical
   graph tools. Simply use 'as(x, "graphNEL")' where 'x' is a
   \code{haploGen} object. This functionality requires the \code{graph}

Modified: pkg/man/seqTrack.Rd
===================================================================
--- pkg/man/seqTrack.Rd	2010-07-21 15:14:58 UTC (rev 656)
+++ pkg/man/seqTrack.Rd	2010-07-31 09:30:05 UTC (rev 657)
@@ -133,7 +133,7 @@
 
   
   === Converting seqTrack objects to graphs ===\cr
-  seqTrack objects can be converted to \linkS4class{graphNEL} objects,
+  seqTrack objects can be converted to \code{\link[graph]{graphNEL-class}} objects,
   which can in turn be plotted and manipulated using classical graph
   tools. Simply use 'as(x, "graphNEL")' where 'x' is a seqTrack
   object. This functionality requires the \code{graph} package. Note

Modified: www/acceuil.html
===================================================================
--- www/acceuil.html	2010-07-21 15:14:58 UTC (rev 656)
+++ www/acceuil.html	2010-07-31 09:30:05 UTC (rev 657)
@@ -1,4 +1,4 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <html>
 <head>
   <meta content="text/html; charset=ISO-8859-1"
@@ -19,8 +19,10 @@
 package dedicated to the multivariate analysis of genetic
 markers. This package is related to <a
  href="http://pbil.univ-lyon1.fr/ADE-4/home.php?lang=eng" target="_top">ade4</a>,
-a R
-package for multivariate analysis, graphics, phylogeny and spatial
+a
+R
+package
+for multivariate analysis, graphics, phylogeny and spatial
 analysis. It is kindly hosted by <a
  href="https://r-forge.r-project.org/projects/adegenet/" target="_top">R-Forge</a>.
 <br>
@@ -67,7 +69,9 @@
 </span>- basic and advanced <span style="font-weight: bold;">data
 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
@@ -82,6 +86,12 @@
 global and local
 structuring, </span><span style="font-weight: bold;">Monmonier
 algorithm<br>
+</span>- the <span style="font-style: italic; font-weight: bold;">seqTrack</span><span
+ style="font-weight: bold;">
+algorithm </span>for reconstructing genealogies of haplotypes<span
+ style="font-weight: bold;"><br>
+</span>- simulation of <span style="font-weight: bold;">genealogies of
+haplotypes<br>
 <br>
 <br>
 </span><span style="text-decoration: underline;">Author:</span> Thibaut

Modified: www/download.html
===================================================================
--- www/download.html	2010-07-21 15:14:58 UTC (rev 656)
+++ www/download.html	2010-07-31 09:30:05 UTC (rev 657)
@@ -18,15 +18,15 @@
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 The
 <span style="font-weight: bold;">current stable version</span>
-(adegenet_1.2-4)
+(adegenet_1.2-5)
 is available as:<br>
-- <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-4.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-4.zip">Windows binary</a><br>
+- linux/unix sources<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_1.2-4)
+<span style="font-weight: bold;">devel version</span> (adegenet_1.2-6)
 is also available
 from <a href="https://r-forge.r-project.org/scm/?group_id=120"
  target="_top">R-Forge's
@@ -47,21 +47,15 @@
 use
 a
 patch.<br>
-- <a href="files/patches/loadingplot.R"><span
- style="font-family: monospace;">loadingplot.R</span></a>: a few checks
-added when the 'at' argument the specified<br>
-- <a href="files/patches/chooseCN.R"><span
- style="font-family: monospace;"><span
- style="text-decoration: underline;">chooseCN</span></span></a><a
- href="files/patches/chooseCN.R"><span style="font-family: monospace;">.R</span></a>:
-new checks
-about duplicated locations, which are problematic with some types of
-graph<br>
 <br>
-<br>
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 <span style="font-weight: bold;">Older
 versions</span>:<br>
+adegenet_1.2-4<br>
+- <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-4.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-4.zip">Windows binary</a><br>
+<br>
 adegenet_1.3-3<br>
 - <a href="files/adegenet_1.2-3.tar.gz">linux/unix sources</a><br>
 - <a href="files/adegenet_1.2-3.tgz">MacOS X binary</a><br>

Modified: www/files/ChangeLog
===================================================================
--- www/files/ChangeLog	2010-07-21 15:14:58 UTC (rev 656)
+++ www/files/ChangeLog	2010-07-31 09:30:05 UTC (rev 657)
@@ -1,3 +1,56 @@
+			CHANGES IN ADEGENET VERSION 1.2-5
+
+
+NEW FEATURES
+
+	o SeqTrack, an algorithm for the reconstruction of genealogies, is
+	now fully implemented and documented.
+
+	o haploGen, a system for simulating genealogies, is now fully
+	implemented and documented.
+
+
+BUG FIXES
+
+	o summary methods for genind and genpop are fixed (again) for the
+	new R version 2.11.1.
+
+
+
+			CHANGES IN ADEGENET VERSION 1.2-4
+
+
+NEW FEATURES
+
+	o Hs computes the theoretical heterozygosity by populations for
+	genpop object
+
+	o propShared is now available for haploid data
+
+	o Discriminant Analysis of Principal Component (DAPC) is
+	implemented by the function DAPC, although the method itself is
+	still under review.
+
+	o The SeqTrack algorithm for reconstructing genealogies is
+	implemented by the function seqTrack, although the method itself
+	is still under review.
+
+	o Pre-release of new simulation tools, still undocumented
+	(haploPop and haploGen).
+
+	o New datasets eHGDP and H3N2
+
+
+BUG FIXES
+
+	o minor bug fixes in df2genind, propShared, and seploc
+
+	o summary issue arised in certain conditions, depending on which
+	package was loaded before adegenet; in some cases, the summary
+	procedure was not found for genind/genpop objects. Fixed now.
+
+
+
 			CHANGES IN ADEGENET VERSION 1.2-3
 
 

Modified: www/images/sshotstart.png
===================================================================
(Binary files differ)

Modified: www/literature.html
===================================================================
--- www/literature.html	2010-07-21 15:14:58 UTC (rev 656)
+++ www/literature.html	2010-07-31 09:30:05 UTC (rev 657)
@@ -64,7 +64,17 @@
 <br>
 <div style="margin-left: 40px;"><span
  style="font-family: monospace; font-weight: bold;"></span><span
- style="font-family: monospace; font-weight: bold;"></span><br>
+ style="font-family: monospace; font-weight: bold;"></span>- the paper
+presenting the <span style="font-style: italic;">SeqTrack </span>algorithm
+(<span style="font-family: monospace; color: rgb(255, 0, 0);">seqTrack</span>),
+and
+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) Reconstructing
+disease outbreaks from genetic data: a graph approach. <span
+ style="font-style: italic;">Heredity</span>. Doi: 10.1038/hdy.2010.78<br>
+<br>
+<br>
 <span style="text-decoration: underline;">Publications citing
 adegenet:</span><br style="text-decoration: underline;">
 <br>

Modified: www/news.html
===================================================================
--- www/news.html	2010-07-21 15:14:58 UTC (rev 656)
+++ www/news.html	2010-07-31 09:30:05 UTC (rev 657)
@@ -18,7 +18,7 @@
  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
-1.2-4 </span>for R.2.11.1.<br>
+1.2-5 </span>for R.2.11.1.<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
@@ -28,9 +28,38 @@
 Next major release will be 1.3-0, and will include the stable versions
 of SeqTrack algorithm, DAPC, and new simulation tools.<br>
 <br>
+<span style="font-weight: bold;"><br>
+30/07/2010 <img style="width: 80px; height: 37px;" alt=""
+ src="images/new.png"></span><span style="font-weight: bold;"></span><br>
+<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-5</span>)
+has
+been
+released
+for R-2.11.1!</big><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);">
+This release includes a stable implementation of the <span
+ style="font-style: italic;">SeqTrack </span>algorithm&nbsp;</span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
+(see literature section for a reference) for reconstructing genealogies
+of haplotypes; see<span style="color: rgb(255, 0, 0);"> </span><span
+ style="font-family: monospace; color: rgb(255, 0, 0);">?seqTrack</span>
+</span></span><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"> for more information. A new tool for
+simulating genealogies of haplotypes has also been implemented (see </span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
+ style="color: rgb(255, 0, 0);"></span><span
+ style="font-family: monospace; color: rgb(255, 0, 0);">?haploGen</span></span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">).
+Minor issues pertaining to the definition of summary methods for genind
+and genpop objects have been fixed. 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 information.</span></span><br>
 <br>
-<span style="font-weight: bold;">19/04/2010 <img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"></span><span
+<br>
+<span style="font-weight: bold;">19/04/2010 </span><span
  style="font-weight: bold;"></span><br>
 <big>New version of the adegenet tutorial online.</big><span
  style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
@@ -42,12 +71,13 @@
 </span></span><span style="color: rgb(255, 0, 0);"><span
  style="color: rgb(0, 0, 0);"></span></span><br>
 <br>
-<span style="font-weight: bold;">19/04/2010 <img
- style="width: 80px; height: 37px;" alt="" src="images/new.png"></span><span
+<span style="font-weight: bold;">19/04/2010 </span><span
  style="font-weight: bold;"></span><br>
 <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-4</span>)
 has
-been released for R-2.10.1 !</big><span style="color: rgb(255, 0, 0);"><span
+been
+released
+for R-2.10.1 !</big><span style="color: rgb(255, 0, 0);"><span
  style="color: rgb(0, 0, 0);">
 This release corrects a few issues and bugs from previous version, and
 includes new material currently under review in scientific journals.
@@ -60,8 +90,7 @@
  style="color: rgb(0, 0, 0);"></span></span><br>
 <br>
 <span style="font-weight: bold;">15/04/2010 </span><span
- style="font-weight: bold;"><img style="width: 80px; height: 37px;"
- alt="" src="images/new.png"></span><span style="font-weight: bold;"></span><br>
+ style="font-weight: bold;"></span><span style="font-weight: bold;"></span><br>
 <big>The adegenet forum's archives can now be searched from this
 website.</big><span style="color: rgb(255, 0, 0);"><span
  style="color: rgb(0, 0, 0);"> Look at the 'contact' section for more
@@ -77,7 +106,9 @@
  style="font-weight: bold;"></span><br>
 <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-3</span>)
 has
-been released for R.2.8.1 !</big><br>
+been
+released
+for R.2.8.1 !</big><br>
 This is a important<span style="color: rgb(255, 0, 0);"><span
  style="color: rgb(0, 0, 0);"> release, including some significant
 improvements
@@ -94,7 +125,9 @@
 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
+the
+tutorial
+has been updated at the same time as the package
 release!<br>
 <br>
 <br>
@@ -102,23 +135,32 @@
  style="font-weight: bold;"></span><br>
 <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-2</span>)
 has
-been released for R.2.8.0 !</big><br>
+been
+released
+for R.2.8.0 !</big><br>
 <span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
 new,
-big release implements many new things and corrects a few bugs
+big
+release
+implements many new things and corrects a few bugs
 (see </span></span><a href="files/ChangeLog">ChangeLog</a><span
  style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
 file). Amongst the biggest news, <span style="font-weight: bold;">several
 levels
-of ploidy</span> are now handled throughout the package, apart
+of
+ploidy</span> are now handled throughout the package, apart
 from a few exceptions. New graphics are available for multivariate
 methods: the <span
  style="font-family: monospace; color: rgb(255, 0, 0);">colorplot</span>,
 which
-can represent genetic diversity using RGB scale, and a <span
+can
+represent
+genetic diversity using RGB scale, and a <span
  style="font-family: monospace; color: rgb(255, 0, 0);">loadingplot</span>,
 which
-can be used to assess the most structuring alleles and loci in an
+can
+be
+used to assess the most structuring alleles and loci in an
 analysis.&nbsp; A new georeferenced genetic dataset is also available
 (dataset <span style="color: rgb(255, 0, 0); font-family: monospace;">rupica</span>).
 And...
@@ -129,24 +171,33 @@
  style="font-weight: bold;"></span><br>
 <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-1</span>)
 has
-been released for R.2.7.1 !</big><br>
+been
+released
+for R.2.7.1 !</big><br>
 <span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
 new
-release corrects a few bugs arising in version 1.2-0 (see </span></span><a
+release
+corrects
+a few bugs arising in version 1.2-0 (see </span></span><a
  href="files/ChangeLog">ChangeLog</a><span
  style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
 file), especially an issue with the detection of NAs. Documentation was
 also improved (have a look at <span
  style="font-family: monospace; color: rgb(255, 0, 0);">?scaleGen</span>).<br>
 </span></span><br>
+<br>
 <span style="font-weight: bold;">09/07/2008 </span><span
  style="font-weight: bold;"></span><br>
 <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-0</span>)
 has
-been released for R.2.7.1 !</big><br>
+been
+released
+for R.2.7.1 !</big><br>
 <span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
 major
-release implements various levels of ploidy and adds some new
+release
+implements
+various levels of ploidy and adds some new
 features (see </span></span><a href="files/ChangeLog">ChangeLog</a><span
  style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
 file):<br>
@@ -168,15 +219,20 @@
 implemented as methods for 'as' and as old S3 coercion (e.g.,
 'as.data.frame([myGenindObject])'). Coercion to matrix, data.frame and
 ktab (from ade4 package).<br>
+<br>
 &nbsp; <br>
 <span style="font-weight: bold;">02/06/2008 </span><span
  style="font-weight: bold;"></span><br>
 <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.1-2</span>)
 has
-been released for R.2.7.0 !</big><br>
+been
+released
+for R.2.7.0 !</big><br>
 <span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
 release
-corrects a few bugs and adds some new features (see </span></span><a
+corrects
+a
+few bugs and adds some new features (see </span></span><a
  href="files/ChangeLog">ChangeLog</a><span
  style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
 file):<br>
@@ -202,22 +258,30 @@
 </span><span style="color: rgb(255, 0, 0);"><span
  style="color: rgb(0, 0, 0);"></span></span><span
  style="font-weight: bold;"><br>
+<br>
 30/04/2008 </span><span style="font-weight: bold;"></span><br>
 The new function '<span
  style="font-family: monospace; color: rgb(255, 0, 0);">propShared</span>'
 is
-available from the devel version of adegenet. It computes the <span
+available
+from
+the devel version of adegenet. It computes the <span
  style="color: rgb(255, 0, 0);">proportion of shared alleles</span>
 among a set of genotypes.<br>
 <br>
+<br>
 <span style="font-weight: bold;">09/04/2008 </span><span
  style="font-weight: bold;"></span><br>
 <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.1-1</span>)
 has
-been released for R.2.6.2 !</big><br>
+been
+released
+for R.2.6.2 !</big><br>
 <span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
 release
-corrects a few bugs and adds some new features:<br>
+corrects
+a
+few bugs and adds some new features:<br>
 &nbsp;&nbsp;&nbsp; - <span style="font-family: monospace;"></span></span></span><span
  style="text-decoration: underline;">I/O:</span> <span
  style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
@@ -240,7 +304,8 @@
 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>
+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 given exponent.<br>
 &nbsp;&nbsp;&nbsp; - <span style="text-decoration: underline;">F
@@ -254,20 +319,26 @@
 slot are now proceeded
 wisely when objects are subsetted using the '[' operator.<br>
 <br>
+<br>
 <span style="font-weight: bold;">15/02/2008 </span><span
  style="font-weight: bold;"><br>
 </span><span style="font-weight: bold;"></span>A tutorial for the new
 version
 of adegenet is available from this website.<br>
 <br>
+<br>
 <span style="font-weight: bold;">14/02/2008 </span><span
  style="font-weight: bold;"></span><big><span style="font-weight: bold;"><br>
 </span><small>New adegenet version (<span style="color: rgb(255, 0, 0);">1.1-0</span>)
 has
-been released for R.2.6.2.</small></big><br>
+been
+released
+for R.2.6.2.</small></big><br>
 <span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
 totally
-new version includes:<br>
+new
+version
+includes:<br>
 &nbsp;&nbsp;&nbsp; - <span style="text-decoration: underline;">Data
 representation:</span> </span></span><span
  style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">S4
@@ -293,12 +364,14 @@
 Accessors to genind and genpop object like with matrices using 'foo[
 chosenGenotypes, chosenAlleles]'.<br>
 <br>
+<br>
 <span style="font-weight: bold;">07/01/2008 </span><span
  style="font-weight: bold;"></span><span style="font-weight: bold;"><br>
 </span>adegenet is now a project on <a
  href="https://r-forge.r-project.org/projects/adegenet/" target="_top">R-Forge</a>.
 <span style="font-weight: bold;"><br>
 </span><br>
+<br>
 <span style="font-weight: bold;">12/09/2007 </span><span
  style="font-weight: bold;"></span><span style="font-weight: bold;"><br>
 </span>Release of a new version of the <span
@@ -306,6 +379,7 @@
 section in this site), showing how to find genetic boundaries using
 Monmonier's algorithm.<br>
 <br>
+<br>
 <span style="font-weight: bold;">12/09/2007 </span><span
  style="font-weight: bold;"></span><span style="font-weight: bold;"><br>
 </span>adegenet version <span style="color: rgb(255, 0, 0);">1.0-2</span>
@@ -313,8 +387,9 @@
 This new version corrects a few bugs (especially in <span
  style="font-family: monospace; color: rgb(255, 0, 0);">optimize.monmonier</span>)
 and
-adds the following elements:<br>
-<br>
+adds
+the
+following elements:<br>
 - <span style="font-family: monospace;"><span
  style="color: rgb(255, 0, 0);">adegenetWeb</span> </span>is a simple
 function opening the adegenet website in the default web browser.<br>
@@ -325,22 +400,25 @@
 - <span style="color: rgb(255, 0, 0); font-family: monospace;">monmonier</span>
 documentation was improved <span style="color: rgb(255, 0, 0);"></span>by
 adding
-a genetic example, using <span
+a
+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>
+<br>
 30/08/2007 </span><span style="font-weight: bold;"><br>
 </span>A new section is added to the <span
  style="color: rgb(255, 0, 0);">download </span>section: <span
  style="color: rgb(255, 0, 0);">patches</span> correcting bugs or
 improving functions of the current version of adegenet.<br>
 <br>
+<br>
 <span style="font-weight: bold;">25/08/2007 </span><span
  style="font-weight: bold;"></span><span style="font-weight: bold;"><br>
 </span>adegenet version 1.0-1 was released for R.2.5.1. <br>
 This new version corrects a few bugs (basically in import/export
 functions) and adds the following functions:<br>
-<br>
 - <span style="font-family: monospace;"><span
  style="color: rgb(255, 0, 0);">chooseCN</span> </span>is a simple
 interactive tool for choosing and building a connection network from
@@ -361,10 +439,12 @@
 boundaries among individuals or populations based on their allelic
 frequencies and spatial coordinates. <br>
 <span style="font-weight: bold;"></span><br>
+<br>
 <span style="font-weight: bold;">24/04/2007</span><span
  style="font-weight: bold;"></span><br>
 <span style="font-weight: bold;"></span>This website arrives on the web.<br>
 <br>
+<br>
 <span style="font-weight: bold;">10/04/2007 <br>
 </span>adegenet first release as an
 official <span style="text-decoration: underline;"><a

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