[adegenet-commits] r651 - pkg pkg/man www

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Wed Jul 14 12:59:18 CEST 2010 

Author: jombart
Date: 2010-07-14 12:59:18 +0200 (Wed, 14 Jul 2010)
New Revision: 651

Modified:
   pkg/ChangeLog
   pkg/DESCRIPTION
   pkg/man/adegenet.package.Rd
   pkg/man/haploGen.Rd
   pkg/man/seqTrack.Rd
   www/news.html
Log:
On my way to the 1.2-5 release.


Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2010-07-14 09:48:16 UTC (rev 650)
+++ pkg/ChangeLog	2010-07-14 10:59:18 UTC (rev 651)
@@ -1,3 +1,22 @@
+			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
 
 
@@ -31,6 +50,7 @@
 	procedure was not found for genind/genpop objects. Fixed now.
 
 
+
 			CHANGES IN ADEGENET VERSION 1.2-3
 
 

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2010-07-14 09:48:16 UTC (rev 650)
+++ pkg/DESCRIPTION	2010-07-14 10:59:18 UTC (rev 651)
@@ -1,6 +1,6 @@
 Package: adegenet
-Version: 1.2-4
-Date: 2009/04/15
+Version: 1.2-5
+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>
   with contributions of: Peter Solymos, Francois Balloux

Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd	2010-07-14 09:48:16 UTC (rev 650)
+++ pkg/man/adegenet.package.Rd	2010-07-14 10:59:18 UTC (rev 651)
@@ -158,8 +158,8 @@
   \tabular{ll}{
     Package: \tab adegenet\cr
     Type: \tab Package\cr
-    Version: \tab 1.2-4\cr
-    Date: \tab 2009-04-15 \cr
+    Version: \tab 1.2-5\cr
+    Date: \tab 2010-07-14 \cr
     License: \tab GPL (>=2)
   }  
 }

Modified: pkg/man/haploGen.Rd
===================================================================
--- pkg/man/haploGen.Rd	2010-07-14 09:48:16 UTC (rev 650)
+++ pkg/man/haploGen.Rd	2010-07-14 10:59:18 UTC (rev 651)
@@ -40,8 +40,8 @@
               repro=function(){round(rnorm(1,2,1))}, max.nb.haplo=1e3,
               geo.sim=TRUE, grid.size=5, lambda.xy=0.5,
               mat.connect=NULL, ini.n=1, ini.xy=NULL)
-% \method{print}{haploGen}(x, \dots)
-% \method{"["}{haploGen}(x, i, j, drop=FALSE)
+\method{print}{haploGen}(x, \dots)
+\method{[}{haploGen}(x, i, j, drop=FALSE)
 \method{labels}{haploGen}(object, \dots)
 \method{as.POSIXct}{haploGen}(x, tz="", origin=as.POSIXct("2000/01/01"), \dots)
 \method{seqTrack}{haploGen}(x, best=c("min","max"), prox.mat=NULL, \dots)
@@ -111,8 +111,9 @@
 }
 \author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
 \references{
-  Jombart T, Eggo R, Dodd P, Balloux F (accepted) Reconstructing disease
-  outbreaks from genetic data: a graph approach. Heredity.
+  Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease
+  outbreaks from genetic data: a graph approach. Heredity. doi:
+  10.1038/hdy.2010.78.
 }
 \value{
   === haploGen class ===\cr

Modified: pkg/man/seqTrack.Rd
===================================================================
--- pkg/man/seqTrack.Rd	2010-07-14 09:48:16 UTC (rev 650)
+++ pkg/man/seqTrack.Rd	2010-07-14 10:59:18 UTC (rev 651)
@@ -90,8 +90,9 @@
   Thibaut Jombart \email{t.jombart at imperial.ac.uk}
 }
 \references{
-  Jombart T, Eggo R, Dodd P, Balloux F (accepted) Reconstructing disease
-  outbreaks from genetic data: a graph approach. Heredity.
+  Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease
+  outbreaks from genetic data: a graph approach. Heredity. doi:
+  10.1038/hdy.2010.78.
 }
 \value{
   === output of seqTrack ===\cr

Modified: www/news.html
===================================================================
--- www/news.html	2010-07-14 09:48:16 UTC (rev 650)
+++ www/news.html	2010-07-14 10:59:18 UTC (rev 651)
@@ -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"
@@ -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.2.10.1.<br>
+1.2-4 </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
@@ -46,8 +46,9 @@
  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);">1.2-4</span>)
-has been released for R-2.10.1 !</big><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
+has
+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.
 Once 'stable', these new functionalities will give rise to the major
@@ -75,7 +76,8 @@
 <span style="font-weight: bold;">02/04/2009 </span><span
  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>
+has
+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
@@ -91,37 +93,46 @@
 ploidy. Another noticeable feature is that SNPs can be obtained from
 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
+time,
+the tutorial has been updated at the same time as the package
 release!<br>
 <br>
 <br>
 </span></span><span style="font-weight: bold;">19/12/2008 </span><span
  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>
+has
+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
+new,
+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
+levels
+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
+which
+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
+which
+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... <a href="files/ChangeLog">several other things</a>!<br>
+And...
+<a href="files/ChangeLog">several other things</a>!<br>
 </span></span><br>
 <br>
 <span style="font-weight: bold;">03/08/2008 </span><span
  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>
+has
+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
+new
+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
@@ -131,9 +142,11 @@
 <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>
+has
+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
+major
+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>
@@ -159,9 +172,11 @@
 <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>
+has
+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
+release
+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>
@@ -190,16 +205,19 @@
 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
+is
+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>
 <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>
+has
+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>
+release
+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
@@ -221,8 +239,8 @@
 given threshold, it is also possible to ask for a given length of
 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>
+The
+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
@@ -245,9 +263,11 @@
 <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>
+has
+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>
+totally
+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
@@ -292,7 +312,8 @@
 was released for R.2.5.1. <br>
 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>
+and
+adds the following elements:<br>
 <br>
 - <span style="font-family: monospace;"><span
  style="color: rgb(255, 0, 0);">adegenetWeb</span> </span>is a simple
@@ -303,7 +324,8 @@
 genotypes sampled from two distinct populations.<br>
 - <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
+adding
+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>

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