[adegenet-commits] r604 - pkg pkg/R pkg/man pkg/misc www www/files
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Apr 19 12:52:24 CEST 2010
Author: jombart
Date: 2010-04-19 12:52:24 +0200 (Mon, 19 Apr 2010)
New Revision: 604
Added:
pkg/misc/FIXED
www/files/adegenet_1.2-4.tar.gz
www/files/adegenet_1.2-4.zip
Modified:
pkg/ChangeLog
pkg/R/basicMethods.R
pkg/R/zzz.R
pkg/TODO
pkg/man/adegenet.package.Rd
www/acceuil.html
www/download.html
www/news.html
Log:
Updated website for new release. zzz now includes a require to methods.
Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog 2010-04-16 11:53:48 UTC (rev 603)
+++ pkg/ChangeLog 2010-04-19 10:52:24 UTC (rev 604)
@@ -1,14 +1,36 @@
- CHANGES IN ADEGENET VERSION 1.3-0
+ 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: pkg/R/basicMethods.R
===================================================================
--- pkg/R/basicMethods.R 2010-04-16 11:53:48 UTC (rev 603)
+++ pkg/R/basicMethods.R 2010-04-19 10:52:24 UTC (rev 604)
@@ -124,7 +124,7 @@
############################
# Method summary for genind
############################
-setMethod ("summary", "genind", function(object, ...){
+setMethod ("summary", signature(object="genind"), function(object, ...){
x <- object
if(!is.genind(x)) stop("Provided object is not a valid genind.")
@@ -230,7 +230,7 @@
############################
# Method summary for genpop
############################
-setMethod ("summary", "genpop", function(object, ...){
+setMethod ("summary", signature(object="genpop"), function(object, ...){
x <- object
if(!inherits(x,"genpop")) stop("To be used with a genpop object")
Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R 2010-04-16 11:53:48 UTC (rev 603)
+++ pkg/R/zzz.R 2010-04-19 10:52:24 UTC (rev 604)
@@ -6,4 +6,5 @@
packageStartupMessage(startup.txt)
+ require(methods)
}
Modified: pkg/TODO
===================================================================
--- pkg/TODO 2010-04-16 11:53:48 UTC (rev 603)
+++ pkg/TODO 2010-04-19 10:52:24 UTC (rev 604)
@@ -30,10 +30,6 @@
# CODE ISSUES:
==============
* fix request 1.2-2.04 (implement adjusted heretozygosity in summary)
-o use packageStartupMessage() instead of cat in .First.lib -- done
-o bug: makefreq does not work after a seploc (bug 1.2-3.03) -- done
-o fix bug 1.2-3.01 (df2genind issue) -- done: was not actually a bug, but the "." used in loc names; no longer a pb now.
-o fix bug 1.2-3.02 (propShared issue) -- done.
# DOCUMENTATION ISSUES:
@@ -56,7 +52,6 @@
===========================
* in spca, when nfposi=0, the returned object actually contains what corresponds to nfposi=1. Comes from multispati in ade4. To correct in ade4.
* use spcaIllus to illustrate global.rtest and local.rtest
-* check all examples and look for possible improvements
* Implement a method to merge different markers for the same individuals
*o* Build accessors for:
- marker names -- done <locNames> (TJ)
@@ -69,7 +64,6 @@
* Implement different levels of ploidy in:
- hybridize - done (TJ)
- read.structure
-*o* propShared -- done for haploid.
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2010-04-16 11:53:48 UTC (rev 603)
+++ pkg/man/adegenet.package.Rd 2010-04-19 10:52:24 UTC (rev 604)
@@ -32,7 +32,7 @@
To import data from any of these formats, you can also use the general
function \code{\link{import2genind}}.\cr
- - DNA files: use \code{\link[pkg]{read.dna}} from the ape package,
+ - DNA files: use \code{\link[ape]{read.dna}} from the ape package,
and then extract SNPs from DNA alignments using
\code{\link{DNAbin2genind}}. \cr
Added: pkg/misc/FIXED
===================================================================
--- pkg/misc/FIXED (rev 0)
+++ pkg/misc/FIXED 2010-04-19 10:52:24 UTC (rev 604)
@@ -0,0 +1 @@
+This bug has been fixed.
\ No newline at end of file
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2010-04-16 11:53:48 UTC (rev 603)
+++ www/acceuil.html 2010-04-19 10:52:24 UTC (rev 604)
@@ -16,7 +16,7 @@
href="http://www.r-project.org/" target="_top"><img alt=""
src="images/R.png"
style="border: 0px solid ; width: 30px; height: 23px;"></a></span>
-package dedicated to the handling and multivariate analysis of genetic
+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
Modified: www/download.html
===================================================================
--- www/download.html 2010-04-16 11:53:48 UTC (rev 603)
+++ www/download.html 2010-04-19 10:52:24 UTC (rev 604)
@@ -18,11 +18,11 @@
<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
The
<span style="font-weight: bold;">current stable version</span>
-(adegenet_1.2-3)
+(adegenet_1.2-4)
is available as:<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>
-- <a href="files/adegenet_1.2-3.zip">Windows binary</a><br>
+- <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
+- MacOS X binary (to come)<br>
+- <a href="files/adegenet_1.2-4.zip">Windows binary</a><br>
<br>
<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
The
@@ -67,6 +67,11 @@
<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
<span style="font-weight: bold;">Older
versions</span>:<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>
+- <a href="files/adegenet_1.2-3.zip">Windows binary</a><br>
+<br>
adegenet_1.2-2<br>
- <a href="files/adegenet_1.2-2.tar.gz">linux/unix sources</a><br>
- <a href="files/adegenet_1.2-2.tgz">MacOS X binary</a><br>
Added: www/files/adegenet_1.2-4.tar.gz
===================================================================
(Binary files differ)
Property changes on: www/files/adegenet_1.2-4.tar.gz
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: www/files/adegenet_1.2-4.zip
===================================================================
(Binary files differ)
Property changes on: www/files/adegenet_1.2-4.zip
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: www/news.html
===================================================================
--- www/news.html 2010-04-16 11:53:48 UTC (rev 603)
+++ www/news.html 2010-04-19 10:52:24 UTC (rev 604)
@@ -12,25 +12,42 @@
style="font-weight: bold;"></span></big></big><span
style="font-weight: bold;"></span><span style="font-weight: bold;"></span><span
style="color: rgb(255, 0, 0);"></span><br>
-<img style="width: 480px; height: 480px;"
- alt="evolution of the adegenet package"
- src="images/evolAdegenetEng.png"><br>
+<br>
<span style="font-weight: bold;"><big><br>
Today</big> </span><span style="font-weight: bold;"></span><span
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
-1.2-3 </span>for R.2.8.1.<br>
+1.2-4 </span>for R.2.10.1.<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 href="files/ChangeLog">ChangeLog</a> for a list of
+See the current <a
+ href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a>
+for a list of
all modifications.<br>
-Next big release will be 1.3-0, and will include lots of new material.<br>
+Next major release will be 1.3-0, and will include the stable versions
+of SeqTrack algorithm, DAPC, and new simulation tools.<br>
<br>
<br>
-<span style="font-weight: bold;">15/04/2010 <img
+<span style="font-weight: bold;">19/04/2010 <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);">1.2-4</span>)
+has been released for R-2.10.1 !</big><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
+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
+release 1.3-0. Look at </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);"> for
+more information about this new version.<br>
+</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;">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>
<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
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