[adegenet-commits] r218 - pkg www www/files

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Dec 19 11:24:44 CET 2008 

Author: jombart
Date: 2008-12-19 11:24:43 +0100 (Fri, 19 Dec 2008)
New Revision: 218

Added:
   www/files/adegenet_1.2-2.tar.gz
Modified:
   pkg/ChangeLog
   pkg/TODO
   www/download.html
   www/files/ChangeLog
   www/files/TODO
   www/news.html
Log:
new release: 1.2-2


Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog	2008-12-15 22:34:22 UTC (rev 217)
+++ pkg/ChangeLog	2008-12-19 10:24:43 UTC (rev 218)
@@ -1,3 +1,54 @@
+			CHANGES IN ADEGENET VERSION 1.2-2
+
+
+NEW FEATURES
+
+	o implement different levels of ploidy in genind / genpop objects
+	(new slot @ploidy). Now, any level of ploidy can be handled by
+	input function df2genind, which has been recoded almost
+	entierely. Different levels of ploidy are now handled by different
+	functions.
+	
+	o a "sep" argument is now handled by df2genind: this allows
+	reading many data formats.
+
+	o implemented a method "scaleGen" for genind / genpop objects,
+	which scales allelic data using different methods.
+
+	o  colorplot: a generic function, with a method for spca
+	objects. Represents up to three principal components based on RGB
+	representation of Cavalli-Sforza.
+
+	o loadingplot for plotting loadings of one axis
+
+	o adegenetTutorial function which opens the online tutorials
+
+	o allow for the use of na.replace and scaleGen in spca function
+
+	o added rupica dataset
+
+	o enable reading data from URL (import2genind, read.[...])
+
+	o permit specification of a matrix of spatial weights in spca 
+	
+
+BUG FIXES
+
+	o fixed bug 1.2-2.01 (read.structure issue): was due to the
+	default of "onerowperind" argument.
+	
+	o fixed bug 1.2-2.02 (read.genetix issue): was due to an
+	error in the data file (wrong nloc); now read.genetix corrects
+	that automatically and issues a warning.
+	
+	o fixed bug 1.2-2.03 (monmonier issue): was a non-detected
+	code 2 due to intersection check with previously drawn segment
+	(was not always removed).
+	
+	o fixed bug 1.2-2.05 (a few fixes/improvement for monmonier)
+
+
+
 			CHANGES IN ADEGENET VERSION 1.2-1
 
 
@@ -44,6 +95,20 @@
 
 
 
+
+			CHANGES IN ADEGENET VERSION 1.1-3
+
+
+NEW FEATURES
+
+	o 'as' methods for genind/genpop objects to matrix, data.frame,
+	and ktab objects. Now, ordination implemented as dudi functions in
+	ade4 (like dudi.pca) can be performed directly using genind/genpop
+	as inputs.
+
+
+
+
 			CHANGES IN ADEGENET VERSION 1.1-2
 
 
@@ -61,8 +126,6 @@
 	validObject now detects duplicates in any kind of names (ind.names,
 	pop.names, etc.) and prints the corresponding items.
 
-
-
 BUG FIXES
 
 	o genind2df does now handles the pop argument correctly.

Modified: pkg/TODO
===================================================================
--- pkg/TODO	2008-12-15 22:34:22 UTC (rev 217)
+++ pkg/TODO	2008-12-19 10:24:43 UTC (rev 218)
@@ -28,15 +28,8 @@
 
 # CODE ISSUES:
 ==============
-o fix bug 1.2-2.01 (read.structure issue) -- fixed: was due to the default of "onerowperind" argument.
-o fix bug 1.2-2.02 (read.genetix issue) -- fixed: was due to an error in the data file (wrong nloc); now read.genetix corrects that automatically and issues a warning. (TJ)
-o fix bug 1.2-2.03 (monmonier issue) -- fixed: was a non-detected code 2 due to intersection check with previously drawn segment (was not always removed). (TJ)
 * fix request 1.2-2.04 (implement adjusted heretozygosity in summary)
-o fix bug 1.2-2.05 (monmonier is such a pain is the ass) -- fixed, done and done (TJ)
-o !! comment the if(DEBUG) in monmonier when it is fixed -- done
-* make the package work after all changes (pass the check)
 
-
 # DOCUMENTATION ISSUES:
 =======================
 * make a tutorial for the sPCA -- done (TJ)
@@ -45,12 +38,7 @@
 
 # NEW IMPLEMENTATIONS:
 =====================
-o color plot for the sPCA results, based on RGB representation of Cavalli-Sforza -- done(TJ)
-o loadingplot for plotting loadings of one axis -- done (TJ)
-o adegenetTutorial function which opens the online tutorials -- done (TJ)
-o allow for the use of na.replace and scaleGen in spca function -- done (TJ)
-o add rupica dataset -- done (TJ)
-o enable reading data from URL (import2genind, read.[...]).
+
 * implement handling of presence/absence data
 * add a type argument to genind/genpop objects
 * make all the required subsequent changes in the package:
@@ -92,10 +80,9 @@
 - hybridize
 - read.structure
 - propShared
-o Permit specification of a matrix of spatial weights in spca (email A. Piotti) -- done (TJ)
-*
 
 
+
 # LONG TERM
 ==========================
 ==========================
@@ -103,7 +90,7 @@
 * export to geneticsBase -- same thing
 * see where code needs tuning, and use C/C++
 * implement global.rtest and local.rtest for genind/genpop objects
-o Implement dudi wrappers for genind / genpop objects -- one step (automatic coercion as data.frames) (TJ)
+
 * Check the formulae provided for Reynolds (consistent with Felsenstein's
 formulae, not straightforward reading the original article)
 * Implement wrappers for spatial function (Moran's I, Mantel's correlogram, etc.).

Modified: www/download.html
===================================================================
--- www/download.html	2008-12-15 22:34:22 UTC (rev 217)
+++ www/download.html	2008-12-19 10:24:43 UTC (rev 218)
@@ -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_1.2-1)
+(adegenet_1.2-2)
 is available as:<br>
-- <a href="files/adegenet_1.2-1.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-1.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-1.zip">Windows binary</a><br>
+- <a href="files/adegenet_1.2-2.tar.gz">linux/unix sources</a><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_1.2-2)
+<span style="font-weight: bold;">devel version</span> (adegenet_1.2-3)
 is also available
 from <a href="https://r-forge.r-project.org/scm/?group_id=120"
  target="_top">R-Forge's
@@ -44,13 +44,15 @@
 (CRAN) ones. Simply download the file in your working directory and
 type <span style="font-family: monospace;">source("[your-patch-file.R]")</span>&nbsp;
 to use a patch.<br>
-- <a href="files/import.R"><span style="font-family: monospace;">import.R</span></a>:
-corrects an important bug arising in adegenet_1.2-0: NA were not
-detected.<br>
 <br>
 <img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
 <span style="font-weight: bold;">Older
 versions</span>:<br>
+adegenet_1.2-1<br>
+- <a href="files/adegenet_1.2-1.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-1.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-1.zip">Windows binary</a><br>
+<br>
 adegenet_1.2-0<br>
 - <a href="files/adegenet_1.2-0.tar.gz">linux/unix sources</a><br>
 - <a href="files/adegenet_1.2-0.tgz">MacOS X binary</a><br>

Modified: www/files/ChangeLog
===================================================================
--- www/files/ChangeLog	2008-12-15 22:34:22 UTC (rev 217)
+++ www/files/ChangeLog	2008-12-19 10:24:43 UTC (rev 218)
@@ -1,3 +1,51 @@
+			CHANGES IN ADEGENET VERSION 1.2-2
+
+
+NEW FEATURES
+
+	o implement different levels of ploidy in genind / genpop objects
+	(new slot @ploidy). Now, any level of ploidy can be handled by
+	input function df2genind, which has been recoded almost
+	entierely. Different levels of ploidy are now handled by different
+	functions.
+	
+	o a "sep" argument is now handled by df2genind: this allows
+	reading many data formats.
+
+	o  colorplot: a generic function, with a method for spca
+	objects. Represents up to three principal components based on RGB
+	representation of Cavalli-Sforza.
+
+	o loadingplot for plotting loadings of one axis
+
+	o adegenetTutorial function which opens the online tutorials
+
+	o allow for the use of na.replace and scaleGen in spca function
+
+	o added rupica dataset
+
+	o enable reading data from URL (import2genind, read.[...])
+
+	o permit specification of a matrix of spatial weights in spca 
+	
+
+BUG FIXES
+
+	o fixed bug 1.2-2.01 (read.structure issue): was due to the
+	default of "onerowperind" argument.
+	
+	o fixed bug 1.2-2.02 (read.genetix issue): was due to an
+	error in the data file (wrong nloc); now read.genetix corrects
+	that automatically and issues a warning.
+	
+	o fixed bug 1.2-2.03 (monmonier issue): was a non-detected
+	code 2 due to intersection check with previously drawn segment
+	(was not always removed).
+	
+	o fixed bug 1.2-2.05 (a few fixes/improvement for monmonier)
+
+
+
 			CHANGES IN ADEGENET VERSION 1.2-1
 
 

Modified: www/files/TODO
===================================================================
--- www/files/TODO	2008-12-15 22:34:22 UTC (rev 217)
+++ www/files/TODO	2008-12-19 10:24:43 UTC (rev 218)
@@ -48,7 +48,6 @@
 * 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 "sep" argument in df2genind
 * Implement a method to merge different markers for the same individuals
 * Build accessors for marker names, indiv names, pop names, spatial coords, ...
 * Return a spatial object from monmonier (class sp?)

Added: www/files/adegenet_1.2-2.tar.gz
===================================================================
(Binary files differ)


Property changes on: www/files/adegenet_1.2-2.tar.gz
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Modified: www/news.html
===================================================================
--- www/news.html	2008-12-15 22:34:22 UTC (rev 217)
+++ www/news.html	2008-12-19 10:24:43 UTC (rev 218)
@@ -20,15 +20,36 @@
  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
-1.2-1 </span>for R.2.8.0.<br>
+1.2-2 </span>for R.2.8.0.<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
 all modifications.<br>
 <br>
-<span style="font-weight: bold;">03/08/2008 <img
+<span style="font-weight: bold;">19/012/2008 <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);">1.2-2</span>)
+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
+(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
+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
+ 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
+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>
+</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>
 <span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This

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