[adegenet-commits] r152 - pkg pkg/man www www/files
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jul 9 23:55:38 CEST 2008
Author: jombart
Date: 2008-07-09 23:55:38 +0200 (Wed, 09 Jul 2008)
New Revision: 152
Modified:
pkg/DESCRIPTION
pkg/man/adegenet.package.Rd
www/files/ChangeLog
www/news.html
Log:
Updates for new release of the package
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2008-07-09 21:41:37 UTC (rev 151)
+++ pkg/DESCRIPTION 2008-07-09 21:55:38 UTC (rev 152)
@@ -1,5 +1,5 @@
Package: adegenet
-Version: 1.2-0
+Version: 1.2-1
Date: 2008/MM/DD
Title: adegenet: a R package for the multivariate analysis of genetic markers.
Author: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>, with contributions from Peter Solymos
@@ -9,4 +9,4 @@
Description: Classes and functions for genetic data analysis within the multivariate framework.
License: GPL (>=2)
LazyLoad: yes
-Collate: classes.R auxil.R genind2genpop.R propTyped.R basicMethods.R old2new.R makefreq.R chooseCN.R dist.genpop.R export.R setAs.R gstat.randtest.R HWE.R import.R monmonier.R coords.monmonier.R spca.R spca.rtests.R zzz.R hybridize.R fstat.R propShared.R scale.R
\ No newline at end of file
+Collate: classes.R auxil.R genind2genpop.R propTyped.R basicMethods.R old2new.R makefreq.R chooseCN.R dist.genpop.R export.R setAs.R gstat.randtest.R HWE.R import.R monmonier.R coords.monmonier.R spca.R spca.rtests.R zzz.R hybridize.R fstat.R propShared.R scale.R
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2008-07-09 21:41:37 UTC (rev 151)
+++ pkg/man/adegenet.package.Rd 2008-07-09 21:55:38 UTC (rev 152)
@@ -99,7 +99,7 @@
\tabular{ll}{
Package: \tab adegenet\cr
Type: \tab Package\cr
- Version: \tab 1.2-0\cr
+ Version: \tab 1.2-1\cr
Date: \tab 2008-MM-DD\cr
License: \tab GPL (>=2)
}
@@ -117,4 +117,4 @@
}
\keyword{manip}
\keyword{multivariate}
-\seealso{The \code{ade4} package for multivariate analysis}
\ No newline at end of file
+\seealso{The \code{ade4} package for multivariate analysis}
Modified: www/files/ChangeLog
===================================================================
--- www/files/ChangeLog 2008-07-09 21:41:37 UTC (rev 151)
+++ www/files/ChangeLog 2008-07-09 21:55:38 UTC (rev 152)
@@ -1,3 +1,49 @@
+ CHANGES IN ADEGENET VERSION 1.2-0
+
+
+NEW FEATURES
+
+ o implement different levels of ploidy in genind / genpop
+ objects. Make necessary adaptations throughout the package.
+
+ o put some stop where needed when ploidy!=2 is not handled.
+
+ o implement a "sep" argument in df2genind.
+
+ o implement accessor for genind/genpop: nLoc.
+
+ o implement "scaleGen" for genind/genpop, which allows for
+ different types of scaling.
+
+ o added several coercion methods, from genind/genpop to
+ data.frame, matrix and ktab objects.
+
+ o implemented propTyped, a function giving the proportion of
+ non-missing data in different ways.
+
+
+
+BUG FIXES
+
+ o missing data indicated in summary corrected (loci with more
+ alleles had more weight in the computations).
+
+
+
+
+ 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
@@ -23,7 +69,7 @@
locus.
-
+
CHANGES IN ADEGENET VERSION 1.1-1
Modified: www/news.html
===================================================================
--- www/news.html 2008-07-09 21:41:37 UTC (rev 151)
+++ www/news.html 2008-07-09 21:55:38 UTC (rev 152)
@@ -12,35 +12,49 @@
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>
-<span style="font-weight: bold;"></span><span style="font-weight: bold;"><big>Incoming</big></span><span
- style="font-weight: bold;"> <img alt="" src="images/new.png"
- style="width: 80px; height: 37px;"></span><span
- style="font-weight: bold;"></span><span style="font-weight: bold;"></span><br>
-<span style="font-weight: bold;"></span>The next version of adegenet is
-<span style="color: rgb(255, 0, 0);">adegenet is
-1.2-0 </span>for R.2.7.0. It is mostly achieved, and awaits testing by
-courageous users by before being released on CRAN. Big news is: the
-package now handles <span style="font-weight: bold;">different levels
-of ploidy</span>, which explains the change from 1.1-2 to 1.2. A few
-new features will be added with this version, like the computation of
-proportions of available (i.e., typed) data by individual/population,
-markers, or both.<br>
<br>
-<br>
<span style="font-weight: bold;"><big>Today</big> </span><span
style="font-weight: bold;"></span><span style="font-weight: bold;"></span><br>
<span style="font-weight: bold;"></span>Current
version of <span style="color: rgb(255, 0, 0);">adegenet is
-1.1-2 </span>for R.2.7.0.<br>
+1.2-0 </span>for R.2.7.1.<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> and <a
href="https://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/*checkout*/pkg/TODO?rev=121&root=adegenet">TODO
list</a> of the package.<br>
<br>
+<span style="font-weight: bold;">09/07/2008 <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);">1.2-0</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
+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>
+ - </span><span style="font-family: monospace;">df2genind</span></span>
+now handles a 'sep' argument, specifying a separator between the input
+alleles. This extends current input capabilities to a wider range of
+software.<br>
+ - <span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"></span><span
+ style="font-family: monospace;">scaleGen</span></span> is a function
+similar to 'scale' for genind/genpop objects. Various scalings adapted
+to genetic markers are proposed.<br>
+ - <span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"></span><span
+ style="font-family: monospace;">propTyped</span></span> is a function
+giving the the proportion of non-missing data in different ways; this
+is particularly useful to detect structuring in missing data.<br>
+ - various coercion method are now available,
+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>
<span style="font-weight: bold;">02/06/2008 </span><span
- style="font-weight: bold;"><img alt="" src="images/new.png"
- style="width: 80px; height: 37px;"></span><br>
+ 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>
<span style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">This
@@ -70,8 +84,7 @@
</span><span style="color: rgb(255, 0, 0);"><span
style="color: rgb(0, 0, 0);"></span></span><span
style="font-weight: bold;"><br>
-30/04/2008 </span><span style="font-weight: bold;"><img alt=""
- src="images/new.png" style="width: 80px; height: 37px;"></span><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
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