[adegenet-commits] r1130 - pkg/R www www/images www/images/gimp
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 15 19:02:18 CEST 2013
Author: jombart
Date: 2013-05-15 19:02:17 +0200 (Wed, 15 May 2013)
New Revision: 1130
Modified:
pkg/R/dapc.R
www/download.html
www/images/acceuil.png
www/images/gimp/acceuil.xcf
www/news.html
Log:
update website for release; added a new function to assess the quality of discrimination with the number of PCs... doesn't seem to kick asses.
Modified: pkg/R/dapc.R
===================================================================
--- pkg/R/dapc.R 2013-05-15 10:57:43 UTC (rev 1129)
+++ pkg/R/dapc.R 2013-05-15 17:02:17 UTC (rev 1130)
@@ -984,14 +984,13 @@
############
-## crossval
+## xvalDapc
############
xvalDapc <- function (x, ...) UseMethod("xvalDapc")
xvalDapc.data.frame <- function(x, grp, n.pca.max, n.da=NULL, training.set = 1/2,
- center=TRUE, scale=FALSE,
- n.pca=NULL, n.rep=10, ...){
+ center=TRUE, scale=FALSE, n.pca=NULL, n.rep=10, ...){
## CHECKS ##
grp <- factor(grp)
@@ -1005,6 +1004,7 @@
N.training <- round(N*training.set)
## GET FULL PCA ##
+ if(missing(n.pca.max)) n.pca.max <- min(dim(x))
pcaX <- dudi.pca(x, nf=n.pca.max, scannf=FALSE, center=center, scale=scale)
n.pca.max <- min(n.pca.max,pcaX$rank,N.training-1)
@@ -1031,14 +1031,64 @@
## GET %SUCCESSFUL OF ACCURATE PREDICTION FOR ALL VALUES ##
res.all <- unlist(lapply(n.pca, get.prop.pred))
- res <- list(success=res.all, n.pca=factor(rep(n.pca, each=n.rep)))
+ res <- data.frame(n.pca=rep(n.pca, each=n.rep), success=res.all)
return(res)
-}
+} # end xvalDapc.data.frame
xvalDapc.matrix <- xvalDapc.data.frame
+
+
+
+
+#############
+## discriVal
+#############
+
+discriVal <- function (x, ...) UseMethod("discriVal")
+
+discriVal.data.frame <- function(x, grp, n.pca.max, n.da=NULL, center=TRUE, scale=FALSE, n.pca=NULL, ...){
+
+ ## CHECKS ##
+ grp <- factor(grp)
+ n.pca <- n.pca[n.pca>0]
+ if(is.null(n.da)) {
+ n.da <- length(levels(grp))-1
+ }
+
+ ## GET FULL PCA ##
+ if(missing(n.pca.max)) n.pca.max <- min(dim(x))
+ pcaX <- dudi.pca(x, nf=n.pca.max, scannf=FALSE, center=center, scale=scale)
+ n.pca.max <- min(n.pca.max,pcaX$rank)
+
+ ## DETERMINE N.PCA IF NEEDED ##
+ if(is.null(n.pca)){
+ n.pca <- round(pretty(1:n.pca.max,10))
+ }
+ n.pca <- n.pca[n.pca>0 & n.pca<n.pca.max]
+
+ ## FUNCTION GETTING THE TOTAL DISCRIMINATION (SUM OF EIGENVALUES) FOR ONE GIVEN NB OF PCA PCs ##
+ ## n.pca is a number of retained PCA PCs
+ get.totdiscr <- function(n.pca){
+ temp.dapc <- suppressWarnings(dapc(x, grp, n.pca=n.pca, n.da=n.da, dudi=pcaX))
+ return(sum(temp.dapc$eig))
+ }
+
+
+ ## GET %SUCCESSFUL OF ACCURATE PREDICTION FOR ALL VALUES ##
+ res.all <- sapply(n.pca, get.totdiscr)
+ res <- data.frame(n.pca=n.pca, success=res.all)
+ return(res)
+} # end discriVal.data.frame
+
+
+discriVal.matrix <- discriVal.data.frame
+
+
+
+
## There's a bunch of problems down there, commenting it for nowé
## xval.dapc <- function(object, n.pca, n.da, training.set = 90, ...){
## training.set = training.set/100
Modified: www/download.html
===================================================================
--- www/download.html 2013-05-15 10:57:43 UTC (rev 1129)
+++ www/download.html 2013-05-15 17:02:17 UTC (rev 1130)
@@ -30,14 +30,14 @@
<br>
<img alt="" src="images/bullet.png" style="width: 10px; height:
10px;"> The <span style="font-weight: bold;">current stable
- version</span> (adegenet_1.3-6) is available as:<br>
- - <a href="files/adegenet_1.3-6.tar.gz">linux sources</a><br>
- - <a href="files/adegenet_1.3-6.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.3-6.zip">Windows binary</a><br>
+ version</span> (adegenet_1.3-8) is available as:<br>
+ - <a href="files/adegenet_1.3-8.tar.gz">linux 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_1.3-7) is also available from <a
+ (adegenet_1.3-9) is also available from <a
href="https://r-forge.r-project.org/scm/?group_id=120"
target="_top">R-Forge's daily snapshots</a>.<br>
It can be installed directly from R console using: <br>
@@ -47,6 +47,8 @@
height: 10px;"> <span style="font-weight: bold;">Patches</span>
+
+
<br>
Patches correct minor bugs or implement new functionnalities, and
will be included into the next CRAN release. It is recommended to
@@ -58,17 +60,31 @@
use
+
+
a patch.<br>
<a href="files/patches/addedFeatures.R"><span style="font-family:
monospace;">addedFeatures.R</span></a>: (for adegenet
>=1.3-1) added features not included in the CRAN version of the
package; includes conversion from <span style="font-family:
monospace;">seqTrack </span>outputs to <span
- style="font-family: monospace;">graphNEL </span>objects.<br>
+ style="font-family: monospace;">graphNEL </span>objects. If you
+ have a choice though, consider using current igraph
+ implementation, which is probably better and still maintained.<br>
<a href="files/patches/export.R"><span style="font-family:
monospace;"></span></a><br>
<img alt="" src="images/bullet.png" style="width: 10px; height:
10px;"> <span style="font-weight: bold;">Older versions</span>:<br>
+ adegenet _1.3-7<br>
+ - <a href="files/adegenet_1.3-7.tar.gz">linux sources</a><br>
+ - <a href="files/adegenet_1.3-7.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.3-7.zip">Windows binary</a><br>
+ <br>
+ adegenet _1.3-6<br>
+ - <a href="files/adegenet_1.3-6.tar.gz">linux sources</a><br>
+ - <a href="files/adegenet_1.3-6.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.3-6.zip">Windows binary</a><br>
+ <br>
adegenet _1.3-5<br>
- <a href="files/adegenet_1.3-5.tar.gz">linux sources</a><br>
- <a href="files/adegenet_1.3-5.tgz">MacOS X binary</a><br>
Modified: www/images/acceuil.png
===================================================================
(Binary files differ)
Modified: www/images/gimp/acceuil.xcf
===================================================================
(Binary files differ)
Modified: www/news.html
===================================================================
--- www/news.html 2013-05-15 10:57:43 UTC (rev 1129)
+++ www/news.html 2013-05-15 17:02:17 UTC (rev 1130)
@@ -28,15 +28,15 @@
0, 0);"></span><br>
<br>
<span style="font-weight: bold;">What's next<big></big></span>?<br>
- Next release (1.3-7) is under development.<br>
+ Next release (1.3-9) is under development.<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 stable version of
- <span style="color: rgb(255, 0, 0);">adegenet is 1.3-6 </span>for
- R.2.15.2.<br>
+ <span style="color: rgb(255, 0, 0);">adegenet is 1.3-8 </span>for
+ R.3.0.0.<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
@@ -44,60 +44,82 @@
for a list of all modifications.<br>
<br>
<br>
- <span style="font-weight: bold;">30/01/2013 </span><span
- style="font-weight: bold;"></span><img style="width: 80px;
- height: 37px;" alt=""
+ 15/05/2013 <img style="width: 80px; height: 37px;" alt=""
src="images/new.png"><br>
+ <big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-8</span>)
+ has been released for R-3.0.0!</big> <span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">New features
+ include a new function for cross-validation of DAPC results,
+ especially useful for assessing the optimal number of PCA
+ components to retain during the dimension reduction step.
+ Check out <span style="font-family: monospace; color:
+ rgb(255, 0, 0);">xvalDapc</span></span><span
+ style="font-family: monospace;"></span><span style="color:
+ rgb(0, 0, 0);">. Other sources of minor excitement
+ include new color palettes, and the function <span
+ style="color: rgb(255, 0, 0); font-family: monospace;">any2col</span>
+ which converts factors and numeric into colors, prodiving info
+ for a legend as well. 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 details.</span></span><br>
+ <br>
+ <span style="font-weight: bold;"><br>
+ ??/??/????<br>
+ </span>At some point in time, version 1.3-7 was released, but
+ never acknowledged on this website.<span style="color: rgb(255, 0,
+ 0);"><span style="color: rgb(0, 0, 0);"> 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 clues about what
+ happened.</span></span><br>
+ <br>
+ <span style="font-weight: bold;"><br>
+ 30/01/2013 </span><span style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-6</span>)
- has
- been
- released
- for R-2.15.2!</big> <span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">New features include a function
- for identifying mutations (position and nature) between pairs
- of DNA sequences (<span style="color: rgb(255, 0, 0);
- font-family: monospace;">findMutations</span>), with a
- possibility of visualization using graphs (</span></span><span
+ has been released for R-2.15.2!</big> <span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">New features
+ include a function for identifying mutations (position and
+ nature) between pairs of DNA sequences (<span style="color:
+ rgb(255, 0, 0); font-family: monospace;">findMutations</span>),
+ with a possibility of visualization using graphs (</span></span><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
0);"><span style="color: rgb(255, 0, 0); font-family:
monospace;">graphMutations</span></span></span><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
- 0);">).
- See the </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><a
+ 0);">). 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 details.</span></span><br>
+ style="color: rgb(0, 0, 0);"> file for more details.</span></span><br>
<br>
<br>
<span style="font-weight: bold;">08/11/2012 </span><span
style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-5</span>)
- has
- been
- released
- for R-2.15.2!</big> <span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">New features include a
- graph-based
- clutering approach (<span style="color: rgb(255, 0, 0);
- font-family: monospace;">gengraph</span>),
+ has been released for R-2.15.2!</big> <span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">New features
+ include a graph-based clutering approach (<span style="color:
+ rgb(255, 0, 0); font-family: monospace;">gengraph</span>),
and a new function for reading fasta alignments into <span
style="font-family: monospace;">DNAbin</span> objects with
- minimum
- memory requirements (</span></span><span style="color:
+ minimum memory requirements (</span></span><span style="color:
rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"><span
style="color: rgb(255, 0, 0); font-family: monospace;">fasta2DNAbin</span></span></span><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
- 0);">).
- See the </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><a
+ 0);">). 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 details.</span></span><br>
+ style="color: rgb(0, 0, 0);"> file for more details.</span></span><br>
<br>
<br>
<span style="font-weight: bold;">10/08/2012 </span><span
@@ -109,140 +131,103 @@
<br>
23/01/2012 </span><span style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-4</span>)
- has
- been
- released
- for R-2.14.1!</big> The package has undergone some
- internal changes in the documentation which should make no
- difference
- to users, except for a drastic reduction in <span style="color:
- rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">download
- and
- installed
- size
- (respectively 4-5MB and 6-7MB). Many examples have
- been 'inactivated' to comply with CRAN check runtime policy,
- meaning
- these won't be run by '<span style="font-family: monospace;">example(myFunction)</span>'
- anymore,
- but
- will
- still be available in the documentation. See the </span></span><span
+ has been released for R-2.14.1!</big> The package has undergone
+ some internal changes in the documentation which should make no
+ difference to users, except for a drastic reduction in <span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
- 0);"></span></span><a
+ 0);">download and installed size (respectively 4-5MB and
+ 6-7MB). Many examples have been 'inactivated' to comply with
+ CRAN check runtime policy, meaning these won't be run by '<span
+ style="font-family: monospace;">example(myFunction)</span>'
+ anymore, but will still be available in the documentation. 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 details.</span></span><br>
+ style="color: rgb(0, 0, 0);"> file for more details.</span></span><br>
<br>
<br>
<span style="font-weight: bold;">23/12/2011 </span><span
style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-3</span>)
- has
- been
- released
- for R-2.14.1!</big> Just in time for Christmas, ain't
- that nice? This release includes a brand new version of <span
- style="color: rgb(255, 0, 0); font-family: monospace;">propShared</span>
- which fixes an important bug, and now allows for any ploidy level
- while
- running core computations in C. The package is also slightly
- smaller
- than before. <span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">See the </span></span><span
+ has been released for R-2.14.1!</big> Just in time for
+ Christmas, ain't that nice? This release includes a brand new
+ version of <span style="color: rgb(255, 0, 0); font-family:
+ monospace;">propShared</span> which fixes an important bug, and
+ now allows for any ploidy level while running core computations in
+ C. The package is also slightly smaller than before. <span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
- 0);"></span></span><a
+ 0);">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 details.</span></span><br>
+ style="color: rgb(0, 0, 0);"> file for more details.</span></span><br>
<br>
<br>
<span style="font-weight: bold;">11/11/2011 </span><span
style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-2</span>)
- has
- been
- released
- for R-2.14.0!</big> This minor release fixes some
- issues in the detection of the number of cores occuring on some
- platforms, as well as a few fixes in manpages. Function <span
+ has been released for R-2.14.0!</big> This minor release fixes
+ some issues in the detection of the number of cores occuring on
+ some platforms, as well as a few fixes in manpages. Function <span
style="font-family: monospace; color: rgb(255, 0, 0);">fstat</span>
- is
- now gone for good as <span style="font-style: italic;">hierfstat
- </span>package
- seems
- to
- be
- gone for good from CRAN, but the documentation shows how to
- use <span style="color: rgb(255, 0, 0); font-family: monospace;">Fst</span>
- from the <span style="font-style: italic;">pegas </span>package
- instead. <span style="color: rgb(255, 0, 0);"><span style="color:
- rgb(0, 0, 0);">See the </span></span><span style="color:
- rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><a
+ is now gone for good as <span style="font-style: italic;">hierfstat
+
+ </span>package seems to be gone for good from CRAN, but the
+ documentation shows how to use <span style="color: rgb(255, 0,
+ 0); font-family: monospace;">Fst</span> from the <span
+ style="font-style: italic;">pegas </span>package instead. <span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
+ 0);">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 details.</span></span><br>
+ style="color: rgb(0, 0, 0);"> file for more details.</span></span><br>
<br>
<br>
<span style="font-weight: bold;">02/09/2011 </span><span
style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-1</span>)
- has
- been
- released
- for R-2.13.1!</big> Less is more: this new release is
- much smaller in size than 1.3-0, while containing the same
- material. It
- also fixes a few minor issues in documentation and in the legend
- of
- dapc scatterplots. <span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">See the </span></span><span
+ has been released for R-2.13.1!</big> Less is more: this new
+ release is much smaller in size than 1.3-0, while containing the
+ same material. It also fixes a few minor issues in documentation
+ and in the legend of dapc scatterplots. <span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">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 details.</span></span><br>
+ style="color: rgb(0, 0, 0);"> file for more details.</span></span><br>
<br>
<br>
<span style="font-weight: bold;">27/06/2011 </span><span
style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-0</span>)
- has
- been
- released
- for R-2.13.0!</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">
- This new major release implements new classes and methods for
- the
+ has been released for R-2.13.0!</big><span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"> This new
+ major release implements new classes and methods for the
handling and analysis of genome-wide SNP data, along with
- several
- improvements to previous tools (especially new graphics for
- DAPC) </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">and
- a few bug fixes. It also include 4 new tutorial distributed as
- vignettes. See the </span></span><span style="color: rgb(255,
- 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><a
+ several improvements to previous tools (especially new
+ graphics for DAPC) </span></span><span style="color: rgb(255,
+ 0, 0);"><span style="color: rgb(0, 0, 0);">and a few bug fixes.
+ It also include 4 new tutorial distributed as vignettes. 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 details of the release.</span></span> Given this is a
- major
- release, version number switched directly from 1.2-8 to 1.3-0.<br>
+ style="color: rgb(0, 0, 0);"> file for details of the release.</span></span>
+ Given this is a major release, version number switched directly
+ from 1.2-8 to 1.3-0.<br>
<br>
<br>
<span style="font-weight: bold;">02/06/2011</span><br>
A new tutorial dedicated to DAPC has been uploaded on the website
- (see
- section "documents").<br>
+ (see section "documents").<br>
<br>
<br>
<span style="font-weight: bold;">14/12/2010 </span><br>
@@ -260,68 +245,50 @@
<span style="font-weight: bold;">05/11/2010 </span><span
style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-8</span>)
- has
- been
- released
- for R-2.12.0!</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">
- This release </span></span><span style="color: rgb(255, 0,
- 0);"><span style="color: rgb(0, 0, 0);">fixes a bug in exports
- from adegenet to
- hierfstat (function <span style="color: rgb(255, 0, 0);
- font-family: monospace;">genind2hierfstat</span>),
- which
- lead
- to
- wrong <span style="font-family: monospace; color: rgb(255, 0,
- 0);">fstat</span>
- computations in some cases. See the </span></span><span
- style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
- 0);"></span></span><a
+ has been released for R-2.12.0!</big><span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"> This
+ release </span></span><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);">fixes a bug in exports from
+ adegenet to hierfstat (function <span style="color: rgb(255,
+ 0, 0); font-family: monospace;">genind2hierfstat</span>),
+ which lead to wrong <span style="font-family: monospace;
+ color: rgb(255, 0, 0);">fstat</span> computations in some
+ cases. 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 details.</span></span><br>
+ style="color: rgb(0, 0, 0);"> file for details.</span></span><br>
<br>
<br>
<span style="font-weight: bold;">29/10/2010 </span><span
style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-7</span>)
- has
- been
- released
- for R-2.12.0!</big><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">
- This release includes the stable implementation of the <span
+ has been released for R-2.12.0!</big><span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"> This
+ release includes the stable implementation of the <span
style="font-style: italic;">Discriminant Analysis of
- Principal
- Components</span> (<span style="font-style: italic;">DAPC</span>,
- <span style="color: rgb(255, 0, 0); font-family: monospace;">?dapc</span>,
- <span style="color: rgb(255, 0, 0); font-family: monospace;">?find.clusters</span>)</span></span><span
+ Principal Components</span> (<span style="font-style:
+ italic;">DAPC</span>, <span style="color: rgb(255, 0, 0);
+ font-family: monospace;">?dapc</span>, <span style="color:
+ rgb(255, 0, 0); font-family: monospace;">?find.clusters</span>)</span></span><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
- 0);">,
- and fixes a bug from the ape package which impacted adegenet
- and
- prevented windows binaries to be generated with R-2.12.0. See
- the </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><a
+ 0);">, and fixes a bug from the ape package which impacted
+ adegenet and prevented windows binaries to be generated with
+ R-2.12.0. 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>
+ style="color: rgb(0, 0, 0);"> file for more information.</span></span><br>
<br>
<br>
<span style="font-weight: bold;">22/09/2010 </span><span
style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.2-6</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 adds the computation of pairwise Fst (</span></span><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 adds the computation of pairwise Fst (</span></span><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);"><span style="color: rgb(255, 0,
@@ -331,102 +298,80 @@
0);"></span></span><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);">and
- a new function for extracting the polymorphism of aligned
- proteic
- sequences (class </span></span><span style="color: rgb(255,
- 0, 0);"><span style="color: rgb(0, 0, 0);"><span
- style="font-family: monospace; color: rgb(255, 0, 0);">alignment
- </span></span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);">in
- the seqinr package) into genind objects (</span></span><span
+ 0);">and a new function for extracting the polymorphism of
+ aligned proteic sequences (class </span></span><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
0);"><span style="font-family: monospace; color: rgb(255, 0,
+ 0);">alignment </span></span></span><span style="color:
+ rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">in the
+ seqinr package) into genind objects (</span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
+ 0);"><span style="font-family: monospace; color: rgb(255, 0,
0);">?alignment2genind</span></span></span><span
style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0,
- 0);">).
- See the </span></span><span style="color: rgb(255, 0, 0);"><span
- style="color: rgb(0, 0, 0);"></span></span><a
+ 0);">). 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, and check out new updates of the
- tutorial.</span></span><br>
+ style="color: rgb(0, 0, 0);"> file for more information, and
+ check out new updates of the tutorial.</span></span><br>
<br>
<span style="font-weight: bold;"><br>
30/07/2010 </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
+ 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 </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
+ 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
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/adegenet -r 1130
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