[adegenet-commits] r708 - in www: . files/patches
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 5 15:34:24 CET 2010
Author: jombart
Date: 2010-11-05 15:34:24 +0100 (Fri, 05 Nov 2010)
New Revision: 708
Added:
www/files/patches/makefreq.R
Modified:
www/download.html
www/news.html
Log:
updated site.
Modified: www/download.html
===================================================================
--- www/download.html 2010-11-05 14:28:00 UTC (rev 707)
+++ www/download.html 2010-11-05 14:34:24 UTC (rev 708)
@@ -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_1.2-7)
+(adegenet_1.2-8)
is available as:<br>
-- <a href="files/adegenet_1.2-7.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-7.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-7.zip">Windows binary</a><br>
+- <a href="files/adegenet_1.2-8.tar.gz">linux/unix sources</a><br>
+- MacOS X binary (to come)<br>
+- <a href="files/adegenet_1.2-8.zip">Windows binary</a><br>
<br>
<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
The
-<span style="font-weight: bold;">devel version</span> (adegenet_1.2-8)
+<span style="font-weight: bold;">devel version</span> (adegenet_1.2-9)
is also available
from <a href="https://r-forge.r-project.org/scm/?group_id=120"
target="_top">R-Forge's
@@ -47,14 +47,25 @@
use
a
patch.<br>
+<a href="files/patches/makefreq.R"><span style="font-family: monospace;">makefreq.R</span></a>:
+(for
+adegenet_1.2-8 or lower) fixes a an issue occuring when trying to
+compute frequences in data consisting in a single monomorphic locus.<br>
<a href="files/patches/export.R"><span style="font-family: monospace;">export.R</span></a>:
-fixes issues in data conversion from adegenet to hierfstat
+(for
+adegenet_1.2-7 or lower) fixes issues in data conversion from adegenet
+to hierfstat
(genind2hierfstat); also fixes <span style="font-family: monospace;">fstat</span>
function.<br>
<br>
<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
<span style="font-weight: bold;">Older
versions</span>:<br>
+adegenet_1.2-7<br>
+- <a href="files/adegenet_1.2-7.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-7.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-7.zip">Windows binary</a><br>
+<br>
adegenet_1.2-6<br>
- <a href="files/adegenet_1.2-6.tar.gz">linux/unix sources</a><br>
- <a href="files/adegenet_1.2-6.tgz">MacOS X binary</a><br>
Added: www/files/patches/makefreq.R
===================================================================
--- www/files/patches/makefreq.R (rev 0)
+++ www/files/patches/makefreq.R 2010-11-05 14:34:24 UTC (rev 708)
@@ -0,0 +1,59 @@
+####################
+# Function makefreq
+####################
+makefreq <- function(x,quiet=FALSE,missing=NA,truenames=TRUE){
+
+ if(!is.genpop(x)) stop("x is not a valid genpop object")
+ ##if(x at type=="PA") stop("frequencies not computable for presence/asbence data")
+ checkType(x)
+
+ if(!quiet) cat("\n Finding allelic frequencies from a genpop object... \n")
+
+ f1 <- function(v){
+ if(all(is.na(v)) || sum(v,na.rm=TRUE)==0) return(rep(NA,length(v)))
+ return(v/(sum(v,na.rm=TRUE)))
+ }
+
+ res <- list()
+
+ tabcount <- x at tab
+
+ eff.pop <- t(apply(tabcount,1,function(r) tapply(r,x at loc.fac,sum,na.rm=TRUE)))
+ if(nLoc(x)==1){ # fix for nloc==1
+ eff.pop <- t(eff.pop)
+ }
+
+ # tabfreq is a pop x loci table of allelic frequencies
+ tabfreq <- t(apply(tabcount,1,function(r) unlist(tapply(r,x at loc.fac,f1))))
+ if(length(x at loc.nall)==1 && x at loc.nall[1]==1) tabfreq <- t(tabfreq) # matrix is transposed by apply if there's a single allele
+ colnames(tabfreq) <- colnames(x at tab)
+
+ # NA treatment
+ # NA can be kept as is, or replaced 0 or by the mean frequency of the allele.
+ if(!is.na(missing)){
+ if(missing==0) tabfreq[is.na(tabfreq)] <- 0
+ if(toupper(missing)=="MEAN") {
+ moy <- apply(tabfreq,2,function(c) mean(c,na.rm=TRUE))
+ for(j in 1:ncol(tabfreq)) {tabfreq[,j][is.na(tabfreq[,j])] <- moy[j]}
+ }
+ }
+
+ if(!quiet) cat("\n...done.\n\n")
+
+ res$tab <- tabfreq
+ res$nobs <- eff.pop
+ res$call <- match.call()
+
+ ## handle truenames
+ if(truenames){
+ temp <- rep(x at loc.names,x at loc.nall)
+ colnames(res$tab) <- paste(temp,unlist(x at all.names),sep=".")
+ rownames(res$tab) <- x at pop.names
+
+ colnames(res$nobs) <- x at loc.names
+ rownames(res$nobs) <- x at pop.names
+ }
+
+ return(res)
+} #end makefreq
+
Modified: www/news.html
===================================================================
--- www/news.html 2010-11-05 14:28:00 UTC (rev 707)
+++ www/news.html 2010-11-05 14:34:24 UTC (rev 708)
@@ -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
-1.2-7 </span>for R.2.12.0.<br>
+1.2-8 </span>for R.2.12.0.<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
@@ -27,9 +27,32 @@
all modifications.<br>
<br>
<br>
-<span style="font-weight: bold;">29/10/2010 </span><span
+<span style="font-weight: bold;">05/11/2010 </span><span
style="font-weight: bold;"></span><img
style="width: 80px; height: 37px;" alt="" src="images/new.png"><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
+ 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>
+<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
@@ -192,7 +215,8 @@
been
updated
at
-the same time as the package
+the
+same time as the package
release!<br>
<br>
<br>
@@ -213,7 +237,8 @@
many
new
things
-and corrects a few bugs
+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
@@ -230,8 +255,8 @@
diversity
using
RGB
-scale, and a <span
- style="font-family: monospace; color: rgb(255, 0, 0);">loadingplot</span>,
+scale,
+and a <span style="font-family: monospace; color: rgb(255, 0, 0);">loadingplot</span>,
which
can
be
@@ -239,7 +264,8 @@
to
assess
the
-most structuring alleles and loci in an
+most
+structuring alleles and loci in an
analysis. A new georeferenced genetic dataset is also available
(dataset <span style="color: rgb(255, 0, 0); font-family: monospace;">rupica</span>).
And...
@@ -263,7 +289,8 @@
few
bugs
arising
-in version 1.2-0 (see </span></span><a href="files/ChangeLog">ChangeLog</a><span
+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
also improved (have a look at <span
@@ -287,7 +314,8 @@
levels
of
ploidy
-and adds some new
+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>
@@ -328,7 +356,8 @@
bugs
and
adds
-some new features (see </span></span><a href="files/ChangeLog">ChangeLog</a><span
+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;">genind2df</span></span>
@@ -364,7 +393,8 @@
devel
version
of
-adegenet. It computes the <span style="color: rgb(255, 0, 0);">proportion
+adegenet.
+It computes the <span style="color: rgb(255, 0, 0);">proportion
of
shared alleles</span>
among a set of genotypes.<br>
@@ -387,7 +417,8 @@
bugs
and
adds
-some new features:<br>
+some
+new features:<br>
- <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
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