[adegenet-commits] r966 - in www: . files/patches
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 17 14:52:49 CEST 2011
Author: jombart
Date: 2011-10-17 14:52:49 +0200 (Mon, 17 Oct 2011)
New Revision: 966
Added:
www/files/patches/addedFeatures.R
Modified:
www/download.html
Log:
added patch for added features.
Modified: www/download.html
===================================================================
--- www/download.html 2011-10-15 17:46:21 UTC (rev 965)
+++ www/download.html 2011-10-17 12:52:49 UTC (rev 966)
@@ -1,205 +1,168 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
- <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
- <title>download</title>
- <script type="text/javascript">
-
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', 'UA-20083187-1']);
- _gaq.push(['_trackPageview']);
-
- (function() {
- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
- })();
-
- </script>
-</head>
-<body>
-<br>
-<br>
-<br>
-<div style="margin-left: 40px;"><img alt="" src="images/bullet.png"
- style="width: 10px; height: 10px;">
-The package adegenet is available from <a
- href="http://cran.r-project.org/mirrors.html">CRAN</a> (stable
-version).<br>
-<br>
-<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
-The
-<span style="font-weight: bold;">current stable version</span>
-(adegenet_1.3-1)
-is available as:<br>
-- <a href="files/adegenet_1.3-1.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.3-1.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.3-1.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_1.3-2)
-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>
-<span style="font-family: monospace;">install.packages("adegenet",repos="http://r-forge.r-project.org")<br>
-<br>
-</span><img alt="" src="images/bullet.png"
- style="width: 10px; height: 10px;">
-<span style="font-weight: bold;">Patches</span> to versions <
-1.3-1 <br>
-Patches correct minor bugs or
-implement new functionnalities, and will be included into the next CRAN
-release. It is recommended to use these versions instead of the current
-(CRAN) ones. Simply download the file (right click -> 'Save link
-as') in your working directory and
-type <span style="font-family: monospace;">source("[your-patch-file.R]")</span>
-to
-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>:
-(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>
-<a href="files/patches/dapc.R"><span style="font-family: monospace;">dapc.R</span></a>:
-(for
-adegenet_1.2-8
-or
-lower)
-implements
-new
-plotting
-options
-for
-dapc scatterplots<span style="font-family: monospace;">
-(scatter</span> on <span style="font-family: monospace;">dapc</span>
-objects).<br>
-<a href="files/patches/auxil.R"><span style="font-family: monospace;">auxil.R</span></a>:
-(for
-adegenet_1.2-8
-or
-lower)
-implements
-useful
-auxiliary
-functions
-for
-plotting data such as <span style="font-family: monospace;">transp</span>
-or <span style="font-family: monospace;">num2col</span>.<br>
-<br>
-<br>
-<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
-<span style="font-weight: bold;">Older
-versions</span>:<br>
-adegenet_1.3-0<br>
-- <a href="files/adegenet_1.3-0.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.3-0.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.3-0.zip">Windows binary<br>
-</a><a href="files/adegenet_1.3-0.zip"></a><br>
-adegenet_1.2-9: there is no adegenet_1.2-9...<br>
-<br>
-adegenet_1.2-8<br>
-- <a href="files/adegenet_1.2-8.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-8.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-8.zip">Windows binary</a><br>
-<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>
-- <a href="files/adegenet_1.2-6.zip">Windows binary</a><br>
-<br>
-adegenet_1.2-5<br>
-- <a href="files/adegenet_1.2-5.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-5.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-5.zip">Windows binary</a><br>
-<br>
-adegenet_1.2-4<br>
-- <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.2-4.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.2-4.zip">Windows binary</a><br>
-<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>
-- <a href="files/adegenet_1.2-2.zip">Windows binary</a><br>
-<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>
-- <a href="files/adegenet_1.2-0.zip">Windows binary</a><br>
-<br>
-adegenet_1.1-2<br>
-- <a href="files/adegenet_1.1-2.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.1-2.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.1-2.zip">Windows binary</a><br>
-<br>
-adegenet_1.1-1<br>
-- <a href="files/adegenet_1.1-1.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.1-1.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.1-1.zip">Windows binary</a><br>
-<br>
-adegenet_1.1-0<br>
-- <a href="files/adegenet_1.1-0.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.1-0.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.1-0.zip">Windows binary</a><br>
-<br>
-adegenet_1.0-2<br>
-- <a href="files/adegenet_1.0-2.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.0-2.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.0-2.zip">Windows binary</a><br>
-<br>
-adegenet_1.0-1<br>
-- <a href="files/adegenet_1.0-1.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.0-1.tgz">MacOS X binary</a><br>
-- <a href="files/adegenet_1.0-1.zip">Windows binary</a><span
- style="text-decoration: underline;"><br>
-<br>
-</span>adegenet_1.0-0<br>
-- <a href="files/adegenet_1.0-0.tar.gz">linux/unix sources</a><br>
-- <a href="files/adegenet_1.0-0.tgz">MacOS X binary</a> <br>
-- <a href="files/adegenet_1.0-0.zip">Windows binary</a><br>
-<span style="font-weight: bold;"></span><br>
-</div>
-</body>
-</html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+ <head>
+ <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+ <title>download</title>
+ <script type="text/javascript">
+
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-20083187-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+ </script>
+ </head>
+ <body>
+ <br>
+ <br>
+ <br>
+ <div style="margin-left: 40px;"><img alt="" src="images/bullet.png"
+ style="width: 10px; height: 10px;">
+ The package adegenet is available from <a
+ href="http://cran.r-project.org/mirrors.html">CRAN</a> (stable
+ version).<br>
+ <br>
+ <img alt="" src="images/bullet.png" style="width: 10px; height:
+ 10px;">
+ The
+ <span style="font-weight: bold;">current stable version</span>
+ (adegenet_1.3-1)
+ is available as:<br>
+ - <a href="files/adegenet_1.3-1.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.3-1.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.3-1.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_1.3-2)
+ 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>
+ <span style="font-family: monospace;">install.packages("adegenet",repos="http://r-forge.r-project.org")<br>
+ <br>
+ </span><img alt="" src="images/bullet.png" style="width: 10px;
+ 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 use these versions instead of the
+ current
+ (CRAN) ones. Simply download the file (right click -> 'Save
+ link
+ as') in your working directory and
+ type <span style="font-family: monospace;">source("[your-patch-file.R]")</span>
+ to
+ 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>
+ <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_1.3-0<br>
+ - <a href="files/adegenet_1.3-0.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.3-0.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.3-0.zip">Windows binary<br>
+ </a><a href="files/adegenet_1.3-0.zip"></a><br>
+ adegenet_1.2-9: there is no adegenet_1.2-9...<br>
+ <br>
+ adegenet_1.2-8<br>
+ - <a href="files/adegenet_1.2-8.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.2-8.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.2-8.zip">Windows binary</a><br>
+ <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>
+ - <a href="files/adegenet_1.2-6.zip">Windows binary</a><br>
+ <br>
+ adegenet_1.2-5<br>
+ - <a href="files/adegenet_1.2-5.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.2-5.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.2-5.zip">Windows binary</a><br>
+ <br>
+ adegenet_1.2-4<br>
+ - <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.2-4.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.2-4.zip">Windows binary</a><br>
+ <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>
+ - <a href="files/adegenet_1.2-2.zip">Windows binary</a><br>
+ <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>
+ - <a href="files/adegenet_1.2-0.zip">Windows binary</a><br>
+ <br>
+ adegenet_1.1-2<br>
+ - <a href="files/adegenet_1.1-2.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.1-2.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.1-2.zip">Windows binary</a><br>
+ <br>
+ adegenet_1.1-1<br>
+ - <a href="files/adegenet_1.1-1.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.1-1.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.1-1.zip">Windows binary</a><br>
+ <br>
+ adegenet_1.1-0<br>
+ - <a href="files/adegenet_1.1-0.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.1-0.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.1-0.zip">Windows binary</a><br>
+ <br>
+ adegenet_1.0-2<br>
+ - <a href="files/adegenet_1.0-2.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.0-2.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.0-2.zip">Windows binary</a><br>
+ <br>
+ adegenet_1.0-1<br>
+ - <a href="files/adegenet_1.0-1.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.0-1.tgz">MacOS X binary</a><br>
+ - <a href="files/adegenet_1.0-1.zip">Windows binary</a><span
+ style="text-decoration: underline;"><br>
+ <br>
+ </span>adegenet_1.0-0<br>
+ - <a href="files/adegenet_1.0-0.tar.gz">linux/unix sources</a><br>
+ - <a href="files/adegenet_1.0-0.tgz">MacOS X binary</a> <br>
+ - <a href="files/adegenet_1.0-0.zip">Windows binary</a><br>
+ <span style="font-weight: bold;"></span><br>
+ </div>
+ </body>
+</html>
Added: www/files/patches/addedFeatures.R
===================================================================
--- www/files/patches/addedFeatures.R (rev 0)
+++ www/files/patches/addedFeatures.R 2011-10-17 12:52:49 UTC (rev 966)
@@ -0,0 +1,29 @@
+###########################
+#
+# Added features for
+# adegenet - not part of
+# the official release.
+#
+# T. Jombart
+###########################
+
+
+##########################
+## as("seqTrack", "graphNEL")
+##########################
+if(require(graph)){
+setOldClass("seqTrack")
+setAs("seqTrack", "graphNEL", def=function(from){
+ if(!require(ape)) stop("package ape is required")
+ if(!require(graph)) stop("package graph is required")
+
+ ori.labels <- rownames(from)
+ from <- from[!is.na(from$ances),,drop=FALSE]
+
+
+ ## CONVERT TO GRAPH
+ res <- ftM2graphNEL(ft=cbind(ori.labels[from$ances], ori.labels[from$id]), W=from$weight, edgemode = "directed", V=ori.labels)
+ return(res)
+ })
+}
+
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