[adegenet-commits] r1178 - in www: . images images/gimp
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 13 06:50:39 CEST 2014
Author: jombart
Date: 2014-05-13 06:50:39 +0200 (Tue, 13 May 2014)
New Revision: 1178
Modified:
www/acceuil.html
www/contact.html
www/documentation.html
www/download.html
www/images/acceuil.png
www/images/gimp/acceuil.xcf
www/links.html
www/literature.html
www/marge.html
www/news.html
www/redirect.html
www/reviewDAPC.html
www/screenshots.html
www/search.html
Log:
New version for 1.4-2; also changed all fonts to Arial.
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2014-05-09 08:59:55 UTC (rev 1177)
+++ www/acceuil.html 2014-05-13 04:50:39 UTC (rev 1178)
@@ -18,9 +18,9 @@
</script>
</head>
<body>
- <div style="margin-left: 40px; text-align: center;"> <img
- style="width: 600px; height: 90px;" alt="title"
- src="images/title.png"><br>
+ <div style="margin-left: 40px; text-align: center; font-family:
+ Helvetica,Arial,sans-serif;"> <img style="width: 600px; height:
+ 90px;" alt="title" src="images/title.png"><br>
<br>
<br>
<br>
@@ -40,8 +40,10 @@
+
Jombart</a>, <a
href="https://sites.google.com/site/caitlincollinswebpage/home">Caitlin
+
Collins</a>, Ismail Ahmed, <a
href="http://www.federicocalboli.com/">Federico Calboli</a>, <a
href="http://www1.imperial.ac.uk/medicine/people/a.cori/">Anne
@@ -75,6 +77,7 @@
+
the bublisher's website</a>]<br>
</li>
</ul>
@@ -85,9 +88,9 @@
<br>
</div>
<div style="text-align: left;">
- <div style="text-align: center;"> <small>sPCA, DAPC,
- typological coherence of markers, Monmonier
- algorithm, ...<br>
+ <div style="text-align: center;"> <small>sPCA, DAPC and its
+ web application, typological coherence of markers,
+ Monmonier algorithm, ...<br>
<br>
</small></div>
<small><br>
@@ -102,12 +105,14 @@
<li>data import from <span style="font-weight: bold;">aligned
+
DNA sequences</span> to <span style="font-weight:
bold;">SNPs</span></li>
<li> data import from <span style="font-weight: bold;">aligned
+
protein sequences</span> to polymorphic sites </li>
<li> data <span style="font-weight: bold;">export</span> to
the R packages genetics, hierfstat, LDheatmap</li>
@@ -125,6 +130,7 @@
+
manipulation</span></li>
<li> basic <span style="font-weight: bold;">data
information </span>(heterozygosity, numbers of alleles,
@@ -144,12 +150,14 @@
+
Fst </span></li>
<li> simulation of <span style="font-weight: bold;">hybridization</span></li>
<li>methods for <span style="font-weight: bold;">spatial
genetics: sPCA, </span><span style="font-weight: bold;">tests
+
for global and local structuring, </span><span
style="font-weight: bold;">Monmonier algorithm</span></li>
<li>the <span style="font-style: italic; font-weight:
@@ -162,6 +170,7 @@
+
</span>for reconstructing genealogies of haplotypes</li>
<li>simulation of <span style="font-weight: bold;">genealogies
@@ -172,6 +181,7 @@
+
of haplotypes</span></li>
<li> Discriminant Analysis of Principal Components (<span
style="font-weight: bold;">DAPC</span>)</li>
@@ -203,6 +213,7 @@
+
Collins (<a href="mailto:caitiecollins17 at gmail.com">caitiecollins at gmail.com</a>),
@@ -212,10 +223,12 @@
+
Ismaïl Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
+
Federico Calboli (<a href="mailto:f.calboli at imperial.ac.uk">f.calboli at imperial.ac.uk</a>),
@@ -223,6 +236,7 @@
+
Anne Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>),
Tobias
@@ -233,6 +247,7 @@
+
Erik Reiners (<a href="mailto:Tobias.Reiners at Senckenberg.de">Tobias.Reiners at Senckenberg.de</a>),
@@ -242,6 +257,7 @@
+
Péter Sólymos (<a href="mailto:solymos at ualberta.ca">solymos at ualberta.ca</a>)<br>
<span style="text-decoration: underline;">Contributors
(datasets/ideas):</span> Christophe Fraser, Katayoun
Modified: www/contact.html
===================================================================
--- www/contact.html 2014-05-09 08:59:55 UTC (rev 1177)
+++ www/contact.html 2014-05-13 04:50:39 UTC (rev 1178)
@@ -18,7 +18,8 @@
</script>
</head>
<body>
- <div style="margin-left: 40px;"><span style="font-weight: bold;
+ <div style="margin-left: 40px; font-family:
+ Helvetica,Arial,sans-serif;"><span style="font-weight: bold;
color: rgb(255, 102, 102);"><br>
Note: I no longer reply to personal emails asking questions that
should be asked on the adegenet forum. </span><span
@@ -27,13 +28,14 @@
questions should go on the adegenet forum. Excitingly, all you
need to know about this forum is just below.</span><br>
</div>
- <br>
- <br>
- <div style="margin-left: 40px;"><img alt="" src="images/bullet.png"
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-family: Helvetica,Arial,sans-serif;">
+ </span><br style="font-family:
+ Helvetica,Arial,sans-serif;">
+ <div style="margin-left: 40px; font-family:
+ Helvetica,Arial,sans-serif;"><img alt="" src="images/bullet.png"
style="width: 10px; height: 10px;"> <span style="font-weight:
- bold;">The
- adegenet
- forum<br>
+ bold;">The adegenet forum<br>
</span>For all discussions/questions related to adegenet.<br>
- one address: adegenet-forum AT lists DOT r-forge DOT r-project
DOT org<br>
@@ -45,117 +47,95 @@
before sending a post<br>
- use the <a style="font-weight: bold;" target="_top"
href="search.html">search engine</a> to look for information in
- the
- archives<br>
+ the archives<br>
- alternatively, you can <a
href="http://lists.r-forge.r-project.org/pipermail/adegenet-forum/">browse
- the
- archives</a> of adegenet forum<br>
+
+ the archives</a> of adegenet forum<br>
- the most frequent questions and their answers are listed at the
bottom of this page.<br>
<br>
<br>
<img alt="" src="images/bullet.png" style="width: 10px; height:
- 10px;">
- For more general questions<span style="font-weight: bold;"> </span>about
-the
-analysis
-of
-genetic
-markers
-in
-R,
-use
- the <a target="_top"
+ 10px;"> For more general questions<span style="font-weight:
+ bold;"> </span>about
+ the
+ analysis
+ of
+ genetic
+ markers
+ in
+ R,
+ use the <a target="_top"
href="https://stat.ethz.ch/mailman/listinfo/r-sig-genetics">R-sig-genetics</a>
mailing list.<br>
<br>
<br>
<img alt="" src="images/bullet.png" style="width: 10px; height:
- 10px;">
- Want
- to track the evolution of the package from the inside ? <br>
+ 10px;"> Want to track the evolution of the package from the
+ inside ? <br>
Subscribe to the commit mailing-list <a
href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-commits"
target="_top">here</a><br>
<br>
<br>
<img alt="" src="images/bullet.png" style="width: 10px; height:
- 10px;">
- Contributions, direct contact with the author: t.jombart AT
- imperial
- DOT ac DOT uk<br>
+ 10px;"> Contributions, direct contact with the author: t.jombart
+ AT imperial DOT ac DOT uk<br>
<br style="color: rgb(0, 102, 0);">
<br style="color: rgb(0, 102, 0);">
<span style="font-weight: bold; color: rgb(255, 102, 102);">Please,
- do use
- the adegenet forum to
- ask questions concerning the
+
+ do use the adegenet forum to ask questions concerning the
package.</span> Browsable archives of this mailing list allow
- other
- users to
- benefit from previous answers.<br>
+ other users to benefit from previous answers.<br>
<br>
<span style="color: rgb(0, 102, 0); font-weight: bold;">Frequently
Asked Questions (and their answers):</span><br>
<br>
<span style="color: rgb(0, 153, 0);"># 1: How do I know which R
- version
- / adegenet version I'm using?</span><br>
+ version / adegenet version I'm using?</span><br>
For R version, type:<br>
- <span style="font-family: monospace;">R.version<br>
- <br>
- </span>For adegenet version, type:<br style="font-family:
- monospace;">
- <span style="font-family: monospace;">packageDescription("adegenet",
- field="Version")</span><br style="font-family: monospace;">
+ R.version<br>
<br>
+ For adegenet version, type:<br>
+ packageDescription("adegenet", field="Version")<br>
<br>
+ <br>
<span style="color: rgb(0, 153, 0);"># 2: Loading adegenet fails
- on
- windows Vista; what's going on?</span><br>
+ on windows Vista; what's going on?</span><br>
This is likely caused by a wrong installation of the package, or
- not
- installing the dependencies.<br>
+ not installing the dependencies.<br>
Start R in 'Administrator' mode (right click on R's icon ->
- "start
- as administrator"), then type:<br>
- <span style="font-family: monospace;">install.packages("adegenet",
- dep=TRUE)</span><br style="font-family: monospace;">
+ "start as administrator"), then type:<br>
+ install.packages("adegenet", dep=TRUE)<br>
<br>
<br>
<span style="color: rgb(0, 153, 0);"># 3: Help pages are not found
- on
- windows...</span><br>
+ on windows...</span><br>
This is likely because your R installation did not include help
- pages
- in html. You need to specify you want to use help in text mode.
- This is
- achieved by typing:<br>
- <span style="font-family: monospace;">options("help_type"="text")<br>
- <br>
- <br>
- </span><span style="color: rgb(0, 153, 0);"># 4: Loading adegenet
- fails
+ pages in html. You need to specify you want to use help in text
+ mode. This is achieved by typing:<br>
+ options("help_type"="text")<br>
+ <br>
+ <br>
+ <span style="color: rgb(0, 153, 0);"># 4: Loading adegenet fails
with this error (R >= 2.13.0): </span><font><font size="2"><br>
<span style="color: rgb(0, 102, 0);">Error in
- as.environment(pos) : no
- item called "newtable" on the search list</span></font></font><br>
+ as.environment(pos) : no item called "newtable" on the
+ search list</span></font></font><br>
This is because the package '<span style="font-style: italic;">graph</span>',
- on
- which
- <span style="font-style: italic;">adegenet</span> depends,
- has been removed from CRAN. You need to install graph from
- bioconductor
- first, and then install adegenet:<br>
- <pre>source("http://bioconductor.org/biocLite.R")<br>biocLite("graph")<span style="font-family: monospace;"><br>install.packages("adegenet", dep=TRUE)</span><br></pre>
- <span style="color: rgb(0, 153, 0);"></span><br
- style="font-family: monospace;">
- <br style="font-family: monospace;">
+
+ on which <span style="font-style: italic;">adegenet</span>
+ depends, has been removed from CRAN. You need to install graph
+ from bioconductor first, and then install adegenet:<br>
+ <pre>source("http://bioconductor.org/biocLite.R")<br>biocLite("graph")<br>install.packages("adegenet", dep=TRUE)<br></pre>
+ <span style="color: rgb(0, 153, 0);"></span><br>
<br>
<br>
<br>
<br>
+ <br>
</div>
</body>
</html>
Modified: www/documentation.html
===================================================================
--- www/documentation.html 2014-05-09 08:59:55 UTC (rev 1177)
+++ www/documentation.html 2014-05-13 04:50:39 UTC (rev 1178)
@@ -21,19 +21,27 @@
<br>
<br>
<br>
- <div style="margin-left: 40px;">As a <span style="text-decoration:
- underline;"><a href="http://www.r-project.org/" target="_top"><img
- alt="" src="images/R.png" style="border: 0px solid ; width:
- 30px; height: 23px;"></a></span> package, each component of
- adegenet is documented in help pages. As a starting point, one can
- type <span style="font-family: monospace; font-weight: bold;">?adegenet</span>
- in R to get an overview of package. Other sources of information
- distributed with the package include a manual and vignettes. This
- website also provides other resources such as lectures and
- practicals.<br>
- <br>
- <span style="font-weight: bold;">To search quickly</span> through
- these resources, use the <a target="_top" href="search.html">search
+ <div style="margin-left: 40px;"><span style="font-family:
+ Helvetica,Arial,sans-serif;">As a </span><span
+ style="text-decoration: underline; font-family:
+ Helvetica,Arial,sans-serif;"><a href="http://www.r-project.org/"
+ target="_top"><img alt="" src="images/R.png" style="border:
+ 0px solid ; width: 30px; height: 23px;"></a></span><span
+ style="font-family: Helvetica,Arial,sans-serif;"> package, each
+ component of adegenet is documented in help pages. As a starting
+ point, one can type </span><span style="font-weight: bold;
+ font-family: Helvetica,Arial,sans-serif;">?adegenet</span><span
+ style="font-family: Helvetica,Arial,sans-serif;"> in R to get an
+ overview of package. Other sources of information distributed
+ with the package include a manual and vignettes. This website
+ also provides other resources such as lectures and practicals.</span><br
+ style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-weight: bold; font-family:
+ Helvetica,Arial,sans-serif;">To search quickly</span><span
+ style="font-family: Helvetica,Arial,sans-serif;"> through these
+ resources, use the </span><a style="font-family:
+ Helvetica,Arial,sans-serif;" target="_top" href="search.html">search
@@ -57,54 +65,62 @@
- engine</a>. <br>
- <br>
- <br>
- <br>
- <span style="font-weight: bold; color: rgb(0, 102, 0);">Manuals</span><br>
- - the adegenet <span style="font-weight: bold;">manual</span> (<a
-href="http://cran.r-project.org/web/packages/adegenet/adegenet.pdf">pdf</a>),
-
-
-
-
-
-
-
-
-
-
-
- which compiles all the manpages of the package.<br>
- <br>
- <br>
- <span style="color: rgb(0, 102, 0); font-weight: bold;">Tutorials*</span><img
- style=" width: 80px; height: 37px;" alt="" src="images/new.png">
+ engine</a><span style="font-family: Helvetica,Arial,sans-serif;">.
+ </span><br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-weight: bold; color: rgb(0, 102, 0);
+ font-family: Helvetica,Arial,sans-serif;">Manuals</span><br
+ style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-family: Helvetica,Arial,sans-serif;"> - the
+ adegenet </span><span style="font-weight: bold; font-family:
+ Helvetica,Arial,sans-serif;">manual</span><span
+ style="font-family: Helvetica,Arial,sans-serif;"> (</span><a
+ style="font-family: Helvetica,Arial,sans-serif;"
+ href="http://cran.r-project.org/web/packages/adegenet/adegenet.pdf">pdf</a><span
+ style="font-family: Helvetica,Arial,sans-serif;">), which
+ compiles all the manpages of the package.</span><br
+ style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="color: rgb(0, 102, 0); font-weight: bold;
+ font-family: Helvetica,Arial,sans-serif;">Tutorials*</span><img
+ style="width: 80px; height: 37px; font-family:
+ Helvetica,Arial,sans-serif;" alt="" src="images/new.png">
<ul>
- <li><a href="files/tutorial-basics.pdf"><span style="font-style:
- italic;">tutorial-basics</span></a>: introduction to the
- package: data classes, inputs/outputs, basic population
- genetics, and exploratory analyses; accessible from R by
- typing <span style="font-family: monospace; color: rgb(255,
- 0, 0);">adegenetTutorial("basics")</span>.</li>
- <li><a href="files/tutorial-dapc.pdf"><span style="font-style:
- italic;">tutorial-dapc</span></a>: a tutorial for the
- analysis of population diversity using Discriminant Analysis
- of Principal Components (DAPC); accessible from R by
- typing <span style="font-family: monospace; color:
- rgb(255, 0, 0);"><span style="font-family: monospace; color:
- rgb(255, 0, 0);">adegenetTutorial</span>("dapc")</span>.</li>
- <li><a href="files/tutorial-genomics.pdf"><span
- style="font-style: italic;">tutorial-genomics</span></a>:
- introduction to the genlight class for storing and handling
- large genome-wide SNP data; accessible from R by typing <span
- style="font-family: monospace;"></span><span
+ <li><a style="font-family: Helvetica,Arial,sans-serif;"
+ href="files/tutorial-basics.pdf"><span style="font-style:
+ italic;">tutorial-basics</span></a><span
+ style="font-family: Helvetica,Arial,sans-serif;">:
+ introduction to the package: data classes, inputs/outputs,
+ basic population genetics, and exploratory analyses;
+ accessible from R by typing </span><span style="color:
+ rgb(255, 0, 0); font-family: Helvetica,Arial,sans-serif;"></span><span
+ style="font-family: monospace; color: rgb(255, 0, 0);">adegenetTutorial("basics")</span>.</li>
+ <li><a style="font-family: Helvetica,Arial,sans-serif;"
+ href="files/tutorial-dapc.pdf"><span style="font-style:
+ italic;">tutorial-dapc</span></a><span style="font-family:
+ Helvetica,Arial,sans-serif;">: a tutorial for the analysis
+ of population diversity using Discriminant Analysis of
+ Principal Components (DAPC); accessible from R by typing</span> <span
+ style="font-family: monospace; color: rgb(255, 0, 0);"><span
+ style="font-family: monospace; color: rgb(255, 0, 0);">adegenetTutorial</span>("dapc")</span>.</li>
+ <li><a style="font-family: Helvetica,Arial,sans-serif;"
+ href="files/tutorial-genomics.pdf"><span style="font-style:
+ italic;">tutorial-genomics</span></a><span
+ style="font-family: Helvetica,Arial,sans-serif;">:
+ introduction to the genlight class for storing and handling
+ large genome-wide SNP data; accessible from R by typing</span>
+ <span style="font-family: monospace;"></span><span
style="font-family: monospace; color: rgb(255, 0, 0);">adegenetTutorial("genomics")</span>.</li>
- <li><a href="files/tutorial-spca.pdf"><span style="font-style:
- italic;">tutorial-spca</span></a>: introduction to spatial
- multivariate analysis using the spatial Principal Component
- Analysis (sPCA); accessible from R by typing <span
+ <li><a style="font-family: Helvetica,Arial,sans-serif;"
+ href="files/tutorial-spca.pdf"><span style="font-style:
+ italic;">tutorial-spca</span></a><span style="font-family:
+ Helvetica,Arial,sans-serif;">: introduction to spatial
+ multivariate analysis using the spatial Principal Component
+ Analysis (sPCA); accessible from R by typing</span> <span
style="font-family: monospace; color: rgb(255, 0, 0);">adegenetTutorial</span><span
style="font-family: monospace; color: rgb(255, 0, 0);">("spca")</span>.</li>
</ul>
@@ -113,9 +129,11 @@
0);"><small>*(note: since adegenet 1.4-0, these tutorials
replace the vignettes which used to be part of the package)</small></span><br>
<br>
- <span style="font-weight: bold; color: rgb(0, 102, 0);"><br>
- Lectures and practicals</span><br>
- <ul>
+ <span style="font-weight: bold; color: rgb(0, 102, 0);
+ font-family: Helvetica,Arial,sans-serif;"><br>
+ Lectures and practicals</span><br style="font-family:
+ Helvetica,Arial,sans-serif;">
+ <ul style="font-family: Helvetica,Arial,sans-serif;">
<li> globaldiv summer school 2009, Piacenza, Italie: <a
href="files/globaldiv-TJ.1.3.pdf">talk</a> - <a
href="files/globaldiv-PC.1.3.pdf">practical course<br>
@@ -143,7 +161,7 @@
<li><a href="files/practical-day3.1.2.pdf">practical 3</a> </li>
</ul>
</ul>
- <ul>
+ <ul style="font-family: Helvetica,Arial,sans-serif;">
<li>MRC methodological session: Introduction to phylogenetics:</li>
<ul>
<li><a href="files/MRCsession2-talk.1.2.pdf">slides</a></li>
@@ -153,8 +171,8 @@
</li>
</ul>
</ul>
- <br>
- <ul>
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <ul style="font-family: Helvetica,Arial,sans-serif;">
<li> RAPID-NGS workshop, Münster (March 2013) - <span
style="font-weight: bold;">Outbreak analysis using <span
style="font-style: italic;">ape </span>and</span> <span
@@ -167,8 +185,8 @@
</li>
</ul>
</ul>
- <br>
- <ul>
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <ul style="font-family: Helvetica,Arial,sans-serif;">
<li>Imperial College - Master <span style="font-style: italic;">Modern
@@ -192,6 +210,7 @@
+
Epidemiology</span> / <i>Public Health</i>: <span
style="font-weight: bold;">Introduction to phylogenetics</span>
(last updated on the 15/13/2013)</li>
@@ -202,8 +221,8 @@
</li>
</ul>
</ul>
- <br>
- <ul>
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <ul style="font-family: Helvetica,Arial,sans-serif;">
<li>Imperial College - Master <span style="font-style: italic;">Modern
@@ -227,6 +246,7 @@
+
Epidemiology</span> / <i>Public Health</i>: <span
style="font-weight: bold;">Introduction to multivariate
analysis / bacterial GWAS</span> (last updated on the
@@ -238,7 +258,7 @@
</li>
</ul>
</ul>
- <ul>
+ <ul style="font-family: Helvetica,Arial,sans-serif;">
<li> GenEpi workshop, London (April 2013) - <span
style="font-weight: bold;">Outbreak analysis using <span
style="font-style: italic;">ape, adegenet,</span> </span><b>and
@@ -257,6 +277,7 @@
+
</b><b><i>outbreaker</i></b></li>
<ul>
<li><a href="files/GenEpiTalk.1.0.pdf">talk</a></li>
@@ -267,13 +288,14 @@
</li>
</ul>
</ul>
- <ul>
+ <ul style="font-family: Helvetica,Arial,sans-serif;">
<li> Molecular Outbreak Epidemiology workshop, Stockholm,
Sweden (November 2013) - <span style="font-weight: bold;">Outbreak
+
analysis using <span style="font-style: italic;">ape,
adegenet,</span> </span><b>and </b><b><i>outbreaker</i></b></li>
<ul>
@@ -285,7 +307,7 @@
</li>
</ul>
</ul>
- <ul>
+ <ul style="font-family: Helvetica,Arial,sans-serif;">
<li>Workshop "<span style="font-weight: bold;">Phylogenetics and
population genetics using R</span>", Montpellier (March
2014) <img style=" width: 80px; height: 37px;" alt=""
@@ -307,53 +329,65 @@
</li>
</ul>
</ul>
- <br>
- <br>
- <br>
- <span style="font-weight: bold; color: rgb(0, 102, 0);">Dirty
- hacks useful for teaching</span><br>
- - a small hack for installing R packages on computers without
- administrative rights: <a href="files/hackLib/hackLib.R">hackLib.R</a>
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- <a href="files/hackLib/README">README</a> <br>
- <br>
- <br>
- <span style="font-weight: bold; color: rgb(0, 102, 0);">Mailing
- lists archives </span><br>
- Use the <a target="_top" href="search.html">search engine</a> to
- browse the <span style="font-weight: bold;">archives</span> of
- the <span style="font-weight: bold;">adegenet forum</span>.<br>
- See the '<a href="contact.html">contact</a>' section of this
- website for further information on mailing lists.<br>
- <br>
- <br>
- <span style="font-weight: bold; color: rgb(0, 102, 0);">Miscellaneous<br>
- </span>- <a href="files/worksOnlyInDiploids.txt">worksOnyInDiploids.txt</a>:
- the list of <span style="font-weight: bold;">functions</span>
- working <span style="font-weight: bold;">only for diploid</span>
- genotypes <br>
- <br>
- <br>
- <span style="font-weight: bold; color: rgb(0, 102, 0);"></span><br>
- <span style="text-decoration: underline;"></span><br>
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-weight: bold; color: rgb(0, 102, 0);
+ font-family: Helvetica,Arial,sans-serif;">Dirty hacks useful for
+ teaching</span><br style="font-family:
+ Helvetica,Arial,sans-serif;">
+ <span style="font-family: Helvetica,Arial,sans-serif;"> - a small
+ hack for installing R packages on computers without
+ administrative rights: </span><a style="font-family:
+ Helvetica,Arial,sans-serif;" href="files/hackLib/hackLib.R">hackLib.R</a><span
+ style="font-family: Helvetica,Arial,sans-serif;"> </span><a
+ style="font-family: Helvetica,Arial,sans-serif;"
+ href="files/hackLib/README">README</a> <br style="font-family:
+ Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-weight: bold; color: rgb(0, 102, 0);
+ font-family: Helvetica,Arial,sans-serif;">Mailing lists archives
+ </span><br style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-family: Helvetica,Arial,sans-serif;"> Use the </span><a
+ style="font-family: Helvetica,Arial,sans-serif;" target="_top"
+ href="search.html">search engine</a><span style="font-family:
+ Helvetica,Arial,sans-serif;"> to browse the </span><span
+ style="font-weight: bold; font-family:
+ Helvetica,Arial,sans-serif;">archives</span><span
+ style="font-family: Helvetica,Arial,sans-serif;"> of the </span><span
+ style="font-weight: bold; font-family:
+ Helvetica,Arial,sans-serif;">adegenet forum</span><span
+ style="font-family: Helvetica,Arial,sans-serif;">.</span><br
+ style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-family: Helvetica,Arial,sans-serif;"> See the '</span><a
+ style="font-family: Helvetica,Arial,sans-serif;"
+ href="contact.html">contact</a><span style="font-family:
+ Helvetica,Arial,sans-serif;">' section of this website for
+ further information on mailing lists.</span><br
+ style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-weight: bold; color: rgb(0, 102, 0);
+ font-family: Helvetica,Arial,sans-serif;">Miscellaneous<br>
+ </span><span style="font-family: Helvetica,Arial,sans-serif;">- </span><a
+ style="font-family: Helvetica,Arial,sans-serif;"
+ href="files/worksOnlyInDiploids.txt">worksOnyInDiploids.txt</a><span
+ style="font-family: Helvetica,Arial,sans-serif;">: the list of </span><span
+ style="font-weight: bold; font-family:
+ Helvetica,Arial,sans-serif;">functions</span><span
+ style="font-family: Helvetica,Arial,sans-serif;"> working </span><span
+ style="font-weight: bold; font-family:
+ Helvetica,Arial,sans-serif;">only for diploid</span><span
+ style="font-family: Helvetica,Arial,sans-serif;"> genotypes </span><br
+ style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="font-weight: bold; color: rgb(0, 102, 0);
+ font-family: Helvetica,Arial,sans-serif;"></span><br
+ style="font-family: Helvetica,Arial,sans-serif;">
+ <span style="text-decoration: underline; font-family:
+ Helvetica,Arial,sans-serif;"></span><br>
<span style="color: rgb(255, 0, 0);"></span></div>
</body>
</html>
Modified: www/download.html
===================================================================
--- www/download.html 2014-05-09 08:59:55 UTC (rev 1177)
+++ www/download.html 2014-05-13 04:50:39 UTC (rev 1178)
@@ -19,72 +19,61 @@
</script>
</head>
<body>
- <br>
- <br>
- <br>
- <div style="margin-left: 40px;"><img alt="" src="images/bullet.png"
- style="width: 10px; height: 10px;"> The package <b>adegenet is
- available from</b> <a
- href="http://cran.r-project.org/mirrors.html">CRAN</a> (stable
- version).<br>
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <br style="font-family: Helvetica,Arial,sans-serif;">
+ <div style="margin-left: 40px; font-family:
+ Helvetica,Arial,sans-serif;"><img alt="" src="images/bullet.png"
+ style="width: 10px; height: 10px;"> The <span
+ style="font-weight: bold;">current stable version</span>
+ (adegenet_1.4-2) <b>is available from</b> <a
+ href="http://cran.r-project.org/web/packages/adegenet/index.html">CRAN</a>.
<br>
+ You can also install adegenet from R by simply typing:<br>
+ <big style="font-family: monospace;">install.packages("adegenet",
+ dep=TRUE)</big><br>
+ <br>
+ <br>
<img alt="" src="images/bullet.png" style="width: 10px; height:
- 10px;"> The <span style="font-weight: bold;">current stable
- version</span> (adegenet_1.4-1) is available as:<br>
+ 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 source("[your-patch-file.R]")
+ to
+ use a patch.<br>
+ <a href="files/patches/addedFeatures.R">addedFeatures.R</a>: (for
+ adegenet >=1.3-1) added features not included in the CRAN
+ version of the package; includes conversion from seqTrack outputs
+ to graphNEL objects. If you have a choice though, consider using
+ current igraph implementation, which is probably better and still
+ maintained.<br>
+ <br>
+ <br>
+ <img alt="" src="images/bullet.png" style="width: 10px; height:
+ 10px;"> <span style="font-weight: bold;">Older versions</span>:<br>
+ adegenet_1.4-1<br>
- <a
href="http://cran.r-project.org/src/contrib/adegenet_1.4-1.tar.gz">linux
+
sources</a><br>
- <a
href="http://cran.r-project.org/bin/macosx/contrib/r-release/adegenet_1.4-0.tgz">MacOS
+
X binary</a><br>
- <a
href="http://cran.r-project.org/bin/windows/contrib/r-release/adegenet_1.4-1.zip">Windows
- binary</a><br>
- <span style="font-family: monospace;"><br>
- <br>
- </span><img alt="" src="images/bullet.png" style="width: 10px;
- height: 10px;"> <span style="font-weight: bold;">Patches</span>
-
-
-
-
-
-
+ binary</a><br>
<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>
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/adegenet -r 1178
More information about the adegenet-commits
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