[adegenet-commits] r1063 - pkg/man www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 29 13:25:37 CET 2013
Author: jombart
Date: 2013-01-29 13:25:36 +0100 (Tue, 29 Jan 2013)
New Revision: 1063
Modified:
pkg/man/SNPbin.Rd
pkg/man/genlight.Rd
pkg/man/glAux.Rd
www/acceuil.html
www/literature.html
Log:
commented examples of SNPbin and genlight
Modified: pkg/man/SNPbin.Rd
===================================================================
--- pkg/man/SNPbin.Rd 2013-01-15 23:57:41 UTC (rev 1062)
+++ pkg/man/SNPbin.Rd 2013-01-29 12:25:36 UTC (rev 1063)
@@ -113,6 +113,7 @@
- \code{\linkS4class{genind}}, for storing other types of genetic markers. \cr
}
\examples{
+\dontrun{
#### HAPLOID EXAMPLE ####
## create a genotype of 100,000 SNPs
dat <- sample(c(0,1,NA), 1e5, prob=c(.495, .495, .01), replace=TRUE)
@@ -157,6 +158,6 @@
ab
identical(c(a,b),cbind(a,b))
as.integer(ab)
-
}
+}
\keyword{classes}
Modified: pkg/man/genlight.Rd
===================================================================
--- pkg/man/genlight.Rd 2013-01-15 23:57:41 UTC (rev 1062)
+++ pkg/man/genlight.Rd 2013-01-29 12:25:36 UTC (rev 1063)
@@ -257,6 +257,7 @@
- \code{\linkS4class{genind}}, for storing other types of genetic markers. \cr
}
\examples{
+\dontrun{
## TOY EXAMPLE ##
## create and convert data
dat <- list(toto=c(1,1,0,0), titi=c(NA,1,1,0), tata=c(NA,0,3, NA))
@@ -286,7 +287,6 @@
as.list(x[c(TRUE,FALSE), c(TRUE,TRUE,FALSE,FALSE)])
-\dontrun{
## REAL-SIZE EXAMPLE ##
## 50 genotypes of 1,000,000 SNPs
dat <- lapply(1:50, function(i) sample(c(0,1,NA), 1e6, prob=c(.5, .49, .01), replace=TRUE))
@@ -297,9 +297,9 @@
x
print(object.size(x), unit="au") # size of the genlight object
object.size(dat)/object.size(x) # conversion efficiency
-}
+
#### cbind, rbind ####
a <- new("genlight", list(toto=rep(1,10), tata=rep(c(0,1), each=5), titi=c(NA, rep(1,9)) ))
@@ -326,6 +326,6 @@
pop(x) <- c("pop1","pop1", "pop2") # set population memberships
pop(x)
seppop(x)
-
}
+}
\keyword{classes}
Modified: pkg/man/glAux.Rd
===================================================================
--- pkg/man/glAux.Rd 2013-01-15 23:57:41 UTC (rev 1062)
+++ pkg/man/glAux.Rd 2013-01-29 12:25:36 UTC (rev 1063)
@@ -96,6 +96,7 @@
}
\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
+\dontrun{
x <- new("genlight", list(c(0,0,1,1,0), c(1,1,1,0,0,1), c(2,1,1,1,1,NA)))
x
as.matrix(x)
@@ -116,6 +117,6 @@
apply(temp,2, function(e) sum(is.na(e))) # NAs
apply(temp,2,sum, na.rm=TRUE) # sum
apply(temp,2,mean, na.rm=TRUE) # mean
-
}
+}
\keyword{multivariate}
\ No newline at end of file
Modified: www/acceuil.html
===================================================================
--- www/acceuil.html 2013-01-15 23:57:41 UTC (rev 1062)
+++ www/acceuil.html 2013-01-29 12:25:36 UTC (rev 1063)
@@ -1,8 +1,7 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
- <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
+ <meta content="text/html; charset=iso-8859-1" http-equiv="content-type">
<title>adegenet on the web</title>
<script type="text/javascript">
@@ -15,128 +14,132 @@
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>
-<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;">
+<img style="width: 600px; height: 90px;" alt="title" src="images/title.png"><br>
<br>
<br>
<br>
-<div style="text-align: left;"><span style="font-weight: bold;">adegenet</span>
-is an <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 dedicated to the exploratory analysis of genetic data. It
-implements a set of tools ranging from multivariate methods to spatial
-genetics and genome-wise SNP data analysis. <br>
+
+
+<div style="text-align: left;">
+<span style="font-weight: bold;">adegenet</span> is an <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
+dedicated to the exploratory analysis of genetic data. It implements a set of
+tools ranging from multivariate methods to spatial genetics and genome-wise SNP
+data analysis. <br>
<br>
-It is developed on <a
- href="https://r-forge.r-project.org/projects/adegenet/" target="_top">R-Forge</a>
-by <a href="http://sites.google.com/site/thibautjombart/">Thibaut
-Jombart</a>, Ismail Ahmed and Anne Cori, and officially released on <a
- href="http://cran.r-project.org">CRAN</a> periodically. <br>
+It is developed on <a href="https://r-forge.r-project.org/projects/adegenet/"
+target="_top">R-Forge</a> by <a
+href="http://sites.google.com/site/thibautjombart/">Thibaut Jombart</a>, Ismail
+Ahmed, Anne Cori and Tobias Erik Reiners, and officially released on <a
+href="http://cran.r-project.org">CRAN</a> periodically. <br>
<br>
adegenet is described in the following application notes:<br>
<span style="font-style: italic;"></span>Jombart T. (<span
- style="font-style: italic;"></span>2008)<span
- style="font-weight: bold;"> </span>adegenet: a R package for the
-multivariate analysis of genetic markers. <span
- style="font-style: italic;">Bioinformatics</span> <span
- style="font-weight: bold;">24</span>: 1403-1405. doi:
+style="font-style: italic;"></span>2008)<span
+style="font-weight: bold;"></span>adegenet: a R package for the multivariate
+analysis of genetic markers. <span
+style="font-style: italic;">Bioinformatics</span> <span
+style="font-weight: bold;">24</span>: 1403-1405. doi:
10.1093/bioinformatics/btn129 [<a
- href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129?ijkey=6sqx5BTXCdYtBZz&keytype=ref">link</a>
+href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129?ijkey=6sqx5BTXCdYtBZz&keytype=ref">link</a>
to a free pdf]<br>
<br>
Jombart T. and Ahmed I. (2011) <span style="font-style: italic;">adegenet
1.3-1</span>: new tools for the analysis of genome-wide SNP data. <span
- style="font-style: italic;">Bioinformatics</span>. doi:
+style="font-style: italic;">Bioinformatics</span>. doi:
10.1093/bioinformatics/btr521 [<a
- href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
-
-to
-the bublisher's website</a>]<br>
+href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
+to the bublisher's website</a>]<br>
<br>
<br>
-<div style="text-align: center;"><img
- style="width: 600px; height: 451px;" alt="" src="images/acceuil.png"><br>
+
+
+<div style="text-align: center;">
+<img style="width: 600px; height: 451px;" alt="" src="images/acceuil.png"><br>
<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, typological coherence of markers, Monmonier algorithm,
+...<br>
<br>
</small></div>
<small><br>
-</small><span style="text-decoration: underline;">Main features of
-adegenet are:</span><br>
+</small><span style="text-decoration: underline;">Main features of adegenet
+are:</span><br>
- data representation (<span style="font-weight: bold;">classes</span>)
suitable for multivariate analysis<br>
</div>
-- data <span style="font-weight: bold;">import</span> from GENETIX,
-STRUCTURE, Genepop, Fstat, Easypop, or any dataframe of genotypes<br>
+- data <span style="font-weight: bold;">import</span> from GENETIX, STRUCTURE,
+Genepop, Fstat, Easypop, or any dataframe of genotypes<br>
- data import from <span style="font-weight: bold;">aligned DNA
sequences</span> to <span style="font-weight: bold;">SNPs</span><br>
- data import from <span style="font-weight: bold;">aligned protein
sequences</span> to polymorphic sites<span style="font-weight: bold;"></span>
<br>
-- data <span style="font-weight: bold;">export</span> to the R
-packages genetics, hierfstat, LDheatmap<br>
-- handling of <span style="font-weight: bold;">different levels of
-ploidy<br>
-</span>- handling of <span style="font-weight: bold;">codominant </span>markers<span
- style="font-weight: bold;"> </span>and<span style="font-weight: bold;">
-presence/absence</span> data<span style="font-weight: bold;"><br>
+- data <span style="font-weight: bold;">export</span> to the R packages
+genetics, hierfstat, LDheatmap<br>
+- handling of <span style="font-weight: bold;">different levels of ploidy<br>
+</span>- handling of <span style="font-weight: bold;">codominant
+</span>markers<span style="font-weight: bold;"></span>and<span
+style="font-weight: bold;">presence/absence</span> data<span
+style="font-weight: bold;"><br>
</span>- basic and advanced <span style="font-weight: bold;">data
manipulation</span><br>
-- basic <span style="font-weight: bold;">data information </span>(heterozygosity,
-
-numbers
-of alleles, sample sizes, ...)<br>
+- basic <span style="font-weight: bold;">data information
+</span>(heterozygosity, numbers of alleles, sample sizes, ...)<br>
- <span style="font-weight: bold;">HWE</span> and <span
- style="font-weight: bold;">G-statistic</span> <span
- style="font-weight: bold;">tests</span>, F statistics implemented for
-adegenet objects<br>
+style="font-weight: bold;">G-statistic</span> <span
+style="font-weight: bold;">tests</span>, F statistics implemented for adegenet
+objects<br>
- computation of <span style="font-weight: bold;">genetic</span> <span
- style="font-weight: bold;">distances<br>
-</span>- computation of <span style="font-weight: bold;">pairwise Fst </span><br>
+style="font-weight: bold;">distances<br>
+</span>- computation of <span style="font-weight: bold;">pairwise Fst
+</span><br>
- simulation of <span style="font-weight: bold;">hybridization<br>
</span><span style="font-weight: bold;"></span>- 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<br>
-</span>- the <span style="font-style: italic; font-weight: bold;">seqTrack</span><span
- style="font-weight: bold;"> algorithm </span>for reconstructing
-genealogies of haplotypes<span style="font-weight: bold;"><br>
+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<br>
+</span>- the <span
+style="font-style: italic; font-weight: bold;">seqTrack</span><span
+style="font-weight: bold;">algorithm </span>for reconstructing genealogies of
+haplotypes<span style="font-weight: bold;"><br>
</span>- simulation of <span style="font-weight: bold;">genealogies of
haplotypes</span><br>
- Discriminant Analysis of Principal Components (<span
- style="font-weight: bold;">DAPC</span>)<span style="font-weight: bold;">
-</span><br>
+style="font-weight: bold;">DAPC</span>)<span
+style="font-weight: bold;"></span><br>
- efficient genome-wise SNP data handling and analysis <br>
- extraction of SNP data from genomic alignments <br>
-- <span style="font-weight: bold;">graph-based clustering</span> of
-genomic data <img style="width: 80px; height: 37px;" alt=""
- src="images/new.png"><br>
+- <span style="font-weight: bold;">graph-based clustering</span> of genomic
+data <img style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
<span style="font-weight: bold;"><br>
-<span style="text-decoration: underline; font-weight: bold;">Maintainer</span></span><span
- style="text-decoration: underline; font-weight: bold;">:</span>
-Thibaut Jombart (<a target="_new"
- href="http://sites.google.com/site/thibautjombart/">website</a>)<br>
-<span style="text-decoration: underline;">Developers:</span> Thibaut
-Jombart (<a href="mailto:tjombart at imperial.ac.uk">tjombart at imperial.ac.uk</a>),
-
-Ismaïl
+<span
+style="text-decoration: underline; font-weight: bold;">Maintainer</span></span><span
+style="text-decoration: underline; font-weight: bold;">:</span> Thibaut Jombart
+(<a target="_new"
+href="http://sites.google.com/site/thibautjombart/">website</a>)<br>
+<span style="text-decoration: underline;">Developers:</span> Thibaut Jombart
+(<a href="mailto:tjombart at imperial.ac.uk">tjombart at imperial.ac.uk</a>), Ismaïl
Ahmed (<a href="mailto:ismail.ahmed at inserm.fr">ismail.ahmed at inserm.fr</a>),
-Anne
-Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>)<br>
+Anne Cori (<a href="mailto:a.cori at imperial.ac.uk">a.cori at imperial.ac.uk</a>),
+Tobias Erik Reiners (<a
+href="mailto:Tobias.Reiners at Senckenberg.de">Tobias.Reiners at Senckenberg.de</a>)<br>
<span style="text-decoration: underline;">Contributors
-(functions/datasets/ideas):</span> Péter Sólymos,
-Christophe
-Fraser, Katayoun Moazami-Goudarzi, Denis Laloë, Francois Balloux,
-Dominique Pontier, Daniel Maillard<span style="font-weight: bold;"><br>
+(functions/datasets/ideas):</span> Péter Sólymos, Christophe Fraser, Katayoun
+Moazami-Goudarzi, Denis Laloë, Francois Balloux, Dominique Pontier, Daniel
+Maillard<span style="font-weight: bold;"><br>
<br>
<br style="font-weight: bold;">
Suggestions, comments and contributions are most welcome!</span><br>
Modified: www/literature.html
===================================================================
--- www/literature.html 2013-01-15 23:57:41 UTC (rev 1062)
+++ www/literature.html 2013-01-29 12:25:36 UTC (rev 1063)
@@ -1,10 +1,9 @@
<!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>documentation</title>
- <script type="text/javascript">
+<head>
+ <meta content="text/html; charset=iso-8859-1" http-equiv="content-type">
+ <title>documentation</title>
+ <script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-20083187-1']);
@@ -15,1447 +14,1049 @@
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>
- <meta http-equiv="content-type" content="text/html;
- charset=ISO-8859-1">
- <meta http-equiv="content-type" content="text/html;
- charset=ISO-8859-1">
- </head>
- <body>
- <br>
- <br>
- <br>
- <div style="margin-left: 40px;"><span style="text-decoration:
- underline;">To cite adegenet:</span><br>
- <br>
- <span style="color: rgb(0, 153, 0);">Jombart T</span><span
- style="color: rgb(0, 153, 0);">.</span><span style="color:
- rgb(0, 153, 0);"> (</span><span style="font-style: italic;
- color: rgb(0, 153, 0);"></span><span style="color: rgb(0, 153,
- 0);">2008)</span><span style="font-weight: bold; color: rgb(0,
- 153, 0);"> </span><span style="color: rgb(0, 153, 0);">adegenet:
- a R package for the
- multivariate analysis of genetic markers. </span><span
- style="font-style: italic; color: rgb(0, 153, 0);">Bioinformatics</span><span
- style="color: rgb(0, 153, 0);"> </span><span
- style="font-weight: bold; color: rgb(0, 153, 0);">24</span><span
- style="color: rgb(0, 153, 0);">: 1403-1405. doi:
- 10.1093/bioinformatics/btn129 [</span><a style="color: rgb(0,
- 153, 0);"
+</head>
+
+<body>
+<br>
+<br>
+<br>
+
+
+<div style="margin-left: 40px;">
+<span style="text-decoration: underline;">To cite adegenet:</span><br>
+<br>
+<span style="color: rgb(0, 153, 0);">Jombart T</span><span
+style="color: rgb(0, 153, 0);">.</span><span
+style="color: rgb(0, 153, 0);">(</span><span
+style="font-style: italic; color: rgb(0, 153, 0);"></span><span
+style="color: rgb(0, 153, 0);">2008)</span><span
+style="font-weight: bold; color: rgb(0, 153, 0);"></span><span
+style="color: rgb(0, 153, 0);">adegenet: a R package for the multivariate
+analysis of genetic markers. </span><span
+style="font-style: italic; color: rgb(0, 153, 0);">Bioinformatics</span><span
+style="color: rgb(0, 153, 0);"></span><span
+style="font-weight: bold; color: rgb(0, 153, 0);">24</span><span
+style="color: rgb(0, 153, 0);">: 1403-1405. doi: 10.1093/bioinformatics/btn129
+[</span><a style="color: rgb(0, 153, 0);"
href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129?ijkey=6sqx5BTXCdYtBZz&keytype=ref">link</a><span
- style="color: rgb(0, 153, 0);"> to a free pdf]</span><br>
- <br>
- <span style="color: rgb(0, 153, 0);">Jombart T. and Ahmed I.
- (2011) </span><span style="font-style: italic; color: rgb(0,
- 153, 0);">adegenet 1.3-1</span><span style="color: rgb(0, 153,
- 0);">: new tools for the analysis of
- genome-wide SNP data. </span><span style="font-style: italic;
- color: rgb(0, 153, 0);">Bioinformatics</span><span style="color:
- rgb(0, 153, 0);">. doi: 10.1093/bioinformatics/btr521 [</span><a
- style="color: rgb(0, 153, 0);"
+style="color: rgb(0, 153, 0);">to a free pdf]</span><br>
+<br>
+<span style="color: rgb(0, 153, 0);">Jombart T. and Ahmed I. (2011)
+</span><span
+style="font-style: italic; color: rgb(0, 153, 0);">adegenet
+1.3-1</span><span style="color: rgb(0, 153, 0);">: new tools for the
+analysis of genome-wide SNP data. </span><span
+style="font-style: italic; color: rgb(0, 153, 0);">Bioinformatics</span><span
+style="color: rgb(0, 153, 0);">. doi: 10.1093/bioinformatics/btr521
+[</span><a style="color: rgb(0, 153, 0);"
href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
- to
- the
- bublisher's
- website</a><span style="color: rgb(0, 153, 0);">]</span> <br
- style="color: rgb(0, 153, 0);">
- <br>
- <br style="color: rgb(0, 153, 0);">
- <br>
- <span style="text-decoration: underline;">Related publications:<br>
- <br style="text-decoration: underline;">
- </span>- a review of applications of multivariate analyses to
- genetic
- markers data:<br>
- <b>Jombart T</b>, Pontier D, Dufour AB. (2009) <span
- style="font-style: italic;"></span> Genetic markers in the
- playground
- of multivariate analysis. <span style="font-style: italic;">Heredity
- </span><span style="font-weight: bold;">102</span>: 330-341.
- doi:10.1038/hdy.2008.130<span style="font-style: italic;">. </span>[<a
+to the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span> <br
+style="color: rgb(0, 153, 0);">
+<br>
+<br style="color: rgb(0, 153, 0);">
+<br>
+<span style="text-decoration: underline;">Related publications:<br>
+<br style="text-decoration: underline;">
+</span>- a review of applications of multivariate analyses to genetic markers
+data:<br>
+<b>Jombart T</b>, Pontier D, Dufour AB. (2009) <span
+style="font-style: italic;"></span> Genetic markers in the playground of
+multivariate analysis. <span style="font-style: italic;">Heredity </span><span
+style="font-weight: bold;">102</span>: 330-341. doi:10.1038/hdy.2008.130<span
+style="font-style: italic;">. </span>[<a
href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy2008130a.pdf">link</a>
- to the journal's pdf - <a target="_new"
+to the journal's pdf - <a target="_new"
href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy2008130a.html">free
- abstract</a>]<br>
- <br>
- - the paper presenting the <span style="font-style: italic;">spatial
-principal
- component analysis</span> (<span style="font-style: italic;">sPCA</span>,
- function
- <span style="font-family: monospace; color: rgb(255, 0, 0);">spca</span>),
-
-global
-and
- local tests (<span style="font-family: monospace; color: rgb(255,
- 0, 0);">global.rtest</span>
- and <span style="font-family: monospace; color: rgb(255, 0, 0);">local.rtest</span>):<br>
- <b>Jombart T, </b>Devillard S, Dufour AB, Pontier D<b> </b>(2008)<b>
- </b>Revealing
- cryptic
- spatial patterns in genetic variability by a new multivariate
- method. <span style="font-style: italic;">Heredity</span> <span
- style="font-weight: bold;">101</span>: 92-103. doi:
- 10.1038/hdy.2008.34 [<a
+abstract</a>]<br>
+<br>
+- the paper presenting the <span style="font-style: italic;">spatial principal
+component analysis</span> (<span style="font-style: italic;">sPCA</span>,
+function <span
+style="font-family: monospace; color: rgb(255, 0, 0);">spca</span>), global and
+local tests (<span
+style="font-family: monospace; color: rgb(255, 0, 0);">global.rtest</span>
+and <span
+style="font-family: monospace; color: rgb(255, 0, 0);">local.rtest</span>):<br>
+<b>Jombart T, </b>Devillard S, Dufour AB, Pontier
+D<b></b>(2008)<b></b>Revealing cryptic spatial patterns in genetic variability
+by a new multivariate method. <span
+style="font-style: italic;">Heredity</span> <span
+style="font-weight: bold;">101</span>: 92-103. doi: 10.1038/hdy.2008.34 [<a
href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy200834a.pdf">link</a>
- on the journal's website - <a target="_new"
+on the journal's website - <a target="_new"
href="http://www.nature.com/hdy/journal/vaop/ncurrent/abs/hdy200834a.html">free
- abstract</a>]<br>
- </div>
- <br>
- <div style="margin-left: 40px;"><span style="font-family: monospace;
- font-weight: bold;"></span><span style="font-family: monospace;
- font-weight: bold;"></span>- the paper
- presenting the <span style="font-style: italic;">SeqTrack </span>algorithm
- (<span style="font-family: monospace; color: rgb(255, 0, 0);">seqTrack</span>),
+abstract</a>]<br>
+</div>
+<br>
-and
-simulations
+<div style="margin-left: 40px;">
+<span style="font-family: monospace; font-weight: bold;"></span><span
+style="font-family: monospace; font-weight: bold;"></span>- the paper
+presenting the <span style="font-style: italic;">SeqTrack </span>algorithm
+(<span style="font-family: monospace; color: rgb(255, 0, 0);">seqTrack</span>),
+and simulations of genealoies of haplotypes (<span
+style="font-family: monospace; color: rgb(255, 0, 0);">haploGen</span>):<br>
+<b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010) Reconstructing disease
+outbreaks from genetic data: a graph approach. <span
+style="font-style: italic;">Heredity</span>. Doi: 10.1038/hdy.2010.78<br>
+<br>
+- the paper introducing the <span style="font-style: italic;">Discriminant
+Analysis of Principal Components</span> (<span
+style="font-style: italic;">DAPC</span>, functions <span
+style="font-family: monospace;"><span
+style="color: rgb(255, 0, 0);">find.clusters</span> </span>and <span
+style="font-family: monospace; color: rgb(255, 0, 0);">dapc</span>):<br>
+<b>Jombart T</b>, Devillard S and Balloux F <b></b>(2010) Discriminant analysis
+of principal components: a new method for the analysis of genetically
+structured populations. <i>BMC Genetics</i>
+<strong>11</strong><strong>:</strong>94.
+<span>doi:10.1186/1471-2156-11-94</span> [<a href="files/DAPCpaper.pdf">free
+pdf</a>] [<a href="http://www.biomedcentral.com/1471-2156/11/94">free html
+version</a>] [<a href="reviewDAPC.html">evaluation by Laurent Excoffier on
+F1000</a>] <br>
+<br>
+<br>
+<br>
+<span style="text-decoration: underline;">Publications citing
+adegenet:</span><br style="text-decoration: underline;">
+<br>
+[1] Cohas A, Yoccoz NG, Bonenfant C, Goossens B, Genton C, Galan M, Kempenaers
+B, Allainé D (2007) The<span style="color: rgb(0, 0, 0);">genetic
+similarity between pair members influences the frequency of extrapair paternity
+in alpine marmots</span>. <i>Animal Behaviour</i><i></i><span
+style="font-weight: bold;">76</span>: 87-95.<br>
+<br>
+[2] Satkoski JA, Malhi RS, Kanthaswamy S, Tito RY, Malladi VS, Smith DG (2008)
+Pyrosequencing as a method for SNP identification in the rhesus macaque
+(<em>Macaca mulatta</em>). <span class="citation-abbreviation"><span
+style="font-style: italic;">BMC Genomics</span></span><span
+class="citation-publication-date"></span><span style="font-weight: bold;"
+class="citation-volume">9</span><span class="citation-issue"></span>: 256.<br>
-of
-genealoies
- of haplotypes (<span style="font-family: monospace; color:
- rgb(255, 0, 0);">haploGen</span>):<br>
- <b>Jombart T, </b>Eggo RM, Dodd PJ, Balloux F (2010)
- Reconstructing
- disease outbreaks from genetic data: a graph approach. <span
- style="font-style: italic;">Heredity</span>. Doi:
- 10.1038/hdy.2010.78<br>
- <br>
- - the paper introducing the <span style="font-style: italic;">Discriminant
- Analysis
- of
- Principal
- Components</span> (<span style="font-style: italic;">DAPC</span>,
- functions <span style="font-family: monospace;"><span
- style="color: rgb(255, 0, 0);">find.clusters</span> </span>and
- <span style="font-family: monospace; color: rgb(255, 0, 0);">dapc</span>):<br>
- <b>Jombart T</b>, Devillard S and Balloux F <b> </b>(2010)
- Discriminant analysis of principal components: a new method for
- the
- analysis of genetically structured populations. <i>BMC Genetics</i>
- <strong>11</strong><strong>:</strong>94.
- <span>doi:10.1186/1471-2156-11-94</span> [<a
- href="files/DAPCpaper.pdf">free
- pdf</a>] [<a href="http://www.biomedcentral.com/1471-2156/11/94">free
-html
- version</a>] [<a href="reviewDAPC.html">evaluation by Laurent
- Excoffier on F1000</a>] <br>
- <br>
- <br>
- <br>
- <span style="text-decoration: underline;">Publications citing
- adegenet:</span><br style="text-decoration: underline;">
- <br>
- [1] Cohas A, Yoccoz NG, Bonenfant C, Goossens B, Genton C, Galan
- M,
- Kempenaers B, Allainé D (2007) The<span style="color:
- rgb(0, 0, 0);"> genetic similarity between pair members
- influences the frequency of extrapair paternity in alpine
- marmots</span>.
- <i>Animal Behaviour</i><i> </i><span style="font-weight: bold;">76</span>:
- 87-95.<br>
- <br>
- [2] Satkoski JA, Malhi RS, Kanthaswamy S, Tito RY, Malladi
- VS,
- Smith DG (2008) Pyrosequencing as a method for SNP identification
- in
- the rhesus macaque (<em>Macaca mulatta</em>). <span
- class="citation-abbreviation"><span style="font-style: italic;">BMC
- Genomics</span></span><span class="citation-publication-date">
- </span><span style="font-weight: bold;" class="citation-volume">9</span><span
- class="citation-issue"></span>: 256.<br>
- <div><span class="citation-flpages"><br>
- [3] </span>Kanthaswamy S, Satkoski J, George D, Kou A,
- Erickson BJ,
- Smith DG. (2008). Interspecies hybridization and the
- stratification of
- nuclear genetic variation of rhesus (<span style="font-style:
- italic;">Macaca
- mulatta</span>) and long-tailed macaques (<span
- style="font-style: italic;">Macaca </span><span
- style="font-style: italic;">fascicularis</span>). <span
- style="font-style: italic;">Int J Primatol</span> <span
- style="font-weight: bold;">29</span>: 1295-1311.<br>
- <br>
- [4] Kidd, AG, Bowman J, Lesbarrères D, Schulte-Hostedde
- AI
- (2009). Hybridization between escaped domestic and wild American
- mink (<span style="font-style: italic;">Neovison vison</span>).
- <span style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 1175-1186.<br>
- <br>
- [5] Cohas E, Bonenfant C, Kempaners B, Allainé D (2009).
- Age-specific effect of heterozygosity on survival in alpine
- marmots, <span class="i"><span style="font-style: italic;">Marmota
- marmota</span>.</span><span style="font-style: italic;">
- Molecular Ecology</span> <span style="font-weight: bold;">18</span>:
- 1491-1503.<br>
- <br>
- [6] O'Brien J, Devillard S, Say L, Vanthomme A, Léger F,
- Ruette
- S, Pontier D (2009). Preserving genetic integrity in a
- hybridising
- world:<br>
- are European Wildcats (<span style="font-style: italic;">Felis
- silvestris silvestris</span>) in eastern France distinct from
- sympatric
- feral domestic cats? <span style="font-style: italic;">Biodivers
- Conserv</span> <span style="font-weight: bold;">18</span>:
- 2351-2360.<br>
- <br>
- [7] Kanthaswamy S <span style="font-style: italic;">et al.</span>
- (2009). Canine Population Data Generated from a Multiplex STR
- Kit for
- Use in Forensic Casework. <span style="font-style: italic;">Journal
- of
- Forensic Sciences</span> <span style="font-weight: bold;">54</span>:
- 829-840.<br>
- <br>
- [8] Lankau R A, Nuzzo V, Spyreas G, Davis A S (2009).
- Evolutionary
- limits ameliorate the negative impact of an invasive plant. <span
- style="font-style: italic;">Proceedings of the National
- Academy of
- Sciences</span> <span style="font-weight: bold;">106</span>:
- 15362-15367.<br>
- <br>
- [9] Dutech C, Fabreguettes O, Capdevielle X, Robin C (2009)
- Multiple
- introductions of divergent genetic lineages in an invasive
- fungal
- pathogen, Cryphonectria parasitica, in France. <span
- style="font-style: italic;">Heredity</span> (advanced online)
- doi:
- 10.1038/hdy.2009.164.<br>
- <br>
- [10] L Y Rutledge, C J Garroway, K M Loveless and
- B
- R Patterson (2010) Genetic differentiation of eastern
- wolves in
- Algonquin Park despite bridging gene flow between coyotes and
- grey
- wolves.<span style="font-style: italic;"> Heredity</span>
- (advanced
- online) doi: 10.1038/hdy.2010.6.<br>
- <br>
- [11] Jennifer Paul, Nicole Vachon,
- Colin J. Garroway and Joanna R. Freeland
- (2010)
- Molecular data provide strong evidence of natural hybridization
- between
- native and introduced lineages of <i>Phragmites australis</i>
- in North
- America. <span style="font-style: italic;">Biological Invasions</span>.
- doi:
- 10.1007/s10530-010-9699-6.<br>
- <br>
- [12] C. BERTHOULY, D. DO NGOC, S. THÉVENON, D. BOUCHEL,
- T. NHU
- VAN, C. DANES, V. GROSBOIS, H. HOANG THANH, C. VU CHI, J.-C.
- MAILLARD
- (2009) How does farmer connectivity influence livestock genetic
- structure? A case-study in a Vietnamese goat population. <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">18</span>: 3980-3991<br>
- <br>
- [13] <span class="name"><span class="forenames">COLIN J.</span>
- <span class="surname">GARROWAY</span><sup><nobr></nobr></sup></span>,
- <span class="name"><span class="forenames">JEFF</span> <span
- class="surname">BOWMAN</span></span>,
- <span class="name"><span class="forenames">TARA J.</span> <span
- class="surname">CASCADEN</span></span>, <span class="name"><span
- class="forenames">GILLIAN L.</span> <span class="surname">HOLLOWAY</span></span>,
- <span class="name"><span class="forenames">CAROLYN G.</span> <span
- class="surname">MAHAN</span></span>, <span class="name"><span
- class="forenames">JAY R.</span> <span class="surname">MALCOLM</span></span>,
- <span class="name"><span class="forenames">MICHAEL A.</span> <span
- class="surname">STEELE</span><sup><nobr></nobr></sup></span>,
- <span class="name"><span class="forenames">GREGORY</span> <span
- class="surname">TURNER</span></span> and <span class="name"><span
- class="forenames">PAUL J.</span> <span class="surname">WILSON</span>
- (2009) </span>Climate change induced hybridization in flying
- squirrels. <span style="font-style: italic;">Global Change
- Biology</span>
- <span style="font-weight: bold;">16</span>: 113-121.<br>
- <br>
- [14] <span class="name"><span class="forenames">JOSSELIN</span>
- <span class="surname">MONTARRY</span></span>, <span
- class="name"><span class="forenames">DIDIER</span> <span
- class="surname">ANDRIVON</span>,</span>
- <span class="name"><span class="forenames">ISABELLE</span> <span
- class="surname">GLAIS</span></span>, <span class="name"><span
- class="forenames">ROSELYNE</span> <span class="surname">CORBIERE</span></span>,
- <span class="name"><span class="forenames">GLADYS</span> <span
- class="surname">MIALDEA</span></span> and <span
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/adegenet -r 1063
More information about the adegenet-commits
mailing list