[adegenet-commits] r968 - pkg/R www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 10 11:31:20 CET 2011
Author: jombart
Date: 2011-11-10 11:31:19 +0100 (Thu, 10 Nov 2011)
New Revision: 968
Modified:
pkg/R/SNPbin.R
pkg/R/glFunctions.R
pkg/R/glHandle.R
pkg/R/import.R
www/literature.html
Log:
Made change required by BR on multicore::: -> parallel:::
+1 ref
Modified: pkg/R/SNPbin.R
===================================================================
--- pkg/R/SNPbin.R 2011-11-08 11:54:09 UTC (rev 967)
+++ pkg/R/SNPbin.R 2011-11-10 10:31:19 UTC (rev 968)
@@ -166,7 +166,7 @@
setMethod("initialize", "genlight", function(.Object, ..., multicore=require("multicore"), n.cores=NULL) {
if(multicore && !require(multicore)) stop("multicore package requested but not installed")
if(multicore && is.null(n.cores)){
- n.cores <- multicore:::detectCores()
+ n.cores <- parallel:::detectCores()
}
x <- .Object
Modified: pkg/R/glFunctions.R
===================================================================
--- pkg/R/glFunctions.R 2011-11-08 11:54:09 UTC (rev 967)
+++ pkg/R/glFunctions.R 2011-11-10 10:31:19 UTC (rev 968)
@@ -178,7 +178,7 @@
## SOME CHECKS ##
if(multicore && !require(multicore)) stop("multicore package requested but not installed")
if(multicore && is.null(n.cores)){
- n.cores <- multicore:::detectCores()
+ n.cores <- parallel:::detectCores()
}
@@ -302,7 +302,7 @@
if(!useC){
if(multicore && !require(multicore)) stop("multicore package requested but not installed")
if(multicore && is.null(n.cores)){
- n.cores <- multicore:::detectCores()
+ n.cores <- parallel:::detectCores()
}
Modified: pkg/R/glHandle.R
===================================================================
--- pkg/R/glHandle.R 2011-11-08 11:54:09 UTC (rev 967)
+++ pkg/R/glHandle.R 2011-11-10 10:31:19 UTC (rev 968)
@@ -254,7 +254,7 @@
if(!is.null(n.block) & !is.null(block.size)) stop("n.block and block.size are both provided.")
if(multicore && !require(multicore)) stop("multicore package requested but not installed")
if(multicore && is.null(n.cores)){
- n.cores <- multicore:::detectCores()
+ n.cores <- parallel:::detectCores()
}
Modified: pkg/R/import.R
===================================================================
--- pkg/R/import.R 2011-11-08 11:54:09 UTC (rev 967)
+++ pkg/R/import.R 2011-11-10 10:31:19 UTC (rev 968)
@@ -727,7 +727,7 @@
if(!quiet) cat("\n Reading biallelic SNP data file into a genlight object... \n\n")
if(multicore && !require(multicore)) stop("multicore package requested but not installed")
if(multicore && is.null(n.cores)){
- n.cores <- multicore:::detectCores()
+ n.cores <- parallel:::detectCores()
}
call <- match.call()
@@ -929,7 +929,7 @@
if(!quiet) cat("\n Reading PLINK raw format into a genlight object... \n\n")
if(multicore && !require(multicore)) stop("multicore package requested but not installed")
if(multicore && is.null(n.cores)){
- n.cores <- multicore:::detectCores()
+ n.cores <- parallel:::detectCores()
}
@@ -1043,7 +1043,7 @@
if(!quiet) cat("\n Converting FASTA alignment into a genlight object... \n\n")
if(multicore && !require(multicore)) stop("multicore package requested but not installed")
if(multicore && is.null(n.cores)){
- n.cores <- multicore:::detectCores()
+ n.cores <- parallel:::detectCores()
}
Modified: www/literature.html
===================================================================
--- www/literature.html 2011-11-08 11:54:09 UTC (rev 967)
+++ www/literature.html 2011-11-10 10:31:19 UTC (rev 968)
@@ -1,763 +1,616 @@
-<!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">
-
- 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;"><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);"
-href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
+<!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">
+ 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);
+ })();
-to
- the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
- <img style="width: 80px; height: 37px;" alt=""
- src="images/new.png"><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"
-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
-href="http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy200834a.pdf">link</a>
- 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>),
+ </script>
+</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);"
+ href="http://bioinformatics.oxfordjournals.org/content/early/2011/09/16/bioinformatics.btr521">link
+to
-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
+the bublisher's website</a><span style="color: rgb(0, 153, 0);">]</span>
+<img style="width: 80px; height: 37px;" alt="" src="images/new.png"><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"
+ 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
-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>):<img style="width: 80px; height: 37px;"
- alt="" src="images/new.png"><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
- class="name"><span class="forenames">FRANCOIS</span> <span
- class="surname">DELMOTTE
- (2010)</span></span> Microsatellite markers reveal two
- admixed genetic
- groups and an ongoing displacement within the French population
- of the
- invasive plant pathogen <span class="i"><span
- style="font-style: italic;">Phytophthora infestans</span>. <span
- style="font-style: italic;">Molecular Ecology</span> <span
- style="font-weight: bold;">19</span>: <span
- style="text-decoration: underline;"></span></span>1965-1977<br>
- <br>
- [15] Gwenaelle Comont, Marie-France Corio-Costet,
- Philippe Larignon and François Delmotte (2010)
- AFLP
- markers reveal two genetic groups in the French population of
- the
- grapevine fungal pathogen <i>Phaeomoniella chlamydospora.
- European
- Journal of Plant Pathology</i> Doi: 10.1007/s10658-010-9611-3<br>
- <br>
- [16] <span class="name"><span class="forenames">Michelle F.</span>
- <span class="surname">DiLeo</span></span>, <span class="name"><span
- class="forenames">Jeffrey R.</span> <span class="surname">Row</span></span>
- and <span class="name"><span class="forenames">Stephen C.</span>
- <span class="surname">Lougheed (2010)</span></span> Discordant
- patterns of
- population structure for two co-distributed snake species across
- a
- fragmented Ontario landscape. <span style="font-style: italic;">Diversity
-and
- Distributions.</span> Doi: <span class="doi">10.1111/j.1472-4642.2010.00667.x<br>
- <br>
- [17] </span><span class="name"><span class="forenames">Francisco</span>
- <span class="surname">Balao</span><sup><nobr></nobr></sup></span>,
- <span class="name"><span class="forenames">Luis M.</span> <span
- class="surname">Valente</span><sup><nobr></nobr></sup></span>,
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