[adegenet-commits] r1053 - pkg pkg/R www

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Nov 20 13:00:42 CET 2012


Author: jombart
Date: 2012-11-20 13:00:42 +0100 (Tue, 20 Nov 2012)
New Revision: 1053

Modified:
   pkg/DESCRIPTION
   pkg/R/sequences.R
   www/literature.html
Log:
+1 ref

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2012-11-15 15:50:59 UTC (rev 1052)
+++ pkg/DESCRIPTION	2012-11-20 12:00:42 UTC (rev 1053)
@@ -10,6 +10,6 @@
 Suggests: genetics, spdep, tripack, pegas, seqinr, adehabitat, multicore, akima, maps, splancs, hierfstat
 Depends: R (>= 2.10), methods, MASS, ade4, igraph, ape
 Description: Classes and functions for genetic data analysis within the multivariate framework.
-Collate: classes.R basicMethods.R handling.R auxil.R setAs.R SNPbin.R glHandle.R glFunctions.R glSim.R find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R chooseCN.R genind2genpop.R loadingplot.R sequences.R gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R coords.monmonier.R haploGen.R old2new.R spca.rtests.R dapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R export.R HWE.R propTyped.R inbreeding.R glPlot.R gengraph.R simOutbreak.R zzz.R
+Collate: classes.R basicMethods.R handling.R auxil.R setAs.R SNPbin.R glHandle.R glFunctions.R glSim.R find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R chooseCN.R genind2genpop.R loadingplot.R sequences.R gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R coords.monmonier.R haploGen.R old2new.R spca.rtests.R dapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R export.R HWE.R propTyped.R inbreeding.R glPlot.R gengraph.R simOutbreak.R mutations.R zzz.R
 License: GPL (>=2)
 LazyLoad: yes

Modified: pkg/R/sequences.R
===================================================================
--- pkg/R/sequences.R	2012-11-15 15:50:59 UTC (rev 1052)
+++ pkg/R/sequences.R	2012-11-20 12:00:42 UTC (rev 1053)
@@ -155,59 +155,59 @@
 
 
 
-#################
-## findMutations
-#################
+## #################
+## ## findMutations
+## #################
 
-## GENERIC
-findMutations <- function(...){
-    UseMethod("findMutations")
-}
+## ## GENERIC
+## findMutations <- function(...){
+##     UseMethod("findMutations")
+## }
 
-## METHOD FOR DNABIN
-findMutations.DNAbin <- function(x, from=NULL, to=NULL, ...){
-    ## CHECKS ##
-    if(!require(ape)) stop("the ape package is needed")
-    if(!inherits(x,"DNAbin")) stop("x is not a DNAbin object")
-    x <- as.matrix(x)
+## ## METHOD FOR DNABIN
+## findMutations.DNAbin <- function(x, from=NULL, to=NULL, ...){
+##     ## CHECKS ##
+##     if(!require(ape)) stop("the ape package is needed")
+##     if(!inherits(x,"DNAbin")) stop("x is not a DNAbin object")
+##     x <- as.matrix(x)
 
-    ## function to pull out mutations from sequence a to b ##
-    NUCL <- c('a','t','g','c')
-    f1 <- function(a,b){
-        seqa <- as.character(x[a,])
-        seqb <- as.character(x[b,])
-        temp <- which(seqa != seqb)
-        ori <- seqa[temp]
-        mut <- seqb[temp]
-        names(ori) <- names(mut) <- temp
-        toRemove <- !ori %in% NUCL | !mut %in% NUCL
-        ori <- ori[!toRemove]
-        mut <- mut[!toRemove]
-        if(all(toRemove)) return(NULL)
-        res <- data.frame(ori,mut)
-        names(res) <- rownames(x)[c(a,b)]
-        res$short <- paste(row.names(res),":",res[,1],"->",res[,2],sep="")
-        return(res)
-    }
+##     ## function to pull out mutations from sequence a to b ##
+##     NUCL <- c('a','t','g','c')
+##     f1 <- function(a,b){
+##         seqa <- as.character(x[a,])
+##         seqb <- as.character(x[b,])
+##         temp <- which(seqa != seqb)
+##         ori <- seqa[temp]
+##         mut <- seqb[temp]
+##         names(ori) <- names(mut) <- temp
+##         toRemove <- !ori %in% NUCL | !mut %in% NUCL
+##         ori <- ori[!toRemove]
+##         mut <- mut[!toRemove]
+##         if(all(toRemove)) return(NULL)
+##         res <- data.frame(ori,mut)
+##         names(res) <- rownames(x)[c(a,b)]
+##         res$short <- paste(row.names(res),":",res[,1],"->",res[,2],sep="")
+##         return(res)
+##     }
 
-    ## GET LIST OF PAIRS TO COMPARE ##
-    ## handle NULL
-    if(is.null(from)) from <- 1:nrow(x)
-    if(is.null(to)) to <- 1:nrow(x)
+##     ## GET LIST OF PAIRS TO COMPARE ##
+##     ## handle NULL
+##     if(is.null(from)) from <- 1:nrow(x)
+##     if(is.null(to)) to <- 1:nrow(x)
 
-    ## get pairs
-    pairs <- expand.grid(from, to)
+##     ## get pairs
+##     pairs <- expand.grid(from, to)
 
-    ## remove unwanted comparisons
-    pairs <- pairs[pairs[,1]!=pairs[,2],,drop=FALSE]
+##     ## remove unwanted comparisons
+##     pairs <- pairs[pairs[,1]!=pairs[,2],,drop=FALSE]
 
-    ## GET NUMBER OF MUTATIONS ##
-    out <- lapply(1:nrow(pairs), function(i) f1(pairs[i,1], pairs[i,2]))
-    names(out) <- paste(rownames(x)[pairs[,1]], rownames(x)[pairs[,2]],sep="->")
+##     ## GET NUMBER OF MUTATIONS ##
+##     out <- lapply(1:nrow(pairs), function(i) f1(pairs[i,1], pairs[i,2]))
+##     names(out) <- paste(rownames(x)[pairs[,1]], rownames(x)[pairs[,2]],sep="->")
 
-    return(out)
+##     return(out)
 
-} # end findMutations
+## } # end findMutations
 
 
 
@@ -215,39 +215,39 @@
 
 
 
-##################
-## graphMutations
-##################
+## ##################
+## ## graphMutations
+## ##################
 
-## GENERIC
-graphMutations <- function(...){
-    UseMethod("graphMutations")
-}
+## ## GENERIC
+## graphMutations <- function(...){
+##     UseMethod("graphMutations")
+## }
 
-## METHOD FOR DNABIN
-graphMutations.DNAbin <- function(x, from=NULL, to=NULL, plot=TRUE, edge.curved=TRUE, ...){
-    if(!require(igraph)) stop("igraph is required")
+## ## METHOD FOR DNABIN
+## graphMutations.DNAbin <- function(x, from=NULL, to=NULL, plot=TRUE, edge.curved=TRUE, ...){
+##     if(!require(igraph)) stop("igraph is required")
 
-    ## GET MUTATIONS ##
-    x <- findMutations(x, from=from, to=to)
+##     ## GET MUTATIONS ##
+##     x <- findMutations(x, from=from, to=to)
 
-    ## GET GRAPH ##
-    from <- gsub("->.*","",names(x))
-    to <- gsub(".*->","",names(x))
-    vnames <- sort(unique(c(from,to)))
-    dat <- data.frame(from,to,stringsAsFactors=FALSE)
-    out <- graph.data.frame(dat, directed=TRUE, vertices=data.frame(vnames, label=vnames))
+##     ## GET GRAPH ##
+##     from <- gsub("->.*","",names(x))
+##     to <- gsub(".*->","",names(x))
+##     vnames <- sort(unique(c(from,to)))
+##     dat <- data.frame(from,to,stringsAsFactors=FALSE)
+##     out <- graph.data.frame(dat, directed=TRUE, vertices=data.frame(vnames, label=vnames))
 
-    ## SET ANNOTATIONS FOR THE BRANCHES ##
-    annot <- unlist(lapply(x, function(e) paste(e$short, collapse="\n")))
-    E(out)$label <- annot
-    E(out)$curved <- edge.curved
+##     ## SET ANNOTATIONS FOR THE BRANCHES ##
+##     annot <- unlist(lapply(x, function(e) paste(e$short, collapse="\n")))
+##     E(out)$label <- annot
+##     E(out)$curved <- edge.curved
 
-    ## PLOT / RETURN ##
-    if(plot) plot(out, ...)
+##     ## PLOT / RETURN ##
+##     if(plot) plot(out, ...)
 
-    return(out)
-} # end graphMutations
+##     return(out)
+## } # end graphMutations
 
 
 

Modified: www/literature.html
===================================================================
--- www/literature.html	2012-11-15 15:50:59 UTC (rev 1052)
+++ www/literature.html	2012-11-20 12:00:42 UTC (rev 1053)
@@ -1,10 +1,10 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<!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']);
@@ -17,1337 +17,961 @@
   })();
 
   </script>
-    <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);"
-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
-        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"
-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>),
-      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>
-      <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>
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-        Philippe Larignon and François Delmotte (2010)
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-        grapevine fungal pathogen <i>Phaeomoniella chlamydospora.
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-          Journal of Plant Pathology</i> Doi: 10.1007/s10658-010-9611-3<br>
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-            class="forenames">Jeffrey R.</span> <span class="surname">Row</span></span>
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-          <span class="surname">Lougheed (2010)</span></span> Discordant
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-            class="surname">Valente</span><sup><nobr></nobr></sup></span>,
-        <span class="name"><span class="forenames">Pablo</span> <span
-            class="surname">Vargas</span><sup><nobr></nobr></sup> </span>,
-        <span class="name"><span class="forenames">Javier</span> <span
-            class="surname">Herrera</span><sup><nobr></nobr></sup> </span>
-        and <span class="name"><span class="forenames">Salvador</span>
-          <span class="surname">Talavera</span> (2010)</span> Radiative
-        evolution of
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-          broteri</span> (Caryophyllaceae).<span class="name"> <sup
-            style="font-style: italic;"><nobr></nobr></sup></span><span
-          class="doi"><span style="font-style: italic;">New Phytologist.
-          </span>Doi:</span><span class="doi">
-          10.1111/j.1469-8137.2010.03280.x<br>
-          <br>
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-        Host-specific differentiation among populations of Venturia
-        inaegualis
-        causing scab on apple, pyracantha and loquat. <span
-          style="font-style: italic;">FUNGAL GENETICS AND BIOLOGY</span>
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-          geo-referenced multiscale and multidisciplinary data for the
-          management
-          of biodiversity in livestock genetic resources. <span
-            style="font-style: italic;">Animal Genetics </span><span
-            style="font-weight: bold;">41</span>: 47-63.<br>
-           </span><span class="authors"><span style="white-space:
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-            Denis
-            Laloë</span>, <span style="white-space: nowrap;">Katayoun
-            Moazami-Goudarzi</span>, <span style="white-space: nowrap;">Johannes
-A.
-            Lenstra</span>, <span style="white-space: nowrap;">Paolo
-            Ajmone
-            Marsan</span>, <span style="white-space: nowrap;">Pedro
-            Azor</span>, <span style="white-space: nowrap;">Roswitha
-            Baumung</span>, <span style="white-space: nowrap;">Daniel
-            G. Bradley</span>, <span style="white-space: nowrap;">Michael
-            W. Bruford</span>, <span style="white-space: nowrap;">Javier
-            Cañón</span>, <span style="white-space:
-            nowrap;">Gaudenz Dolf</span>, <span style="white-space:
-            nowrap;">Susana Dunner</span>, <span style="white-space:
-            nowrap;">Georg Erhardt</span>, <span style="white-space:
-            nowrap;">Godfrey Hewitt</span>, <span style="white-space:
-            nowrap;">Juha Kantanen</span>, <span style="white-space:
-            nowrap;">Gabriela Obexer-Ruff</span>, <span
-            style="white-space: nowrap;">Ingrid Olsaker</span>, <span
-            style="white-space: nowrap;">Clemen Rodellar</span>, <span
-            style="white-space: nowrap;">Alessio Valentini</span>, <span
-            style="white-space: nowrap;">Pamela Wiener</span> and <span
-            style="white-space: nowrap;"> European Cattle Genetic
-            Diversity
-            Consortium and Econogene Consortium</span></span> (2010) <span
-          class="title">Spatial Trends of Genetic Variation of Domestic
-          Ruminants in Europe</span>. <span class="idnt"><em>Diversity</em>
-          <b>2010</b>,
-          <em>2</em>(6), 932-945; doi:10.3390/d2060932</span><br>
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-        </span><span class="citation_author">[21] Gautier M, </span> <span
-          class="citation_author">Laloë D, </span> <span
-          class="citation_author">Moazami-Goudarzi K, </span> <span
-          class="citation_date">2010</span> <span
-          class="citation_article_title">Insights
-          into
-          the
-          Genetic
-          History
-          of French Cattle from Dense SNP Data on 47
-          Worldwide Breeds. </span> <span style="font-style: italic;"
-          class="citation_journal_title">PLoS ONE</span><span
-          class="citation_issue"> <span style="font-weight: bold;">5(9)</span>:</span>
-        <span class="citation_start_page">e13038.</span> <span
-          class="citation_doi">doi:10.1371/journal.pone.0013038</span><span
-          class="citation_author">a<br>
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-        Montarry, B.
-        Oakley, et al. 2010. Inferring the evolutionary history of the
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-        pathogen <em>Pseudomonas syringae</em> from its biogeography in
-        headwaters of rivers in North America, Europe, and New Zealand.
-        <span style="font-style: italic;">mBio </span>1(3):e00107-10.
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-          R,
-          Nisbet RE, Hill EW, Howe CJ, Binns M (2010) The cosmopolitan
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-          contribution from British and Irish native mares. <a
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-          ROSSI,
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-        </p>
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-          Stagioni,
-          Giulia Riccioni, Piero Addis, Angelo Cau, Corrado Piccinetti,
-          FaustoTinti (2010) Fishery genetics of mediterranean bluefin
-          tuna:
-          review of existing data, on-going studies and perspectives. <span
-            style="font-style: italic;">Collect. Vol. Sci. Pap. ICCAT</span>,
-          65(3): 988-995</p>
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-            S, </span>
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-            class="citation_date">2010</span> <span
-            class="citation_article_title">Population
-            Genetic
-            Differences
-            along
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-            Latitudinal Cline between Original and
-            Recently Colonized Habitat in a Butterfly. </span> <span
-            style="font-style: italic;" class="citation_journal_title">PLoS
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-            class="citation_start_page">e13810.</span> <span
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-          Malladi and
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-          size on estimation of population genetic data for Chinese and
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-            class="doi"><span class="label">DOI:</span> <span
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-          MAES, G. E.,
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-            italic;">Molecular
[TRUNCATED]

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