<div dir="ltr">Dear Ole and Team, <div><br></div><div>sorry, this message was stuck in the moderation limbos for a while. Best subscribe to skip this. </div><div><br></div><div>There's been a bunch of changes since the older version, but the main one I can think of in this case is that a bug has been fixed in predict.dapc when supplementary individuals are used. In some versions prior to 2.0, data were not scaled before being projected onto the discriminant functions, resulting in some erroneous predictions. In practice, it seems supplementary individuals tended to be too drastically assigned to a given group, though not too wrongly (in the microbov example predictions still made sense). This said, I'm not aware of any systematic study of the issue. </div><div><br></div><div>At any rate, trust the current version. </div><div><br></div><div>Best</div><div>Thibaut</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div><div><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology, <span style="font-size:12.8px">Imperial College London</span></div></div><div><span style="font-size:12.8px">Head of RECON: </span><span style="font-size:12.8px"><a href="http://repidemicsconsortium.org" target="_blank">repidemicsconsortium.org</a></span><br></div></div><div><a href="http://sites.google.com/site/thibautjombart/" style="font-size:12.8px" target="_blank">sites.google.com/site/thibautjombart/</a><br></div><div><a href="http://github.com/thibautjombart" target="_blank">github.com/thibautjombart</a></div>Twitter: <a href="http://twitter.com/TeebzR" target="_blank">@TeebzR</a><br></div><div dir="ltr">+44(0)20 7594 3658</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 14 December 2016 at 14:05, Ole Henriksen <span dir="ltr"><<a href="mailto:ohen@aqua.dtu.dk" target="_blank">ohen@aqua.dtu.dk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">Hi Thibaut and Co<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif";background:white">We're a team who have used <i>adegenet</i>'s (version </span><i><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">1-4.1 </span></i><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">and <i>1-4.2 </i><span style="background:white">) <wbr>DAPC
assignment method for some earlier studies. We are now encountering problems using the assignment method. The problem is that the new version </span><i>adegenet 2.0.1 </i>assigns "old individuals", which we have used in earlier studies,<i> </i>differently
compared to assignments with earlier versions of the package.<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">We use SNP data, and our gen-files look as shown below. A<span style="background:white">lleles
are coded by three digits. Se example below</span><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman","serif"">______________________________<wbr>________________</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">GenePop file, with 5 samples & 96 loci</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">cgpGmo-S1017</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">cgpGmo-S1018a</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">cgpGmo-S1026</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">cgpGmo-S1070</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">cgpGmo-S1095</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">cgpGmo-S1103</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">POP</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">DAB08_01 , 001001 002002 001002 002001 001001 001001 </span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">DAB08_02 , 001001 002002 001001 002002 001001 002002 </span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">DAB08_03 , 001001 002002 001001 002002 001001 002001 </span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">POP</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">INC02_01 , 001001 002002 001002 002002 001001 002001 </span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">INC02_02 , 001001 002002 002002 002002 001001 002002</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">INC02_03 , 001001 002002 001002 002002 001001 002001 </span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman","serif"">______________________________<wbr>____________<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">We have two issues<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
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<span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman","serif"">1) Last year we assigned individuals using version <i><span style="background:white">adegenet </span>1-4.1.</i>We
suspected that is must be something with how the file are read, and we wanted to check and compare with older versions (<i>1-4.1 </i>and <i>1-4.2</i>). We've tried to use older versions with </span><i><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">install_version()</span></i><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">
to make the comparison between versions </span><span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman","serif"">(<i>1-4.1</i>, <i>1-4.2
</i>and </span><i><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">2.0.1</span></i><span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman","serif"">)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">,
but we keep getting following error message when using older versions.<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">______________________________<wbr>_____________<u></u><u></u></span></p>
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<i><span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> Converting data from a Genepop .gen file to a genind object... </span></i><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""> </span></p>
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<i><span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">File description: GenePop file, with 5 samples & 96 loci </span></i><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<i><span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">Error in while (keepCheck) { : missing value where TRUE/FALSE needed</span></i><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<i><span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">______________________________<wbr>______________________________</span></i><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">We do not understand why we get this error message, when we use the exact same files
as we have always used. Any idea? <u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> <u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif";background:white">2) When we use the newest version, we get a different assignment result </span><span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman","serif"">compared
to assignments with earlier versions of the </span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">package<span style="background:white">.</span><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">I have my previous assignment results for assigned individuals (<i>1-4.1 </i>and <i>1-4.2</i>).
I reassigned these individuals with the new package (<i>2.0.1</i>). Thereafter, I've compared the assignment between package versions and they are different, <span style="background:white">e</span>ven though we retain the same number of PC's, use same reference
file and use the same script with some minor corrections for reading files to accommodate the new version. Any idea why this is the case? Any changes to how each locus and allele are read from version to version?<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">I have noticed that there is a difference between assignment when using adegenet (<i>2.0.1</i>)
depending on the individuals I include in a gen-file for assignment. When I assign all my individuals from all years in one file, it will give a different assignment result than when I assign single files where they are divided up into years.<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">Can it be the positioning of alleles at each locus which have changed? We are not sure
what is going wrong, but we suspect that it is something with the reading of our files. <u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">Below is some R-history, which hopefully. might be helpful <u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">R-script:<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif"">______________________________<wbr>________________<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">#Reading files</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">Ref <- read.genepop("Ref.gen", ncode = 3)</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">Assign <- read.genepop("TBA_All.gen", ncode = 3)</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">#DAPC</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">DAPC_Ref<-dapc(Ref, pop(Ref), n.pca=100, n.da=3)</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">#Assignment<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">Predict=predict.dapc(DAPC_Ref, newdata=Assign)<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">Predict$assign</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman","serif"">Genind objects after <i>read.genepop()</i>:</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif"">______________________________<wbr>_____<u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">>Reference</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">/// GENIND OBJECT /////////</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> // 487 individuals; 96 loci; 192 alleles; size: 451.5 Kb</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> // Basic content</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @tab: 487 x 192 matrix of allele counts</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @loc.n.all: number of alleles per locus (range: 2-2)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @loc.fac: locus factor for the 192 columns of @tab</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @all.names: list of allele names for each locus</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @ploidy: ploidy of each individual (range: 2-2)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @type: codom</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @call: read.genepop(file = "Ref.gen", ncode = 3)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> // Optional content</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @pop: population of each individual (group size range: 62-215)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">>AssignAll #All individuals for all years</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">/// GENIND OBJECT /////////</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> // 1,357 individuals; 96 loci; 192 alleles; size: 1.1 Mb</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> // Basic content</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @tab: 1357 x 192 matrix of allele counts</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @loc.n.all: number of alleles per locus (range: 2-2)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @loc.fac: locus factor for the 192 columns of @tab</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @all.names: list of allele names for each locus</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @ploidy: ploidy of each individual (range: 2-2)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @type: codom</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @call: read.genepop(file = "TBA_All.gen", ncode = 3)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> // Optional content</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @pop: population of each individual (group size range: 1357-1357)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> <u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">> Assign2015 #individuals for year 2015 only</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif"">/// GENIND OBJECT /////////</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> // 469 individuals; 96 loci; 192 alleles; size: 434.2 Kb</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> // Basic content</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @tab: 469 x 192 matrix of allele counts</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @loc.n.all: number of alleles per locus (range: 2-2)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @loc.fac: locus factor for the 192 columns of @tab</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @all.names: list of allele names for each locus</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @ploidy: ploidy of each individual (range: 2-2)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @type: codom</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @call: read.genepop(file = "TBA_Fisk2015.gen", ncode = 3)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> // Optional content</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:"Times New Roman","serif""> @pop: population of each individual (group size range: 469-469)</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:13.5pt;font-family:"Segoe UI",sans-serif"> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12pt;font-family:"Times New Roman",serif">Assignment result showing different assignment depending on which individuals one include in a input-file (gen-file) for assignment is after <i>predict.dapc()</i>:</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif">______________________________<wbr>_________________________<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif">> Predict$assign </span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif">#All individuals for all years<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [1] TAS10_30 TAS10_30 TAS10_30 TAS10_30 UMM45_39 UMM45_39</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [7] UMM45_39 UMM45_39 TAS10_30 TAS10_30 UMM45_39 UMM45_39</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [13] ISC02_39 UMM45_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [19] UMM45_39 QOR08_30 ISC02_39 UMM45_39 TAS10_30 UMM45_39</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [25] QOR08_30 QOR08_30 UMM45_39 QOR08_30 QOR08_30 UMM45_39</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [31] UMM45_39 UMM45_39 QOR08_30 UMM45_39 UMM45_39 ISC02_39</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [37] ISC02_39 UMM45_39 UMM45_39 QOR08_30 UMM45_39 QOR08_30</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [43] UMM45_39 UMM45_39 UMM45_39 UMM45_39 QOR08_30 UMM45_39</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> etc.</span><span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:10pt;font-family:Arial,sans-serif"> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif">> Predict$assign #individuals for year 2015 only<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [1] TAS10_30 TAS10_30 TAS10_30 TAS10_30 TAS10_30 TAS10_30<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [7] TAS10_30 TAS10_30 TAS10_30 TAS10_30 UMM45_39 UMM45_39<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [13] UMM45_39 UMM45_39 UMM45_39 UMM45_39 UMM45_39 UMM45_39<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [19] UMM45_39 UMM45_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [25] ISC02_39 ISC02_39 TAS10_30 ISC02_39 ISC02_39 ISC02_39<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [31] ISC02_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39 TAS10_30<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [37] ISC02_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39 TAS10_30<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> [43] ISC02_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39 ISC02_39<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:7.5pt;font-family:Arial,sans-serif"> etc.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:13.5pt;font-family:"Segoe UI",sans-serif"> </span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12pt;font-family:"Times New Roman",serif">Thank you<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12pt;font-family:"Times New Roman",serif">Sincerely<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span lang="EN-US" style="font-size:12pt;font-family:"Times New Roman",serif">Ole and team</span><span lang="EN-US" style="font-size:13.5pt;font-family:"Segoe UI",sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
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