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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Mark<br>
<br>
I think you identified the problem. genind object keep only polymorphic sites. <br>
<br>
You would need to 'repool' your supplementary individuals to make sure loci/alleles match, and then just extract the relevant individuals for the prediction.<br>
<br>
Makes sense?<br>
<br>
Best<br>
Thibaut<br>
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<div class="PlainText"> <br>
==============================<br>
Dr Thibaut Jombart<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - School of Public Health<br>
Norfolk Place, London W2 1PG, UK<br>
Tel. : 0044 (0)20 7594 3658<br>
http://sites.google.com/site/thibautjombart/<br>
http://sites.google.com/site/therepiproject/<br>
http://adegenet.r-forge.r-project.org/<br>
Twitter: @thibautjombart<br>
<br>
<br>
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<div style="direction: ltr;" id="divRpF790746"><font face="Tahoma" color="#000000" size="2"><b>From:</b> adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Mark Coulson [Mark.Coulson.ic@uhi.ac.uk]<br>
<b>Sent:</b> 19 June 2015 11:23<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> [adegenet-forum] supplementary individuals<br>
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<p class="MsoNormal">Hi Thibault,</p>
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<p class="MsoNormal">I am trying to use the pred.sup function to assign ‘test’ individuals against my baseline data. Both baseline and supplementary individuals files load fine in adegenet but when I run the pred.sup function I get the following:</p>
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<p class="MsoNormal"><span style="color:red">Error in predict.dapc(dapc1, newdata=sup):</span></p>
<p class="MsoNormal"><span style="color:red"> Number of variables in newdata does not match original data.</span></p>
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<p class="MsoNormal"> </p>
<p class="MsoNormal">Looking at the dataframes, the baseline says it’s a matrix of 1800 x 70 (which I expect), however the supplementary says 69 for the latter(?). I have found that when interrogating @loc.fac for the supplementary file, locus27 is only listed
once, while all others are listed 2x. Perhaps a coincidence but this locus is the only one that is monomorphic in the supplementary individuals but it is polymorphic in the baseline – would this have any effect?</p>
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<p class="MsoNormal">Suggestions?</p>
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<p class="MsoNormal">Thanks,</p>
<p class="MsoNormal">Mark</p>
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Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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