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<div>Hi there, <br>
<br>
this is not an error but a warning, which in this case is most likely harmless. I posted an issue for it:<br>
<a href="https://github.com/thibautjombart/adegenet/issues/103" target="_blank">https://github.com/thibautjombart/adegenet/issues/103</a><br>
<br>
However with 4 individuals in your smallest cluster I'm afraid cross validation is not really practicable, and I would not trust the results.
<br>
<br>
Missing data are replaced by the mean value of the variable. I suspect you use a different method for replacement of missing values, and/or use (implicitly, probably), a different scaling option when passing different types of data to the function.
<br>
<br>
Cheers<br>
Thibaut<br>
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<div style="direction: ltr;" id="divRpF462435"><font color="#000000" face="Tahoma" 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 LAURA NICOLE WOODINGS [17869067@students.latrobe.edu.au]<br>
<b>Sent:</b> 01 November 2015 02:22<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> [adegenet-forum] xval warning<br>
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<div>Hi,</div>
<div><br>
</div>
<div>I am trying to use xval to cross-validate the number of PCs to retain for a DAPC using the below command and I am getting the following error msg:</div>
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<div>xval_nopopbp75_cnt75_cl96_maf5to1 <- xvalDapc(nopop_bp75_cnt75_cl96_maf5to1NoNA@tab, nopop_clust$grp)</div>
<div><br>
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<div>There were 50 or more warnings (use warnings() to see the first 50)</div>
<div>> warnings()</div>
<div>Warning messages:</div>
<div>1: In if (result == "overall") { ... :</div>
<div> the condition has length > 1 and only the first element will be used</div>
<div>2: In if (result == "groupMean") { ... :</div>
<div> the condition has length > 1 and only the first element will be used</div>
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</span></div>
<div>Using find.clusters 2 groups are found but 1 group has 83 individuals and the other group has 4. Is the discrepancy in sample size causing the problem with xval? And if so how can I determine the optimal number of PC’s to keep? I have attached my input
file and the script that I use.</div>
<div><br>
</div>
<div>Also when conduction DAPC should you remove the NA’s in the data? The DAPC seems to work when the Nas are not removed, but when I run it with them removed I get different results.</div>
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<div>Thanks for your help!</div>
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<div>Cheers, </div>
<div><span style="font-family:Calibri">Laura</span></div>
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<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri"><br>
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<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri">PhD Candidate</font></font></div>
<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri">Department of Ecology, Environment and Evolution| La Trobe University | Bundoora 3086 | Australia</font></font></div>
<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri"><br>
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<div><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" face="Calibri">m: +61 408 642 006 | e: 17869067@students.latrobe.edu.au</font></font></div>
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