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<p class="MsoNormal">Hi, I’m trying to perform a sPCA and am getting an error when I attempt to make a screeplot showing the spatial and variance components of the eigenvalues. The error seems to be coming from the summary command that gets run within screeplot
as I get the following error message:<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Console";color:blue;background:#E1E2E5;mso-fareast-language:EN-AU">> summary(possum.spca2)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-AU"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-AU">Spatial principal component analysis<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-AU"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-AU">Call: spca(obj = nonapossum, cn = possum.graph, scannf = FALSE, nfposi = 2,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-AU"> nfnega = 0)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Console";color:#C5060B;background:#E1E2E5;mso-fareast-language:EN-AU">Error in min(eigL) : invalid 'type' (complex) of argument</span><span style="font-size:10.0pt;font-family:"Lucida Console";color:black;background:#E1E2E5;mso-fareast-language:EN-AU"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Looking at the step in summary just before it breaks, all (or nearly all) values of eigL are complex numbers (e.g. 1.025750e+00+0.000000e+00i).
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Other than this, I am able to go through all of the steps in the examples provided in adegenet-spca.pdf, so I’m not sure if this is a sign of problems with my data set or if it could be something else? I am pointing to problems in my data
set as there is quite a bit of missing data in my genotypes (~12.4%) and I have 1605 individuals.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The code I’m running is:<o:p></o:p></p>
<p class="MsoNormal">…<o:p></o:p></p>
<p class="MsoNormal">data organization steps to prepare my genind object dpossum<o:p></o:p></p>
<p class="MsoNormal">…<o:p></o:p></p>
<p class="MsoNormal">nonapossum<-na.replace(dpossum,met=0)<o:p></o:p></p>
<p class="MsoNormal">possum.graph<-chooseCN(nonapossum$other$xy,type=5,d1=0,d2=5000,plot=FALSE,res="listw")<o:p></o:p></p>
<p class="MsoNormal">possum.spca2<-spca(nonapossum,cn=possum.graph,scannf=FALSE,nfposi=2,nfnega=0)<o:p></o:p></p>
<p class="MsoNormal">screeplot(possum.spca2)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any help in solving this would be greatly appreciated. <o:p>
</o:p></p>
<p class="MsoNormal">-Aaron<o:p></o:p></p>
<p class="MsoNormal">p.s. I think there may be a small typo on page 3 of the manual (adegenet-spca.pdf), I think the page reference for Numerical Ecology should be pp. 752-756 rather than pp. 572-576.
<o:p></o:p></p>
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