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<p class="MsoNormal">Dear all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My dataset consists of 699 individuals sampled at 36 locations (colonies) and genotyped at 10 microsatellites. I have uploaded my dataset in a STRUCTURE format and performed a DAPC analysis on the genind object.<o:p></o:p></p>
<p class="MsoNormal">I wanted to compare these results with results from a sPCA on the genpop object using Delauney triangulation as connection network.<o:p></o:p></p>
<p class="MsoNormal">When calling for the spca plot, the connection network, 3 x score 1 and eigenvalues plots are displayed but the spatial and variance components of the eigenvalues plot doesn’t appear.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When calling for it separately using screeplot, it doesn’t come up either.<o:p></o:p></p>
<p class="MsoNormal">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:black">Error in apply(X, 2, f1) : object 'X' not found<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The same message appears when calling for the summary of the spca.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<pre><span class="gjwpqfqdn4"><span style="font-family:"Lucida Console";color:blue">> </span></span><span class="gjwpqfqdb4"><span style="font-family:"Lucida Console";color:blue">delauney<-spca(pop,ask=F,type=1,scannf=F,nfposi=2,nfnega=0) #select 2 axes for positive, 0 negative<o:p></o:p></span></span></pre>
<pre><span class="gjwpqfqdn4"><span style="font-family:"Lucida Console";color:blue">> </span></span><span class="gjwpqfqdb4"><span style="font-family:"Lucida Console";color:blue">plot(delauney)<o:p></o:p></span></span></pre>
<pre><span class="gjwpqfqdf4"><span style="font-family:"Lucida Console";color:black">Error in apply(X, 2, f1) : object 'X' not found<o:p></o:p></span></span></pre>
<pre><span class="gjwpqfqdn4"><span style="font-family:"Lucida Console";color:blue">> </span></span><span class="gjwpqfqdb4"><span style="font-family:"Lucida Console";color:blue">screeplot(delauney)<o:p></o:p></span></span></pre>
<pre><span class="gjwpqfqdf4"><span style="font-family:"Lucida Console";color:black">Error in apply(X, 2, f1) : object 'X' not found<o:p></o:p></span></span></pre>
<pre><span class="gjwpqfqdn4"><span style="font-family:"Lucida Console";color:blue">> </span></span><span class="gjwpqfqdb4"><span style="font-family:"Lucida Console";color:blue">summary(delauney)<o:p></o:p></span></span></pre>
<pre><span style="font-family:"Lucida Console";color:black"><o:p> </o:p></span></pre>
<pre><span style="font-family:"Lucida Console";color:black">Spatial principal component analysis<o:p></o:p></span></pre>
<pre><span style="font-family:"Lucida Console";color:black"><o:p> </o:p></span></pre>
<pre><span style="font-family:"Lucida Console";color:black">Call: spca(obj = pop, scannf = F, nfposi = 2, nfnega = 0, type = 1, <o:p></o:p></span></pre>
<pre><span style="font-family:"Lucida Console";color:black"> ask = F)<o:p></o:p></span></pre>
<pre><span class="gjwpqfqdf4"><span style="font-family:"Lucida Console";color:black">Error in apply(X, 2, f1) : object 'X' not found</span></span><span style="font-family:"Lucida Console";color:black"><o:p></o:p></span></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The same issue occurs when I used other connection networks.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am at loss trying to figure out what went wrong and how I could obtain the screeplot. Would anyone be able to help?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks a lot.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Caro<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="color:#7030A0">Caroline Moussy<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="color:#7030A0">PhD Spatial ecology of the serotine bat<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#7030A0"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#7030A0">Centre for Ecology and Conservation<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#7030A0">University of Exeter<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#7030A0">Tremough campus<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#7030A0">Penryn<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#7030A0">Cornwall<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#7030A0">TR10 9EZ<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#7030A0">UK<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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