<div dir="ltr"><div> Hello Emma,<br></div><div dir="ltr"><br>You are correct that you can use both find.clusters() and dapc() with your morphometric data. Both of these functions take data frames or matrices of samples in rows and characters in columns. I'll answer you questions below<br><br>> My dataset is a list but when I looked up the pop function, it can only take genind and genepop objects, is that correct?<br><br></div><div>Yes. Genetic data can be placed into the genind/genpop objects because they represent counts of alleles.<br><br>> If so, is there another way to find out how the actual groups compare to the find.cluster output so that I can continue on to correctly perform a DAPC on my data?<br></div><div><br></div><div>The pop() function gives you back a vector of population assignments. If you have that in your original data set, you can compare the column of the population assignments to the $grp element in the output of find.clusters. A caveat, however: You don't NEED to run find.clusters() for DAPC if you already know the group assignments. DAPC creates a multivariate model based on known group definitions, so your previously defined groups should work well. If you want to compare your groups to the find.clusters output, you can test those with chisq.test().<br><br>> I tried to run a DAPC with the following code mydata.dapc <- dapc(mydata) but there were no data points on the graph.<br><br></div><div>If you are using a data frame, you will need to include a vector of population assignments as the pop argument.<br><br></div><div>Hope that helps,</div><div>Zhian<br></div><div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Nov 23, 2019 at 11:00 AM <<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">adegenet-forum-request@lists.r-forge.r-project.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send adegenet-forum mailing list submissions to<br>
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1. Using adegenet with morphometric data (Emma White)<br>
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Date: Fri, 22 Nov 2019 16:25:50 +0000<br>
From: Emma White <Emma.White@Marine.ie><br>
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Subject: [adegenet-forum] Using adegenet with morphometric data<br>
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Hello!<br>
<br>
I had a look through the archive for morphometric related questions and I only found one so hopefully I'm not duplicating any questions.<br>
<br>
I am trying to compare morphometric data with some genetic data from the same samples and my colleague has used adegenet to carry out some analysis which I would like to replicate. I have successfully used the find.cluster function but when I go to use the pop function to see how well the function clustered my data compared with the actual groups I get the following error: "Error in (function (classes, fdef, mtable) : unable to find an inherited methof for function 'pop' for signature '"data.frame"'". My dataset is a list but when I looked up the pop function, it can only take genind and genepop objects, is that correct? If so, is there another way to find out how the actual groups compare to the find.cluster output so that I can continue on to correctly perform a DAPC on my data? I tried to run a DAPC with the following code mydata.dapc <- dapc(mydata) but there were no data points on the graph.<br>
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Thanks for your help.<br>
<br>
Emma<br>
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