Answers.Body: <p>If we consult the <a href="https://www.ccg.unam.mx/%7Evinuesa/tlem09/docs/structure_doc.pdf" rel="nofollow noreferrer">structure docs</a>, we observe that they directly address the idea of a <span class="math-container">$Q$</span> distribution for each individual (p. 24), in the form of a Bayesian credible interval, which can be obtained by using the <code>ANCESTDIST</code> flag. Example output is shown on p.34.</p>
  <p>It is not clear to me how to summarize across runs given the different initializations, but I'd trust the internal methods more.</p>
  <p>I am unsure how to integrate this with CLUMPAK. I'd say that they are probably two different ways of getting at a conceptually similar interpretation.</p>
  
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Answers.Text: Thanks--setting the ANCESTDIST flag to 1 did generate Bayesian Credible intervals surrounding each value in the Q matrix, for each STRUICTURE run. 
  
  I will look into how to combine these results across runs.
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Body: <p><strong>Context</strong>: I've run <a href="https://web.stanford.edu/group/pritchardlab/structure.html" rel="nofollow noreferrer">STRUCTURE</a> on a set of 84 individuals (RADseq data) for a range of K values (2--7). I've specified 20 replicate STRUCTURE runs per K value, and these were passed to <a href="https://tau.evolseq.net/clumpak/index.html" rel="nofollow noreferrer">CLUMPAK</a> to summarize results within and across K values, generating a summary Q-matrix for each K value.</p>
  <p><strong>Question</strong>: is there a way to calculate confidence intervals surrounding these summary Q-matrices? My preference is to do so using CLUMPAK, but I am open to other options if they're available. The output of each STRUCTURE run generates a text file containing a Q-matrix, but it isn't clear to me how to combine these for multiple runs to generate confidence intervals.</p>
  <p>Thanks for any suggestions!</p>
  
Tags: <clustering><radseq><population-genetics><admixture>
Title: Confidence intervals around Q-matrix values from multiple STRUCTURE runs
ThreadText: # Confidence intervals around Q-matrix values from multiple STRUCTURE runs
  
  (Asked by: username_0 on 2024-05-09)
  
  **Context**: I've run [STRUCTURE](https://web.stanford.edu/group/pritchardlab/structure.html) on a set of 84 individuals (RADseq data) for a range of K values (2--7). I've specified 20 replicate STRUCTURE runs per K value, and these were passed to [CLUMPAK](https://tau.evolseq.net/clumpak/index.html) to summarize results within and across K values, generating a summary Q-matrix for each K value.
  
  **Question**: is there a way to calculate confidence intervals surrounding these summary Q-matrices? My preference is to do so using CLUMPAK, but I am open to other options if they're available. The output of each STRUCTURE run generates a text file containing a Q-matrix, but it isn't clear to me how to combine these for multiple runs to generate confidence intervals.
  
  Thanks for any suggestions!
  
  **Tags:** clustering, radseq, population-genetics, admixture
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-05-10. Score: 1 | Accepted answer
  
  If we consult the [structure docs](https://www.ccg.unam.mx/%7Evinuesa/tlem09/docs/structure_doc.pdf), we observe that they directly address the idea of a $Q$ distribution for each individual (p. 24), in the form of a Bayesian credible interval, which can be obtained by using the `ANCESTDIST` flag. Example output is shown on p.34.
  
  It is not clear to me how to summarize across runs given the different initializations, but I'd trust the internal methods more.
  
  I am unsure how to integrate this with CLUMPAK. I'd say that they are probably two different ways of getting at a conceptually similar interpretation.
  
  > **Comments:**
  > **username_0**: Thanks--setting the ANCESTDIST flag to 1 did generate Bayesian Credible intervals surrounding each value in the Q matrix, for each STRUICTURE run.   I will look into how to combine these results across runs.  
  
  ---
  
  