Answers.Body: <p><strong>Disclaimer</strong>: I'm the author of godon. The question above comes from the real communication with a software user.</p>
  
  <p>In the godon implementation of the branch-site model I performed the following reparametrization:</p>
  
  <p><span class="math-container">$p_{01sum} = p_0 + p_1$</span></p>
  
  <p><span class="math-container">$p_{0prop} = \frac{p_0}{p_0 + p_1}$</span>.</p>
  
  <p>This has the following advantages:</p>
  
  <ul>
  <li>Both parameters have a well defined range <span class="math-container">$(0, 1)$</span>.</li>
  <li>There is less dependency between the two. E.g., <span class="math-container">$p_2=1-p_0-p_1$</span> (proportion of sites under positivie selection) does not depend on <span class="math-container">$p_{0prop}$</span>.</li>
  <li>Both properties are very helpful for both likelihood maximization and MCMC.</li>
  </ul>
  
  <p>In case you are interested in <span class="math-container">$p_0$</span> and <span class="math-container">$p_1$</span> there is a straightforward way to go back to the original parameters:</p>
  
  <p><span class="math-container">$p_0=p_{0prop}*p_{01sum}$</span></p>
  
  <p><span class="math-container">$p_1=p_{01sum}-p_0$</span>.</p>
  
  <p>P.S. I also added this information to the <a href="https://github.com/idavydov/godon-tutorial" rel="nofollow noreferrer">tutorial</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-03T13:23:03.470Z
Answers.Text: Damn, I totally missed this package. Godon is seriously nice, great work!
Answers.UserDisplayName: NatWH
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-03T08:00:42.307Z
Answers.LastActivityDate: 2020-06-03T08:25:54.353Z
Answers.LastEditDate: 2020-06-03T08:25:54.353Z
Answers.UserDisplayName: Iakov Davydov
Body: <p>When using branch-site model in <a href="https://bitbucket.org/Davydov/godon/" rel="nofollow noreferrer">Godon</a>, model optimization results include the following parameters: <code>p01sum</code> and <code>p0prop</code>. What are those and how do they relate to <code>p0</code> and <code>p1</code> in the branch-site model?</p>
  
Tags: <codon><positive-selection><godon>
Title: What are the p01sum and p0prop parameters in godon?
ThreadText: # What are the p01sum and p0prop parameters in godon?
  
  (Asked by: username_0 on 2020-06-03)
  
  When using branch-site model in [Godon](https://bitbucket.org/username_0/godon/), model optimization results include the following parameters: `p01sum` and `p0prop`. What are those and how do they relate to `p0` and `p1` in the branch-site model?
  
  **Tags:** codon, positive-selection, godon
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2020-06-03. Score: 1 | Accepted answer
  
  **Disclaimer**: I'm the author of godon. The question above comes from the real communication with a software user.
  
  In the godon implementation of the branch-site model I performed the following reparametrization:
  
  $p\_{01sum} = p\_0 + p\_1$
  
  $p\_{0prop} = \frac{p\_0}{p\_0 + p\_1}$.
  
  This has the following advantages:
  
  * Both parameters have a well defined range $(0, 1)$.
  * There is less dependency between the two. E.g., $p\_2=1-p\_0-p\_1$ (proportion of sites under positivie selection) does not depend on $p\_{0prop}$.
  * Both properties are very helpful for both likelihood maximization and MCMC.
  
  In case you are interested in $p\_0$ and $p\_1$ there is a straightforward way to go back to the original parameters:
  
  $p\_0=p\_{0prop}\*p\_{01sum}$
  
  $p\_1=p\_{01sum}-p\_0$.
  
  P.S. I also added this information to the [tutorial](https://github.com/idavydov/godon-tutorial).
  
  > **Comments:**
  > **username_1**: Damn, I totally missed this package. Godon is seriously nice, great work!  
  
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