text: user752: I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping factor and "Error")
  I have two questions:
  
  What does "error" stand for?
  How do I calculate Fst? Which values do I have to use?
  
  A genind object in R is an object which contains allelic information about a set of individuals.
  This is the table that I get: 
  Analysis of Molecular Variance
  
  Call: amova(formula = plantula.dist ~ g, nperm = 100)  
  
             SSD         MSD  df  
  g     354992.9 354992.9297   1  
  Error 310814.9    693.7834 448 
  Total 665807.9   1482.8683 449 
  
  Variance components:  
         sigma2 P.value  
  g     1574.69       0  
  Error  693.78         
  
  Variance coefficients:  
         a   
  224.9956   
  
  
  user48: Error is the estimation that can't be fitted by your parameters (in this case g). 
  The amova function in pegas package does the following: 
  
  This function performs a hierarchical analysis of molecular variance as described in Excoffier et al.
    (1992). This implementation accepts any number of hierarchical levels
  
  And as per the definition of Fixation index, you need the variance in the frequency of the allele between different subpopulations, weighted by the sizes of the subpopulations, the variance of the allelic state in the total population. Which is not provided by amova. Thus you cannot compute the fixation index from amova results. 
  
original_text: 752: <p>I calculated an AMOVA from a genind object, with one hierarchical factor. In the table I obtain there are SSD values (for my grouping factor,"Error" and total) and sigma2 values (for my grouping factor and "Error")</p>
  
  <p>I have two questions:</p>
  
  <ul>
  <li>What does "error" stand for?</li>
  <li>How do I calculate Fst? Which values do I have to use?</li>
  </ul>
  
  <p>A genind object in R is an object which contains allelic information about a set of individuals.<br>
  This is the table that I get: </p>
  
  <pre><code>Analysis of Molecular Variance
  
  Call: amova(formula = plantula.dist ~ g, nperm = 100)  
  
             SSD         MSD  df  
  g     354992.9 354992.9297   1  
  Error 310814.9    693.7834 448 
  Total 665807.9   1482.8683 449 
  
  Variance components:  
         sigma2 P.value  
  g     1574.69       0  
  Error  693.78         
  
  Variance coefficients:  
         a   
  224.9956   
  </code></pre>
   48: <p>Error is the estimation that can't be fitted by your parameters (in this case g). 
  The amova function in pegas package does the following: </p>
  
  <blockquote>
    <p>This function performs a hierarchical analysis of molecular variance as described in Excoffier et al.
    (1992). This implementation accepts any number of hierarchical levels</p>
  </blockquote>
  
  <p>And as per the definition of Fixation index, you need the variance in the frequency of the allele between different subpopulations, weighted by the sizes of the subpopulations, the variance of the allelic state in the total population. Which is not provided by amova. Thus you cannot compute the fixation index from amova results. </p>
  