title: Does SIMPER in Vegan show percentage dissimilarities or similarities and is there a way to show both?
body: <p>The summary function for simper in vegan provides an output that looks like this for my data:</p>
  
  <pre><code>summary(with(env, simper(species, env$Habitat)))
  
  Contrast: Fringe_Mudflat 
                             average       sd  ratio     ava     avb cumsum
  Bairdiella ronchus        0.255035 0.142025 1.7957 48.3333 50.6667 0.4708
  Diapterus rhombeus        0.054406 0.086815 0.6267  6.1667  1.8333 0.5712
  Stellifer colonensis      0.048659 0.086382 0.5633  5.5000  3.5000 0.6611
  Sphoeroides testudineus   0.038510 0.041463 0.9288  0.0000  5.3333 0.7322
  Anchovia clupeoides       0.026492 0.026885 0.9854  1.5000  3.6667 0.7811
  </code></pre>
  
  <p>and from what Ive read it seems these percentages (average and cumsum) are showing the percentage contribution to the dissimilarity between groups. However the first species clearly has very close means in each group (ava and avb), it really therefore looks like it is picking up this species because of its similarity between groups rather than dissimilarity. Does anyone know if this is definitely dissimilarity or similarity or a mix?</p>
  
  <p>Why is the 'average' so different from the first 'cumsum' and which one should be presented in a paper?</p>
  
  <p>Is there a way to display both percentages for dissimilarity and similarity. I see people presenting this in papers and I assume they get it from Primer but I would like to do it in R.</p>