title: Options for multiple comparisons in vegan::simper
body: <p>I am using the <code>adonis</code> function in the <code>vegan</code> package to determine differences in dissimilarities in a community (PCB congeners) between several different factors. I also have decided to use the <code>simper</code> function to assess which community members contributed most to the observed differences. Is there a way for to include multiple factors in the <code>simper</code> function? I ran the <code>adonis</code> model shown below successfully, but the corresponding code for the <code>simper</code> function doesn't work. Many thanks.</p>
  <pre><code># Adonis model
  pcbtest3 &lt;- adonis(pcbcong ~ FISH_CLASS+REACH+BASIN,
                     data=pcbcov,
                     method=&quot;bray&quot;,
                     permutations=999
                     )
  # pcbcong=matrix of community dissimilarities
  # FISH_CLASS,REACH, BASIN are factors
  # Simper
  simp &lt;- with(pcbcov, simper(pcbcong,(FISH_CLASS, BASIN, REACH)))
  </code></pre>