title: metaMDS {vegan} distances instead of community matrix
body: <p>The help file of <code>metaMDS</code> {vegan} mentions that one can also use a <code>dist</code> object instead of community data in the <code>comm</code> argument.</p>
  
  <p>So if I run the following, why do I get different results? Am I doing something wrong here and is <code>metaMDS</code> ending up computing dissimilarities of dissimilarities?</p>
  
  <pre><code>library(vegan)
  data(varespec)
  vare_dist &lt;- vegdist(varespec, method="bray")
  vare_mds &lt;- metaMDS(comm = vare_dist, autotransform = FALSE) 
  # actually autotransform = FALSE doesn't seem to change the results
  plot(vare_mds, type = "t")
  
  vare_mds_2 &lt;- metaMDS(comm = varespec, distance = "bray", k =2)
  plot(vare_mds_2, display = "sites", type = "t")
  
  # plots above are different and the stress values below as well
  vare_mds$stress; vare_mds_2$stress
  # [1] 0.1000211
  # [1] 0.1843196
  </code></pre>
  
  <p>Fallowing this <a href="https://stackoverflow.com/questions/25629645/r-metamds-ordination-distances">SO question</a> I though that using the <code>autotransform = FALSE</code> would fix the issue. However, I think values are not that extreme to trigger a transformation need, so seems not to apply here. Also this <a href="http://r.789695.n4.nabble.com/metaMDS-NMDS-use-of-alternative-distances-td905826.html" rel="nofollow noreferrer">discussion</a> didn't help me much. 
  Specifically, I have a <code>dist</code> object from running <code>unifrac {picante}</code> and I thought I could use it in <code>metaMDS {vegan}</code>.
  PS: unfortunately I'm not an ecologist and I'm trying my best to fallow the jargon. I can only ask for your extreme patience.</p>