title: Error when performing an NMDS in R using package vegdist
body: <p>I'm trying to perform an NMDS in R using the vegan package on a data set that has plots as columns and species counts as columns. My data is in the format of a text file (tab delimited) and contains a lot of '0' species counts. However, when I try to create a distance matrix I get the following error message:</p>
  <pre><code>bray &lt;- vegdist(data1, method = &quot;bray&quot;)                              
  </code></pre>
  <blockquote>
  <p>Warning messages:
  1: In vegdist(data1, method = &quot;bray&quot;) :
  you have empty rows: their dissimilarities may be meaningless in method “bray”
  2: In vegdist(data1, method = &quot;bray&quot;) : missing values in results</p>
  </blockquote>
  <p>This prevents me from performing an NMDS:</p>
  <pre><code>nmds &lt;- metaMDS(data1, k = 2, 
  +           distance = 'bray', autotransform = FALSE)
  </code></pre>
  <blockquote>
  <p>Error in if (any(dist &lt; -sqrt(.Machine$double.eps))) warning(&quot;some dissimilarities are negative -- is this intentional?&quot;) :
  missing value where TRUE/FALSE needed
  In addition: Warning messages:
  1: In distfun(comm, method = distance, ...) :
  you have empty rows: their dissimilarities may be meaningless in method “bray”
  2: In distfun(comm, method = distance, ...) : missing values in results</p>
  </blockquote>
  <p>How can I fix this?</p>
  <p>Thank you for your answers!</p>