title: R package cooccur - help interpreting unintuitive P_lt and P_gt results
body: <p>I was hoping to run visNetwork on some benthic data I have. My first step was to use the cooccur package in RStudio.</p>
  <p>As described <a href="https://medium.com/analytics-vidhya/how-to-create-co-occurrence-networks-with-the-r-packages-cooccur-and-visnetwork-f6e1ceb1c523" rel="nofollow noreferrer">here</a> and similarly in the cooccur publication: &quot;Columns p_lt and p_gt give us our p-values. If p_lt &lt; 0.05, then the species pair co-occurs at a frequency lower than we would expect to find by chance. If p_gt &lt; 0.05, the pair co-occurs at a rate higher than we would expect to find by chance. Since we’ve stored only significant interactions, either p_lt or p_gt will be less than 0.05 for each row.&quot;</p>
  <p>The program says it only stores the significant interactions. However, all of my P_lt values are &lt;0.05 and all of my P_gt values are .99+. Wouldn't this indicate that all of the associations in my cooccurrence network are essentially random (or that the association would be less likely to occur than even by chance)? Does this mean this data is useless for a true network analysis? Why would it say that it only keeps the significant interactions when the stored associations have P values that suggest otherwise?</p>
  <p>Furthermore, the cooccur <a href="https://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2012.00789.x" rel="nofollow noreferrer">paper</a> indicates that P_lt+P_gt+P_et should equal 1; however, in all of my results, P_gt=~1 while the associated P_lt also holds some value between ~.01-.04, which obviously totals to &gt;1. Not sure how to interpret this.</p>
  <p>Any advice would be greatly appreciated! Thanks.</p>