So I'm trying to run an NMDS (using the vegan package in R) for a species X site matrix. Unfortunately the abundances of species are not inherently equal (If you can use that word) meaning that not all the sites had equal sampling efforts for this data. Therefore I standardized the abundances of everything by dividing the abundance by the number of months that were actively sampled per site. For example, if site A only sampled 5 out of 12 months and had an abundance of 30 for species B, then the new standardized value would be 30/5 or 6. I realized that when I run the NMDS, the default method in vegan is to utilize bray-curtis distances to calculate distances between sites in terms of dissimilarity or turnover. My question is: Can we use that measure of beta diversity for data that has now been altered and don't reflect true abundances but rather abundances per sampling effort? Maybe the better question is: Is it right to do so? If not then what other sort of measure should I be using.

  • $\begingroup$ Looking at Bray-Curtis distance (or similarity) one can say there is absolutely no restrictions whether the data values be integer, counts, proportions, etc. Any nonnegative values support the formula and its meaning. $\endgroup$ – ttnphns Oct 13 '18 at 19:05
  • $\begingroup$ I'm far not an expert in bioecosystem field but I know many special measures are used to compare abundances, including Ellenberg, Gleason and Pandeya similarities. Maybe they worth to consider for you too. (You can see their formulas in the doc. "Various proximities" on my web-page.) $\endgroup$ – ttnphns Oct 13 '18 at 19:08

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