I've sampled 2 sites for wasps. At each site, I used 20 traps to catch wasps. I sampled each site once a month for 3 months:
Site 1 = 20 samples + 20 samples + 20 samples
Site 2 = 20 samples + 20 samples + 20 samples
So sampling effort and sample size are identical for each site. The traps at each site were setup in the same spots each time. But because I had 20 available, they were not set up simultaneously (one lot were set up for a week, then moved to the other site for a week).
I'm now wanting to construct MDS plots to look at how the wasp species, sites, plant species, trap placement, climate data etc are all related.
My question: When constructing a (dis)similarity table for MDS analysis, do I have to have 120 samples, or can I pool the site data together to just have 40 samples (20 from each site).
Put another way, do I need to split my data up into 3 chunks relating to sampling period or can I pool the data from each period?