In particular, my questions are:
-How to deal with abundances recorded during multiple visits (2 or more) to each sampling unit? I see that a common practice is to consider the maximum over the visits as the abundance in the sampling unit. I wonder whether is it possible to account for species detectability directly in the RDA (as in unmarked for univariate models).
-Is it possible in RDA to account for spatial non-independence of
sampling units?
Finally:
-Is it better to consider occurrence (presence-absence) or abundance in RDA analysis? Which give more robust and reliable results?
Yes, RDA accounts for spatial non-independence. Presence-abscence or abundance are just different ways of measuring biodiversity. You have to decide what you want to measure and choose the one you like best, or use both! :)
Thank you Elia, the subsequent question is: how to implement random factors in RDA (in R vegan)? By partial-RDA?
Andrew, RDA per se doesn't account for spatial non-independence, I suppose. Probably there are specific techniquest to deal with it in RDA. I am wondering how...
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