Vectors for biodiversity indices in RDA plot I'm doing partial distance based (db-)RDA analysis of nematode community data.
I have got the triplots already. They contain vectors of environmental data.
Is it possible to overlay a second set of vectors, describing the relationship of biodiversity/nematode community Indices with community structure of the sites? Or do i have do perform a second db-RDA with these Indices as explanatory variables, and hence replace the environmental data for these Indices.
Or is the use of Biodiversity indices, calculated on the basis of species communities, to explain these communities a circle reasoning?
 A: So it is possible to do a constrained ordination of a species matrix by environmental variables then extract these reduced-space site scores and examine their relationship with vectors of biodiversity/any other variables. But the question it answers is only related to the proportion of variation in the primary (community) matrix explained by those secondary (environmental) variables. I.e. is the structure of the primary matrix constrained by environmental variables in any way related to vectors of biodiversity, if that’s what the question is.
Alternatively, you can constrain the species matrix by vectors of biodiversity, i.e. using them as the secondary ‘environmental’ matrix, which is what you are probably referring to in ‘replace the environmental matrix’. This is an entirely different analysis/question of what biodiversity vectors/metrics are most important in explaining/describing the variation in community composition. I think those two are mixed up a bit in the question above or else the goal is not entirely clear.
