Similarity within and between groups of sites with different species compositions


I' struggling to find descriptions of how to calculate similarity indices (jaccard, sorensen or other) for groups, both within groups and between. Can anyone help me? I have looked at the jaccard(x,y) and sorensen(x,y) functions but as I understand it they can only calculate similarity between two sites which mean I would have to make a lot (!) of calculations so hope someone knows an easier way!

I have 65 sites with different species compositions and the sites are divided into 5 groups of unequal size (5, 15, 15, 15, 15) and I want to explore whether the species compositions are more similar within each group than between groups. Should I use count of species, percentage or binary data?

Are the species data binary (present/not present) or census (number observed)?

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