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?