These intermediate products of calculation are useful: the normalized abundance vectors, and the products of Z with these (the Zp vectors.)
These are not _in_accessible through the API currently-- After all, there are no private member variables in Python, and we don't call del on these. After instantiating a Metacommunity object m with the abundance matrix and whatever it needs to make the similarity matrix, you can access the p(x) as m.abundance.normalized_subcommunity_abundance[:,p_index] and the Zp and Zq vectors as m.components.normalized_subcommunity_similarity[:,p_index] and m.components.normalized_subcommunity_similarity[:,q_index].
However, this is not obvious, and the member names are confusing. Trivially, we can make this deliberately visible in the Metacommunity's interface, with sensible names.
These intermediate products of calculation are useful: the normalized abundance vectors, and the products of Z with these (the Zp vectors.)
These are not _in_accessible through the API currently-- After all, there are no private member variables in Python, and we don't call
delon these. After instantiating a Metacommunity objectmwith the abundance matrix and whatever it needs to make the similarity matrix, you can access the p(x) asm.abundance.normalized_subcommunity_abundance[:,p_index]and the Zp and Zq vectors asm.components.normalized_subcommunity_similarity[:,p_index]andm.components.normalized_subcommunity_similarity[:,q_index].However, this is not obvious, and the member names are confusing. Trivially, we can make this deliberately visible in the Metacommunity's interface, with sensible names.
What should the sensible names be?