PINA does not get computed in prepare.community_similarity_data.R

defleury / Schmidt_et_al_2016_community_similarity

Analysis code for a manuscript on community similarity computation

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PINA does not get computed in prepare.community_similarity_data.R #3

Closed karchern closed 7 years ago

karchern commented 7 years ago

both call community.similarity.corr.par (which computes TINA). Needs fix.

defleury commented 7 years ago

The call to the same function is correct. The difference is in the "S" matrix provided: TINA will take a SparCC-based S matrix, PINA will take one based on cophenetic distances. In the uploaded code this is indeed a bug. In the script used for the original paper, the correct S matrix was used.

Fixed by replacing S.sparcc w/ S.phylo in the code.