Including multiPhylo objects #44
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added 8 commits
August 23, 2024 19:27
erik-ringen
approved these changes
Sep 26, 2024
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Awesome work on this! One of the reasons I was thinking this would be a pain is I thought it was possible that different trees would have a vary number of segments. But after seeing a constant N_seg in your code and thinking it through I realized that this wouldn't make sense. For bifurcating trees of the same species there must be a constant number of segments...
A minor note: I realized we don't actually need 1/N_tree in the likelihood, because uniform mixing ratios drop out when using log_sum_exp(). https://mc-stan.org/docs/stan-users-guide/finite-mixtures.html#dropping-uniform-mixture-ratios
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These changes allow the user to enter a multiPhylo object instead of a phylo object. The Stan model iterates over all the trees and combines the results in the posterior. I have made the requisite changes to post-processing functions and have implemented tests.