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isaacovercast / PIED

A model of coevolving community abundance and phylogenetic birth/death processes.
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Implement fully integrated popgen process #1

Open isaacovercast opened 4 years ago

isaacovercast commented 4 years ago

Right now pi is only generated at the tips using abundance and therefore assuming no incomplete lineage sorting. Since we have the tree we could construct a giant coalescent model and simulate data at the tips in more integrated fashion, but this involves some potentially nasty housekeeping to build the msprime demographic model.

isaacovercast commented 4 years ago

This is now done in PIED.nucleotide_diversity_ILS(), but it returns much different info than PIED.nucleotide_diversity(), so it hasn't been worked into the full model yet