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Implement fully integrated popgen process #1

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isaacovercast opened this issue Jun 8, 2020 · 1 comment
Open

Implement fully integrated popgen process #1

isaacovercast opened this issue Jun 8, 2020 · 1 comment

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@isaacovercast
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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
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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

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