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UT-Covid / episimlab

Framework for development of epidemiological models
https://ut-covid.github.io/episimlab/
BSD 3-Clause "New" or "Revised" License
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Re-implement incidence compartments #37

Closed ethho closed 3 years ago

ethho commented 3 years ago

Re-implement reporting of incidence compartments. Formatted like <compt>2<compt> , e.g. Iy2Ih. Currently, can only track the net incident change in a compartment's state, which includes in and out edges applied during that time step. The ask is to expose the contribution of connected compartments to a given compartment at each time step. In the case of Iy2Ih: how many people went from Iy to Ih at this timestep, which is not the same as "how much did Ih change?

These incidence compartments are still calculated in SEIR functions for Cython:

https://github.com/eho-tacc/episimlab/blob/9e639575e5c8810b1d811d381944dfed557b9f2b/episimlab/seir/bf_cython_engine.pyx#L592-L592

and for plain Python:

https://github.com/eho-tacc/episimlab/blob/9e639575e5c8810b1d811d381944dfed557b9f2b/episimlab/seir/brute_force.py#L228-L228

They are also still included in the default compartment coordinates:

https://github.com/eho-tacc/episimlab/blob/9e639575e5c8810b1d811d381944dfed557b9f2b/episimlab/setup/coords.py#L22-L22

...but are expected by this test to be NaNs as implemented currently on the 27-housekeeping branch:

https://github.com/eho-tacc/episimlab/blob/0f33f2dd25f448b490d79db9db370b2649c03e6c/tests/test_seir/test_bf_cython_seir.py#L31-L34

kellypierce commented 3 years ago

resolved in https://github.com/eho-tacc/episimlab/pull/38