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Add notebook illustrating force of infection generation without use o…
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{ | ||
"cells": [ | ||
{ | ||
"cell_type": "markdown", | ||
"id": "90759a2a-40e5-431a-a8bd-26e51a650aff", | ||
"metadata": {}, | ||
"source": [ | ||
"Illustration of how to construct the force of infection\n", | ||
"(frequency-dependent) without using `summer2`'s built-in\n", | ||
"`add_infection_frequency_flow`.\n", | ||
"(I think this is correct, but may need David to confirm\n", | ||
"and haven't tested in detail.)\n", | ||
"Also, note that this is not an epidemiologically sensible model." | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": null, | ||
"id": "b7f879ec-74d9-4e2c-975f-a5cb3c670a8e", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"from summer2 import CompartmentalModel\n", | ||
"from summer2.parameters import Parameter, Function, CompartmentValues" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": null, | ||
"id": "758c8abb-8e5f-43e4-a76d-47a505e6f932", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"comps = [\"susceptible\", \"infectious\", \"recovered\"]\n", | ||
"epi_model = CompartmentalModel([0.0, 100.0], comps, [\"infectious\"])" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": null, | ||
"id": "13199b5d-d8b5-4c1f-8506-2e313fae2e43", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"def get_force_infection(comp_vals):\n", | ||
" \"\"\"Manually construct the force of infection calculation.\n", | ||
" \"\"\"\n", | ||
" infect_comps = epi_model.query_compartments({\"name\": \"infectious\"}, as_idx=True)\n", | ||
" infect_pop = comp_vals[infect_comps]\n", | ||
" all_comps = epi_model.query_compartments({\"name\": comps}, as_idx=True)\n", | ||
" total_pop = comp_vals[all_comps].sum()\n", | ||
" return infect_pop / total_pop\n", | ||
"\n", | ||
"epi_model.add_transition_flow(\n", | ||
" \"infection\", \n", | ||
" Function(get_force_infection, [CompartmentValues]) * Parameter(\"beta\"),\n", | ||
" \"susceptible\",\n", | ||
" \"infectious\",\n", | ||
")" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": null, | ||
"id": "0fd8b13c-af6b-4170-9e61-95ec7cbaa566", | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"epi_model.set_initial_population({\"susceptible\": 100.0})\n", | ||
"epi_model.run({\"beta\": 1.0})" | ||
] | ||
} | ||
], | ||
"metadata": { | ||
"kernelspec": { | ||
"display_name": "Python 3 (ipykernel)", | ||
"language": "python", | ||
"name": "python3" | ||
}, | ||
"language_info": { | ||
"codemirror_mode": { | ||
"name": "ipython", | ||
"version": 3 | ||
}, | ||
"file_extension": ".py", | ||
"mimetype": "text/x-python", | ||
"name": "python", | ||
"nbconvert_exporter": "python", | ||
"pygments_lexer": "ipython3", | ||
"version": "3.10.13" | ||
} | ||
}, | ||
"nbformat": 4, | ||
"nbformat_minor": 5 | ||
} |