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Update and streamline notebook
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@bgyori
bgyori committed Apr 9, 2024
1 parent c91eb39 commit 102ddf5
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Showing 2 changed files with 36 additions and 53 deletions.
6 changes: 3 additions & 3 deletions notebooks/evaluation_2024.03/epi_scenario3/SEIR_scenario3_petrinet.json
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Expand Up @@ -129,7 +129,7 @@
"ido": "0000514"
},
"modifiers": {
"status": "young"
"status": "old"
}
},
"units": {
Expand Down Expand Up @@ -557,8 +557,8 @@
"id": "N",
"value": 37742307.0,
"units": {
"expression": "1/day",
"expression_mathml": "<apply><power/><ci>day</ci><cn>-1</cn></apply>"
"expression": "person",
"expression_mathml": "<ci>person</ci>"
}
},
{
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83 changes: 33 additions & 50 deletions notebooks/evaluation_2024.03/epi_scenario3/epi_eval_sc3_seir.ipynb
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Expand Up @@ -18,7 +18,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 16,
"id": "efd146e7-0742-4e39-a374-39fe931df029",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -53,7 +53,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 17,
"id": "f8d81322-226a-4676-a0b8-923e7220e10d",
"metadata": {},
"outputs": [],
Expand All @@ -75,7 +75,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 18,
"id": "5e2c1d9f-51a9-46a4-aa06-5aa862b8b081",
"metadata": {},
"outputs": [],
Expand All @@ -88,7 +88,7 @@
"c = {\n",
" 'S_y': _susceptible.with_context(status=\"young\"),\n",
" 'S_m': _susceptible.with_context(status=\"middle\"),\n",
" 'S_o': _susceptible.with_context(status=\"young\"),\n",
" 'S_o': _susceptible.with_context(status=\"old\"),\n",
" 'E_y': _exposed.with_context(status=\"young\"),\n",
" 'E_m': _exposed.with_context(status=\"middle\"),\n",
" 'E_o': _exposed.with_context(status=\"old\"),\n",
Expand All @@ -99,18 +99,9 @@
" 'R_m': _recovered.with_context(status=\"middle\"),\n",
" 'R_o': _recovered.with_context(status=\"old\"),\n",
"}\n",
"c['S_y'].name = 'S_y'\n",
"c['S_m'].name = 'S_m'\n",
"c['S_o'].name = 'S_o'\n",
"c['E_y'].name = 'E_y'\n",
"c['E_m'].name = 'E_m'\n",
"c['E_o'].name = 'E_o'\n",
"c['I_y'].name = 'I_y'\n",
"c['I_m'].name = 'I_m'\n",
"c['I_o'].name = 'I_o'\n",
"c['R_y'].name = 'R_y'\n",
"c['R_m'].name = 'R_m'\n",
"c['R_o'].name = 'R_o'"
"\n",
"for concept in c:\n",
" c[concept].name = concept"
]
},
{
Expand All @@ -123,7 +114,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 19,
"id": "b4774d31-1ad4-4027-a82b-6bee06907e03",
"metadata": {},
"outputs": [],
Expand All @@ -138,7 +129,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 20,
"id": "a902e806-0dad-4bf6-a264-0172324257b0",
"metadata": {},
"outputs": [],
Expand All @@ -148,7 +139,7 @@
" distribution=Distribution(type='StandardUniform1',\n",
" parameters={'minimum': 0.05,\n",
" 'maximum': 0.8})), # Infection rate\n",
" 'N': Parameter(name='total_population', value=sympy.Float(37742307.0), units=per_day_units()), # Total population\n",
" 'N': Parameter(name='total_population', value=sympy.Float(37742307.0), units=person_units()), # Total population\n",
" 'mew': Parameter(name='mew', value=sympy.Float(0.0), units=per_day_units()), # Mask efficacy\n",
" 'mcw': Parameter(name='mcw', value=sympy.Float(0.0), units=per_day_units()), # Mask compliance\n",
" 'r_EI': Parameter(name='r_EI', value=sympy.Float(0.08), units=per_day_units()), # Rate of progressing E -> I\n",
Expand All @@ -175,7 +166,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 21,
"id": "802ce5dd-9f50-43c3-8d0b-f1e7a692d7b0",
"metadata": {},
"outputs": [],
Expand All @@ -196,24 +187,24 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 22,
"id": "f892e033-55da-44c6-b309-459dee0cae1a",
"metadata": {},
"outputs": [],
"source": [
"initials = {\n",
" \"S_y\": Initial(concept=Concept(name=\"S_y\"), expression=sympy.Float(10305660.0)),\n",
" \"S_m\": Initial(concept=Concept(name=\"S_m\"), expression=sympy.Float(15281905.0)),\n",
" \"S_o\": Initial(concept=Concept(name=\"S_o\"), expression=sympy.Float(12154442.0)),\n",
" \"E_y\": Initial(concept=Concept(name=\"E_y\"), expression=sympy.Float(50.0)),\n",
" \"E_m\": Initial(concept=Concept(name=\"E_m\"), expression=sympy.Float(50.0)),\n",
" \"E_o\": Initial(concept=Concept(name=\"E_o\"), expression=sympy.Float(50.0)),\n",
" \"I_y\": Initial(concept=Concept(name=\"I_y\"), expression=sympy.Float(50.0)),\n",
" \"I_m\": Initial(concept=Concept(name=\"I_m\"), expression=sympy.Float(50.0)),\n",
" \"I_o\": Initial(concept=Concept(name=\"I_o\"), expression=sympy.Float(50.0)),\n",
" \"R_y\": Initial(concept=Concept(name=\"R_y\"), expression=sympy.Float(0.0)),\n",
" \"R_m\": Initial(concept=Concept(name=\"R_m\"), expression=sympy.Float(0.0)),\n",
" \"R_o\": Initial(concept=Concept(name=\"R_o\"), expression=sympy.Float(0.0)),\n",
" \"S_y\": Initial(concept=c[\"S_y\"], expression=10305660.0),\n",
" \"S_m\": Initial(concept=c[\"S_m\"], expression=15281905.0),\n",
" \"S_o\": Initial(concept=c[\"S_o\"], expression=12154442.0),\n",
" \"E_y\": Initial(concept=c[\"E_y\"], expression=50.0),\n",
" \"E_m\": Initial(concept=c[\"E_m\"], expression=50.0),\n",
" \"E_o\": Initial(concept=c[\"E_o\"], expression=50.0),\n",
" \"I_y\": Initial(concept=c[\"I_y\"], expression=50.0),\n",
" \"I_m\": Initial(concept=c[\"I_m\"], expression=50.0),\n",
" \"I_o\": Initial(concept=c[\"I_o\"], expression=50.0),\n",
" \"R_y\": Initial(concept=c[\"R_y\"], expression=0.0),\n",
" \"R_m\": Initial(concept=c[\"R_m\"], expression=0.0),\n",
" \"R_o\": Initial(concept=c[\"R_o\"], expression=0.0),\n",
"}"
]
},
Expand All @@ -227,7 +218,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 23,
"id": "5f186c10-7b95-4678-8737-ebca86c1f856",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -350,16 +341,16 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 24,
"id": "38e21c50-8b53-4288-a8ef-73f6e02ac63a",
"metadata": {},
"outputs": [],
"source": [
"observables_seir = {\n",
" 'susceptible': Observable(name='susceptible', expression=SympyExprStr(S_y+S_m+S_o)),\n",
" 'exposed': Observable(name='exposed', expression=SympyExprStr(E_y+E_m+E_o)),\n",
" 'infected': Observable(name='infected', expression=SympyExprStr(I_y+I_m+I_o)),\n",
" 'recovered': Observable(name='recovered', expression=SympyExprStr(R_y+R_m+R_o)),\n",
" 'susceptible': Observable(name='susceptible', expression=S_y+S_m+S_o),\n",
" 'exposed': Observable(name='exposed', expression=E_y+E_m+E_o),\n",
" 'infected': Observable(name='infected', expression=I_y+I_m+I_o),\n",
" 'recovered': Observable(name='recovered', expression=R_y+R_m+R_o),\n",
"}"
]
},
Expand All @@ -373,7 +364,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 25,
"id": "4c523830-dfc3-4b8a-b584-5dad7f95c729",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -418,7 +409,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 26,
"id": "12219f8d-566f-466d-b35e-6bb70af5cea7",
"metadata": {},
"outputs": [],
Expand All @@ -438,14 +429,6 @@
"with open('update_parameters_example.json', 'w') as fh:\n",
" json.dump(template_model_to_petrinet_json(tm), fh, indent=1)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c0f18783-7a00-4484-a1ac-8e5e1697f921",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -464,7 +447,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.9"
"version": "3.10.13"
}
},
"nbformat": 4,
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