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[WIP] Add functions to form rates and initial values for stratified models #52

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[WIP] Add functions to form rates and initial values for stratified models #52

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fd5eda7
feat(petrinet): start adding StratifiedASKEMPetriNets
mehalter Jun 23, 2023
1ca0a43
feat(petrinet)!: improve API for ASKEMPetriNets
mehalter Jun 23, 2023
dfb3d79
feat(petrinet): start implementing json update/creation for stratifie…
mehalter Jun 24, 2023
db0307a
Added new constructors, including from dictionaries and including for…
p-stokes Jul 11, 2023
2cd1a0e
Changed call of form_type_map to type_map. Added back in constructor …
p-stokes Jul 12, 2023
89fe3b8
Set up test_rates.jl script to make and test functions for combining …
p-stokes Jul 12, 2023
04f13e1
In function to form_ode_semantics, added bit to concatenate parameter…
p-stokes Jul 13, 2023
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121 changes: 121 additions & 0 deletions petrinet/examples/flux_typed.json
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{
"name": "Two City Stratification Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Stratification spatially between two cities model created by Micah. Modified by Patrick.",
"model_version": "0.1",
"model": {
"states": [
{
"id": "Rgn_1",
"name": "Region 1",
"description": "Number of individuals physically located in region 1 relative to the total population"
},
{
"id": "Rgn_2",
"name": "Region 2",
"description": "Number of individuals physically located in region 2 relative to the total population"
}
],
"transitions": [
{
"id": "travel_1_2",
"input": ["Rgn_1"],
"output": ["Rgn_2"],
"properties": {
"name": "Traveling 1 -> 2",
"description": "Individuals traveling from region 1 to region 2"
}
},
{
"id": "travel_2_1",
"input": ["Rgn_2"],
"output": ["Rgn_1"],
"properties": {
"name": "Traveling 2 -> 1",
"description": "Individuals traveling from region 2 to region 1"
}
}
]
},
"semantics": {
"ode": {},
"typing": {
"system": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"model": {
"states": [
{
"id": "Pop",
"name": "Pop",
"description": "Compartment of individuals in a human population"
},
{
"id": "Vaccine",
"name": "Vaccine",
"description": "Compartment of vaccine doses available for use in a vaccination campaign"
}
],
"transitions": [
{
"id": "Infect",
"input": ["Pop", "Pop"],
"output": ["Pop", "Pop"],
"properties": {
"name": "Infect",
"description": "2-to-2 interaction that represents infectious contact between two human individuals"
}
},
{
"id": "Disease",
"input": ["Pop"],
"output": ["Pop"],
"properties": {
"name": "Disease",
"description": "1-to-1 interaction that represents a change in th edisease status of a human individual."
}
},
{
"id": "Strata",
"input": ["Pop"],
"output": ["Pop"],
"properties": {
"name": "Strata",
"description": "1-to-1 interaction that represents a change in the demographic division of a human individual."
}
},
{
"id": "Vaccinate",
"input": ["Pop", "Vaccine"],
"output": ["Pop"],
"properties": {
"name": "Vaccinate",
"description": "2-to-1 interaction that represents an human individual receiving a vaccine dose."
}
},
{
"id": "Produce_Vaccine",
"input": [],
"output": ["Vaccine"],
"properties": {
"name": "Produce Vaccine",
"description": "0-to-1 interaction that represents the production of a single vaccine dose."
}
}
]
},
"semantics": {},
"metadata": {}
},
"map": [
["Rgn_1", "Pop"],
["Rgn_2", "Pop"],
["travel_1_2", "Strata"],
["travel_2_1", "Strata"]
]
}
},
"metadata": {}
}
157 changes: 157 additions & 0 deletions petrinet/examples/flux_typed_aug.json
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{
"name": "Two City Stratification Model",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Stratification spatially between two cities model created by Micah",
"model_version": "0.1",
"model": {
"states": [
{
"id": "Rgn_1",
"name": "Region 1",
"description": "Number of individuals physically located in region 1 relative to the total population"
},
{
"id": "Rgn_2",
"name": "Region 2",
"description": "Number of individuals physically located in region 2 relative to the total population"
}
],
"transitions": [
{
"id": "Rgn1_dis",
"input": ["Rgn_1"],
"output": ["Rgn_1"],
"properties": {
"name": "Rgn1_disease"
}
},
{
"id": "Rgn1_inf",
"input": ["Rgn_1", "Rgn_1"],
"output": ["Rgn_1", "Rgn_1"],
"properties": {
"name": "Rgn1_infection"
}
},
{
"id": "Rgn2_dis",
"input": ["Rgn_2"],
"output": ["Rgn_2"],
"properties": {
"name": "Rgn2_disease"
}
},
{
"id": "Rgn2_inf",
"input": ["Rgn_2", "Rgn_2"],
"output": ["Rgn_2", "Rgn_2"],
"properties": {
"name": "Rgn2_infection"
}
},
{
"id": "travel_1_2",
"input": ["Rgn_1"],
"output": ["Rgn_2"],
"properties": {
"name": "Traveling 1 -> 2",
"description": "Individuals traveling from region 1 to region 2"
}
},
{
"id": "travel_2_1",
"input": ["Rgn_2"],
"output": ["Rgn_1"],
"properties": {
"name": "Traveling 2 -> 1",
"description": "Individuals traveling from region 2 to region 1"
}
}
]
},
"semantics": {
"ode": {},
"typing": {
"system": {
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"model": {
"states": [
{
"id": "Pop",
"name": "Pop",
"description": "Compartment of individuals in a human population"
},
{
"id": "Vaccine",
"name": "Vaccine",
"description": "Compartment of vaccine doses available for use in a vaccination campaign"
}
],
"transitions": [
{
"id": "Infect",
"input": ["Pop", "Pop"],
"output": ["Pop", "Pop"],
"properties": {
"name": "Infect",
"description": "2-to-2 interaction that represents infectious contact between two human individuals"
}
},
{
"id": "Disease",
"input": ["Pop"],
"output": ["Pop"],
"properties": {
"name": "Disease",
"description": "1-to-1 interaction that represents a change in th edisease status of a human individual."
}
},
{
"id": "Strata",
"input": ["Pop"],
"output": ["Pop"],
"properties": {
"name": "Strata",
"description": "1-to-1 interaction that represents a change in the demographic division of a human individual."
}
},
{
"id": "Vaccinate",
"input": ["Pop", "Vaccine"],
"output": ["Pop"],
"properties": {
"name": "Vaccinate",
"description": "2-to-1 interaction that represents an human individual receiving a vaccine dose."
}
},
{
"id": "Produce_Vaccine",
"input": [],
"output": ["Vaccine"],
"properties": {
"name": "Produce Vaccine",
"description": "0-to-1 interaction that represents the production of a single vaccine dose."
}
}
]
},
"semantics": {},
"metadata": {}
},
"map": [
["Rgn_1", "Pop"],
["Rgn_2", "Pop"],
["Rgn1_dis", "Disease"],
["Rgn1_inf", "Infect"],
["Rgn2_dis", "Disease"],
["Rgn2_inf", "Infect"],
["travel_1_2", "Strata"],
["travel_2_1", "Strata"]
]
}
},
"metadata": {}
}
69 changes: 69 additions & 0 deletions petrinet/examples/ont_pop_vax.json
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{
"name": "Ontology Model w/ Pop and Vax States",
"schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json",
"description": "Ontology Model w/ Population and Vaccine-Unit States. File created by Patrick based ontology created by Nelson",
"model_version": "0.1",
"model": {
"states": [
{
"id": "Pop",
"name": "Pop",
"description": "Compartment of individuals in a human population"
},
{
"id": "Vaccine",
"name": "Vaccine",
"description": "Compartment of vaccine doses available for use in a vaccination campaign"
}
],
"transitions": [
{
"id": "Infect",
"input": ["Pop", "Pop"],
"output": ["Pop", "Pop"],
"properties": {
"name": "Infect",
"description": "2-to-2 interaction that represents infectious contact between two human individuals"
}
},
{
"id": "Disease",
"input": ["Pop"],
"output": ["Pop"],
"properties": {
"name": "Disease",
"description": "1-to-1 interaction that represents a change in th edisease status of a human individual."
}
},
{
"id": "Strata",
"input": ["Pop"],
"output": ["Pop"],
"properties": {
"name": "Strata",
"description": "1-to-1 interaction that represents a change in the demographic division of a human individual."
}
},
{
"id": "Vaccinate",
"input": ["Pop", "Vaccine"],
"output": ["Pop"],
"properties": {
"name": "Vaccinate",
"description": "2-to-1 interaction that represents an human individual receiving a vaccine dose."
}
},
{
"id": "Produce_Vaccine",
"input": [],
"output": ["Vaccine"],
"properties": {
"name": "Produce Vaccine",
"description": "0-to-1 interaction that represents the production of a single vaccine dose."
}
}
]
},
"semantics": {},
"metadata": {}
}
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