def _add_flow(self, requested_flow):
flow = None
f_source = requested_flow.get("origin")
f_source = Compartment.deserialize(f_source) if f_source else None
f_dest = requested_flow.get("to")
f_dest = Compartment.deserialize(f_dest) if f_dest else None
f_param = requested_flow["parameter"]
f_type = requested_flow["type"]
if f_type == Flow.STANDARD:
flow = StandardFlow(
source=f_source,
dest=f_dest,
param_name=f_param,
param_func=self.get_parameter_value,
)
elif f_type == Flow.INFECTION_FREQUENCY:
flow = InfectionFrequencyFlow(
source=f_source,
dest=f_dest,
param_name=f_param,
param_func=self.get_parameter_value,
find_infectious_multiplier=self.get_infection_frequency_multiplier,
)
elif f_type == Flow.INFECTION_DENSITY:
flow = InfectionDensityFlow(
source=f_source,
dest=f_dest,
param_name=f_param,
param_func=self.get_parameter_value,
find_infectious_multiplier=self.get_infection_density_multiplier,
)
elif f_type == Flow.DEATH:
flow = InfectionDeathFlow(
source=f_source, param_name=f_param, param_func=self.get_parameter_value
)
elif f_type == Flow.IMPORT:
flow = ImportFlow(
dest=self.entry_compartment,
param_name=f_param,
param_func=self.get_parameter_value,
)
if flow:
self.flows.append(flow)
return flow
def __init__(
self,
times: List[float],
compartment_names: List[str],
initial_conditions: Dict[str, float],
parameters: Dict[str, float],
requested_flows: List[dict],
infectious_compartments: List[str],
birth_approach: str,
entry_compartment: str,
starting_population: int,
):
super().__init__(
times=times,
compartment_names=compartment_names,
initial_conditions=initial_conditions,
parameters=parameters,
requested_flows=requested_flows,
infectious_compartments=infectious_compartments,
birth_approach=birth_approach,
entry_compartment=entry_compartment,
starting_population=starting_population,
)
# Keeps track of Stratifications that have been applied.
self.stratifications = []
# Keeps track of original, pre-stratified compartment names.
self.original_compartment_names = [Compartment.deserialize(n) for n in compartment_names]
# A list of the different sub-categories ('strains') of the diease that we are modelling.
self.disease_strains = [self.DEFAULT_DISEASE_STRAIN]
# Strata-based multipliers for compartmental infectiousness levels.
self.infectiousness_levels = {}
# Compartment-based overwrite values for compartmental infectiousness levels.
self.individual_infectiousness_adjustments = []
# Mixing matrices a list of NxN arrays used to calculate force of infection.
self.mixing_matrices = []
# A list of dicts that has the strata required to match a row in the mixing matrix.
self.mixing_categories = [{}]
def test_deserialzie():
s = "infectedXlocation_hawaiiXage_15"
c = Compartment.deserialize(s)
assert c == Compartment(
"infected",
strat_names=["location", "age"],
strat_values={
"location": "hawaii",
"age": "15"
},
)
assert c != Compartment(
"infected",
strat_names=["age", "location"],
strat_values={
"location": "hawaii",
"age": "15"
},
)
assert str(c) == "infectedXlocation_hawaiiXage_15"
assert hash(c) == hash("infectedXlocation_hawaiiXage_15")
def __init__(
self,
times: List[float],
compartment_names: List[str],
initial_conditions: Dict[str, float],
parameters: Dict[str, float],
requested_flows: List[dict],
birth_approach: str,
starting_population: int,
infectious_compartments: List[str],
entry_compartment: str,
):
model_kwargs = {
"times": times,
"compartment_names": compartment_names,
"initial_conditions": initial_conditions,
"parameters": parameters,
"requested_flows": requested_flows,
"birth_approach": birth_approach,
"starting_population": starting_population,
"infectious_compartments": infectious_compartments,
"entry_compartment": entry_compartment,
}
validate_model(model_kwargs)
# Flows
self.flows = []
self.time_variants = {}
self.parameters = {}
# Compartments
self.compartment_names = [Compartment(n) for n in compartment_names]
self.infectious_compartments = [Compartment(n) for n in infectious_compartments]
# Derived outputs
self.derived_outputs = {}
self._derived_calc = DerivedOutputCalculator()
self.times = times
# Populate model compartments with the values set in `initial conditions`.
self.compartment_values = np.zeros(len(compartment_names))
pop_remainder = starting_population - sum(initial_conditions.values())
for idx, comp_name in enumerate(compartment_names):
if comp_name in initial_conditions:
self.compartment_values[idx] = initial_conditions[comp_name]
if comp_name == entry_compartment:
self.compartment_values[idx] += pop_remainder
self.birth_approach = birth_approach
self.parameters = parameters
self.parameters["crude_birth_rate"] = self.parameters.get("crude_birth_rate", 0)
self.parameters["universal_death_rate"] = self.parameters.get("universal_death_rate", 0)
# Add user-specified flows
self.entry_compartment = Compartment.deserialize(entry_compartment)
self.flows = []
for requested_flow in requested_flows:
self._add_flow(requested_flow)
# Add birth flows.
if (
self.birth_approach == BirthApproach.ADD_CRUDE
and self.parameters["crude_birth_rate"] > 0
):
flow = CrudeBirthFlow(
dest=self.entry_compartment,
param_name="crude_birth_rate",
param_func=self.get_parameter_value,
)
self.flows.append(flow)
elif self.birth_approach == BirthApproach.REPLACE_DEATHS:
self.total_deaths = 0
flow = ReplacementBirthFlow(
dest=self.entry_compartment, get_total_deaths=self.get_total_deaths
)
self.flows.append(flow)
# Add non-disease death flows if requested
if self.parameters["universal_death_rate"] > 0:
for compartment_name in self.compartment_names:
flow = UniversalDeathFlow(
source=compartment_name,
param_name="universal_death_rate",
param_func=self.get_parameter_value,
)
self.flows.append(flow)
# Update indices for quick lookups.
self._update_flow_compartment_indices()
for idx, c in enumerate(self.compartment_names):
c.idx = idx
def test_create_ageing_flows():
strat = Stratification(
name="age",
strata=["0", "10", "30", "40"],
compartments=["S", "I"],
comp_split_props={},
flow_adjustments={},
)
previous_compartments = [
Compartment("S", strat_names=["location"], strat_values={"location": "home"}),
Compartment("S", strat_names=["location"], strat_values={"location": "work"}),
Compartment("I", strat_names=["location"], strat_values={"location": "home"}),
Compartment("I", strat_names=["location"], strat_values={"location": "work"}),
Compartment("R", strat_names=["location"], strat_values={"location": "home"}),
Compartment("R", strat_names=["location"], strat_values={"location": "work"}),
]
ageing_flows, ageing_params = AgeingFlow.create(strat, previous_compartments, _get_param_value)
assert ageing_params == {"ageing0to10": 0.1, "ageing10to30": 0.05, "ageing30to40": 0.1}
flow = ageing_flows[0]
assert flow.source == Compartment.deserialize("SXlocation_homeXage_0")
assert flow.dest == Compartment.deserialize("SXlocation_homeXage_10")
assert flow.param_name == "ageing0to10"
assert flow.param_func == _get_param_value
flow = ageing_flows[1]
assert flow.source == Compartment.deserialize("SXlocation_workXage_0")
assert flow.dest == Compartment.deserialize("SXlocation_workXage_10")
assert flow.param_name == "ageing0to10"
assert flow.param_func == _get_param_value
flow = ageing_flows[2]
assert flow.source == Compartment.deserialize("IXlocation_homeXage_0")
assert flow.dest == Compartment.deserialize("IXlocation_homeXage_10")
assert flow.param_name == "ageing0to10"
assert flow.param_func == _get_param_value
flow = ageing_flows[3]
assert flow.source == Compartment.deserialize("IXlocation_workXage_0")
assert flow.dest == Compartment.deserialize("IXlocation_workXage_10")
assert flow.param_name == "ageing0to10"
assert flow.param_func == _get_param_value
flow = ageing_flows[4]
assert flow.source == Compartment.deserialize("SXlocation_homeXage_10")
assert flow.dest == Compartment.deserialize("SXlocation_homeXage_30")
assert flow.param_name == "ageing10to30"
assert flow.param_func == _get_param_value
flow = ageing_flows[5]
assert flow.source == Compartment.deserialize("SXlocation_workXage_10")
assert flow.dest == Compartment.deserialize("SXlocation_workXage_30")
assert flow.param_name == "ageing10to30"
assert flow.param_func == _get_param_value
flow = ageing_flows[6]
assert flow.source == Compartment.deserialize("IXlocation_homeXage_10")
assert flow.dest == Compartment.deserialize("IXlocation_homeXage_30")
assert flow.param_name == "ageing10to30"
assert flow.param_func == _get_param_value
flow = ageing_flows[7]
assert flow.source == Compartment.deserialize("IXlocation_workXage_10")
assert flow.dest == Compartment.deserialize("IXlocation_workXage_30")
assert flow.param_name == "ageing10to30"
assert flow.param_func == _get_param_value
flow = ageing_flows[8]
assert flow.source == Compartment.deserialize("SXlocation_homeXage_30")
assert flow.dest == Compartment.deserialize("SXlocation_homeXage_40")
assert flow.param_name == "ageing30to40"
assert flow.param_func == _get_param_value
flow = ageing_flows[9]
assert flow.source == Compartment.deserialize("SXlocation_workXage_30")
assert flow.dest == Compartment.deserialize("SXlocation_workXage_40")
assert flow.param_name == "ageing30to40"
assert flow.param_func == _get_param_value
flow = ageing_flows[10]
assert flow.source == Compartment.deserialize("IXlocation_homeXage_30")
assert flow.dest == Compartment.deserialize("IXlocation_homeXage_40")
assert flow.param_name == "ageing30to40"
assert flow.param_func == _get_param_value
flow = ageing_flows[11]
assert flow.source == Compartment.deserialize("IXlocation_workXage_30")
assert flow.dest == Compartment.deserialize("IXlocation_workXage_40")
assert flow.param_name == "ageing30to40"
assert flow.param_func == _get_param_value
