def update_parameters(i, *input_values) -> List[dict]:
"""Reads html form outputs and converts them to a parameter instance
Returns Parameters
"""
inputs_dict = SidebarCallbacks.get_formated_values(i, input_values)
dt = inputs_dict["doubling_time"] if inputs_dict[
"doubling_time"] else None
dfh = inputs_dict["date_first_hospitalized"] if not dt else None
pars = Parameters(
current_hospitalized=inputs_dict["current_hospitalized"],
date_first_hospitalized=dfh,
doubling_time=dt,
hospitalized=Disposition.create(
days=inputs_dict["hospitalized_los"],
rate=inputs_dict["hospitalized_rate"] / 100,
),
icu=Disposition(
days=inputs_dict["icu_los"],
rate=inputs_dict["icu_rate"] / 100,
),
infectious_days=inputs_dict["infectious_days"],
market_share=inputs_dict["market_share"] / 100,
n_days=inputs_dict["n_days"],
population=inputs_dict["population"],
recovered=0, #FIXME input or pass through from defaults is required!
relative_contact_rate=inputs_dict["relative_contact_rate"] / 100,
ventilated=Disposition.create(
days=inputs_dict["ventilated_los"],
rate=inputs_dict["ventilated_rate"] / 100,
))
return [{
"inputs_dict": inputs_dict,
"parameters": parameters_serializer(pars)
}]
def halving_param():
return Parameters(
current_date=datetime(year=2020, month=3, day=28),
current_hospitalized=100,
doubling_time=6.0,
hospitalized=Disposition.create(rate=0.05, days=7),
icu=Disposition.create(rate=0.02, days=9),
infectious_days=14,
market_share=0.05,
mitigation_date=datetime(year=2020, month=3, day=28),
n_days=60,
population=500000,
recovered=0,
relative_contact_rate=0.7,
ventilated=Disposition.create(rate=0.01, days=10),
)
def fixture_penn_chime_setup() -> Tuple[Parameters, Sir]:
"""Initializes penn_chime parameters and SIR model
"""
p = Parameters(
current_hospitalized=69,
date_first_hospitalized=date(2020, 3, 7),
doubling_time=None,
hospitalized=Disposition.create(days=7, rate=0.025),
icu=Disposition.create(days=9, rate=0.0075),
infectious_days=14,
market_share=0.15,
n_days=100,
population=3600000,
recovered=0,
relative_contact_rate=0.3,
ventilated=Disposition.create(days=10, rate=0.005),
)
return p, Sir(p)
def parameters(self):
'''
return penn_chime Parameters object populated with instance values
'''
doubling_time = self.doubling_time
if self.date_first_hospitalized:
doubling_time = None
mitigation_date = self.mitigation_date
relative_contact_rate = max(self.relative_contact_rate, EPSILON)
if relative_contact_rate == EPSILON:
mitigation_date = None
return Parameters(
current_date=timezone.localdate(),
population=self.population,
current_hospitalized=self.current_hospitalized,
date_first_hospitalized=self.date_first_hospitalized,
doubling_time=doubling_time,
hospitalized=Disposition(
days=self.hospitalized_days,
rate=self.hospitalized_rate,
),
icu=Disposition(
days=self.icu_days,
rate=self.icu_rate,
),
infectious_days=self.infectious_days,
market_share=self.market_share,
n_days=self.n_days,
mitigation_date=mitigation_date,
relative_contact_rate=relative_contact_rate,
ventilated=Disposition(
days=self.ventilated_days,
rate=self.ventilated_rate,
),
recovered=0, # not implemented
)
def parameters_deserializer(p_json: str):
values = loads(p_json)
dates = {
key: parse_date(values[key]).date() if values[key] else None
for key in (
"current_date",
"date_first_hospitalized",
"mitigation_date",
)
}
return Parameters(
current_date=dates["current_date"],
current_hospitalized=values["current_hospitalized"],
hospitalized=Disposition.create(
days=values["hospitalized"][0],
rate=values["hospitalized"][1],
),
icu=Disposition.create(
days=values["icu"][0],
rate=values["icu"][1],
),
infectious_days=values["infectious_days"],
date_first_hospitalized=dates["date_first_hospitalized"],
doubling_time=values["doubling_time"],
market_share=values["market_share"],
max_y_axis=values["max_y_axis"],
mitigation_date=dates["mitigation_date"],
n_days=values["n_days"],
population=values["population"],
recovered=values["recovered"],
region=values["region"],
relative_contact_rate=values["relative_contact_rate"],
ventilated=Disposition.create(
days=values["ventilated"][0],
rate=values["ventilated"][1],
),
)
def defaults():
return Parameters(
region=Regions(
delaware=564696,
chester=519293,
montgomery=826075,
bucks=628341,
philly=1581000,
),
current_date=datetime(year=2020, month=3, day=28),
current_hospitalized=14,
date_first_hospitalized=datetime(year=2020, month=3, day=7),
doubling_time=4.0,
hospitalized=Disposition.create(rate=0.025, days=7),
icu=Disposition.create(rate=0.0075, days=9),
infectious_days=14,
n_days=60,
market_share=0.15,
mitigation_date=datetime(year=2020, month=3, day=28),
recovered=0,
relative_contact_rate=0.3,
ventilated=Disposition.create(rate=0.005, days=10),
)