def test_scenario_with_model_change(self):
# Instance to save population values
population_data = PopulationData(filename=None)
# Set tau value and start date of records
example_data = ExampleData(tau=1440, start_date="01Jan2020")
# Preset of SIR-F parameters
preset_dict = SIRF.EXAMPLE["param_dict"]
# Create dataset from 01Jan2020 to 31Jan2020
area = {"country": "Theoretical"}
example_data.add(SIRF, step_n=30, **area)
# Register population value
population_data.update(SIRF.EXAMPLE["population"], **area)
# Create Scenario class
snl = Scenario(example_data, population_data, tau=1440, **area)
# Set 0th phase from 02Jan2020 to 31Jan2020 with preset parameter values
snl.clear(include_past=True)
snl.add(end_date="31Jan2020", model=SIRF, **preset_dict)
# Add main scenario
snl.add(end_date="31Dec2020", name="Main")
# Add lockdown scenario
rho_lock = snl.get("rho", phase="0th") / 2
snl.add(end_date="31Dec2020", name="Lockdown", rho=rho_lock)
# Add medicine scenario
kappa_med = snl.get("kappa", phase="0th") / 2
sigma_med = snl.get("sigma", phase="0th") * 2
snl.add(end_date="31Dec2020",
name="Medicine",
kappa=kappa_med,
sigma=sigma_med)
# Add vaccine scenario
snl.add(end_date="31Dec2020", name="Vaccine", model=SIRFV, omega=0.001)
# Summarize
snl.summary()
# Compare scenarios
snl.describe(y0_dict={"Vaccinated": 0})
def test_ode(self, model):
# Setting
eg_tau = 1440
area = {"country": "Full", "province": model.NAME}
# Population
population_data = PopulationData(filename=None)
population_data.update(model.EXAMPLE["population"], **area)
# Simulation
example_data = ExampleData(tau=eg_tau, start_date="01Jan2020")
example_data.add(model, **area)
# Model-specialized records
spe_df = example_data.specialized(**area)
assert set(spe_df.columns) == set(
[*Term.STR_COLUMNS, *model.VARIABLES])
# Non-dimensional records
nondim_df = example_data.non_dim(**area)
assert set(nondim_df.columns) == set(
[Term.TS, *list(model.VAR_DICT.keys())])
# JHU-type records
jhu_df = example_data.subset(**area)
assert set(jhu_df.columns) == set(Term.NLOC_COLUMNS)
# Calculate Rt/day parameters when parameters are None
param_dict = {p: 0 for p in model.PARAMETERS}
model_instance = model(population_data.value(**area), **param_dict)
model_instance.calc_r0()
model_instance.calc_days_dict(eg_tau)
def test_scenario(self):
area = {"country": "Theoretical"}
# Set-up example dataset (from 01Jan2020 to 31Jan2020)
example_data = ExampleData(tau=1440, start_date="01Jan2020")
example_data.add(SIRF, step_n=30, **area)
# Population value
population_data = PopulationData(filename=None)
population_data.update(SIRF.EXAMPLE["population"], **area)
# Set-up Scenario instance
snl = Scenario(tau=1440, **area)
snl.register(example_data, population_data)
# Check records
record_df = snl.records(variables="CFR")
assert set(record_df.columns) == set(
[Term.DATE, Term.C, Term.F, Term.R])
# Add a past phase to 31Jan2020 with parameter values
snl.add(model=SIRF, **SIRF.EXAMPLE["param_dict"])
# Check summary
df = snl.summary()
assert not df.empty
assert len(df) == 1
assert Term.RT in df
# Main scenario
snl.add(end_date="31Dec2020", name="Main")
assert snl.get(Term.RT, phase="last", name="Main") == 2.50
# Lockdown scenario
snl.clear(name="Lockdown")
rho_lock = snl.get("rho", phase="0th") * 0.5
snl.add(end_date="31Dec2020", name="Lockdown", rho=rho_lock)
assert snl.get(Term.RT, phase="last", name="Lockdown") == 1.25
# Medicine scenario
snl.clear(name="Medicine")
kappa_med = snl.get("kappa", phase="0th") * 0.5
sigma_med = snl.get("sigma", phase="0th") * 2
snl.add(end_date="31Dec2020",
name="Medicine",
kappa=kappa_med,
sigma=sigma_med)
assert snl.get(Term.RT, phase="last", name="Medicine") == 1.31
# Add vaccine scenario
snl.clear(name="Vaccine")
rho_vac = snl.get("rho", phase="0th") * 0.8
kappa_vac = snl.get("kappa", phase="0th") * 0.6
sigma_vac = snl.get("sigma", phase="0th") * 1.2
snl.add(end_date="31Dec2020",
name="Vaccine",
rho=rho_vac,
kappa=kappa_vac,
sigma=sigma_vac)
assert snl.get(Term.RT, phase="last", name="Vaccine") == 1.72
# Description
snl.describe()
# History
snl.history("Rt")
snl.history("rho")
snl.history("Infected")
snl.history_rate(name="Medicine")
snl.simulate(name="Vaccine")
def test_update(self):
population_data = PopulationData(filename=None)
population_data.update(1000, "Moon")
assert population_data.value("Moon") == 1000
population_data.update(2000, "Moon")
assert population_data.value("Moon") == 2000