def test_estimate_with_fixed(self, jhu_data, population_data, country):
# Dataset
population = population_data.value(country)
record_df = jhu_data.subset(country, population=population)
# Setting
unit = PhaseUnit("27May2020", "27Jun2020", population)
unit.set_ode(model=SIR, tau=360, rho=0.01)
# Parameter estimation
unit.estimate(record_df=record_df)
assert unit.tau == unit.to_dict()[Term.TAU] == 360
assert unit.to_dict()["rho"] == 0.01
def test_set_ode(self):
unit = PhaseUnit("01Jan2020", "01Feb2020", 1000)
unit.set_ode(model=SIR, tau=720, rho=0.2)
assert issubclass(unit.model, SIR)
summary_dict = unit.to_dict()
assert summary_dict[Term.TAU] == 720
assert summary_dict[Term.ODE] == SIR.NAME
assert summary_dict["rho"] == 0.2
assert summary_dict["sigma"] is None
def test_estimate(self, jhu_data, population_data, country):
# Dataset
population = population_data.value(country)
record_df = jhu_data.subset(country, population=population)
# Parameter estimation
unit = PhaseUnit("27May2020", "27Jun2020", population)
with pytest.raises(NameError):
unit.estimate()
unit.set_ode(model=SIR)
with pytest.raises(ValueError):
unit.estimate()
unit.record_df = record_df
assert set(unit.record_df.columns) == set(Term.SUB_COLUMNS)
unit.estimate(timeout=20)
# Check results
assert isinstance(unit.estimator, Estimator)
assert set(SIR.PARAMETERS).issubset(unit.to_dict())
assert set(SIR.DAY_PARAMETERS).issubset(unit.to_dict())
assert None not in unit.to_dict().values()
def test_simulate(self, jhu_data, population_data, country):
# Dataset
population = population_data.value(country)
record_df = jhu_data.subset(country, population=population)
# Parameter setting
unit = PhaseUnit("27May2020", "27Jun2020", population)
with pytest.raises(UnExecutedError):
unit3 = PhaseUnit("27May2020", "27Jun2020", population)
unit3.set_ode(model=SIR, tau=240, rho=0.006)
unit3.simulate()
unit.set_ode(model=SIR, tau=240, rho=0.006, sigma=0.011)
summary_dict = unit.to_dict()
assert summary_dict[Term.RT] == 0.55
assert summary_dict["1/beta [day]"] == 27
assert summary_dict["1/gamma [day]"] == 15
# Set initial values
unit.set_y0(record_df)
# Simulation
sim_df = unit.simulate()
assert set(sim_df.columns) == set(Term.NLOC_COLUMNS)
def test_start(self):
unit = PhaseUnit("01Jan2020", "01Feb2020", 1000)
assert str(unit) == "Phase (01Jan2020 - 01Feb2020)"
summary_dict = unit.to_dict()
assert summary_dict[Term.START] == "01Jan2020"
assert summary_dict[Term.END] == "01Feb2020"
assert summary_dict[Term.N] == 1000
summary_df = unit.summary()
assert set(summary_df.columns) == set([Term.START, Term.END, Term.N])
with pytest.raises(NotImplementedError):
assert unit == "phase"
unit2 = PhaseUnit("01Jan2020", "01Feb2020", 100000)
assert unit == unit2
unit3 = PhaseUnit("01Jan2020", "01Mar2020", 1000)
assert unit != unit3
assert "31Dec2019" not in unit
assert "01Jan2020" in unit
assert "15Jan2020" in unit
assert "01Feb2020" in unit
assert "01Mar2020" not in unit
def test_set_tau(self):
unit = PhaseUnit("01Jan2020", "01Feb2020", 1000)
unit.set_ode(model=None, tau=240, rho=0.006)
assert unit.tau == 240
assert "rho" not in unit.to_dict()