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_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_simulate_y0_direct(self, jhu_data, population_data, country):
# Dataset
population = population_data.value(country)
# Parameter setting
unit = PhaseUnit("27May2020", "27Jun2020", population)
unit.set_ode(model=SIR, tau=240, rho=0.006, sigma=0.011)
# Simulation
y0_dict = {
"Susceptible": 126512455, "Infected": 1806, "Fatal or Recovered": 14839
}
sim_df = unit.simulate(y0_dict=y0_dict)
assert set(sim_df.columns) == set(Term.NLOC_COLUMNS)
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_replace(self, jhu_data, population_data, country):
# Setting
population = population_data.value(country)
series = PhaseSeries("01Apr2020", "01Aug2020", population)
series.add(end_date="01May2020")
series.add(end_date="01Jun2020")
series.add(end_date="01Jul2020")
series.add()
# Replace one old phase with one new phase
unit_old = series.unit("0th")
unit_new = PhaseUnit(
unit_old.start_date, unit_old.end_date, population
)
unit_new.set_ode(tau=360)
series.replace("0th", unit_new)
assert series.unit("0th") == unit_new
# Replace one old phase with two new phases
unit_old = series.unit("1st")
change_date = Term.date_change(unit_old.end_date, days=-7)
unit_pre = PhaseUnit(
unit_old.start_date, Term.yesterday(change_date), population)
unit_pre.set_ode(tau=360)
unit_fol = PhaseUnit(change_date, unit_old.end_date, population)
unit_fol.set_ode(tau=360)
series.replaces(phase="1st", new_list=[unit_pre, unit_fol])
print(series.unit("1st"), unit_pre)
assert series.unit("1st") == unit_pre
assert series.unit("2nd") == unit_fol
# TypeError of new_list
with pytest.raises(TypeError):
series.replaces(phase="3rd", new_list=[unit_pre, Term])
# ValueError with tense
with pytest.raises(ValueError):
future_unit = PhaseUnit("01Sep2020", "01Dec2020", population)
series.replaces(phase="3rd", new_list=[future_unit])
# Add phase without deletion of any phases
new1 = PhaseUnit("02Aug2020", "01Sep2020", population)
new2 = PhaseUnit("02Sep2020", "01Oct2020", population)
series.replaces(phase=None, new_list=[new1, new2])
assert series.unit("last") == new2
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()