def test_results(self):
approx = lambda x: _approx(x, rel=0.005)
m = SIR(disease="covid-19", region="BR")
m.set_ic(cases=1e6)
m.run(60)
# Data
assert m.results["data.attack_rate"] == approx(0.919)
assert m.results["data.cases"] == approx(194236068)
assert m.results["data.infectious"] == approx(4045)
assert m.results["data.recovered"] == approx(194632955)
assert m.results["data.susceptible"] == approx(17118720)
assert m.results["data"] == approx({
"attack_rate": 0.919,
"cases": 194236068,
"infectious": 4045,
"recovered": 194632955,
"susceptible": 17118720,
})
# Parameters
assert m.results["params.R0"] == m.R0
assert m.results["params.gamma"] == m.gamma
assert m.results["params.infectious_period"] == m.infectious_period
assert m.results["params"] == approx({
"R0": 2.74,
"infectious_period": 3.47
})
# Dates
dates = m.results["dates"]
assert dates["start"] < dates["peak"] < dates["end"]
def test_info(self):
approx = lambda x: _approx(x, rel=0.005)
disease = get_disease("covid-19")
m = SIR(disease="covid-19", region="BR")
m.set_ic(cases=1e6)
m.run(60)
# Disease
infectious_period = disease.infectious_period(region="BR")
assert m.info["disease.CFR"] == approx(disease.CFR(region="BR"))
assert m.info["disease.IFR"] == approx(disease.IFR(region="BR"))
assert m.info["disease.infectious_period"] == approx(infectious_period)
assert set(m.info["disease"]) == {
"R0",
"case_fatality_ratio",
"critical_delay",
"critical_period",
"death_delay",
"hospital_fatality_ratio",
"hospitalization_overflow_bias",
"hospitalization_period",
"hospitalization_table",
"icu_fatality_ratio",
"icu_period",
"incubation_period",
"infection_fatality_ratio",
"infectious_period",
"mortality_table",
"prob_aggravate_to_icu",
"prob_critical",
"prob_severe",
"prob_symptoms",
"rho",
"serial_period",
"severe_delay",
"severe_period",
"symptom_delay",
}
# Region
br = mundi.region("BR")
keys = {
"population",
"age_distribution",
"age_pyramid",
"hospital_capacity",
"icu_capacity",
}
assert m.info["region.population"] == br.population
assert all(m.info["region.age_distribution"] == br.age_distribution)
assert all(m.info["region.age_pyramid"] == br.age_pyramid)
assert set(m.info["region"]) == keys
def test_can_store_information_in_results(self):
m = SIR(disease="covid-19", region="BR")
m.run(10)
expect = {"bar": 42, "spam": "eggs"}
m.results["foo.bar"] = 42
m.results["foo.spam"] = "eggs"
assert m.results["foo"] == expect
assert "foo" in m.results.keys()
assert "foo" in m.results.to_dict()
assert "foo.bar" in m.results.to_dict(flat=True)
m.run(10)
assert m.results.get("foo") == {}