def test_add_phase_with_model(self, jhu_data, population_data, country):
# Setting
population = population_data.value(country)
series = PhaseSeries("01Apr2020", "01Aug2020", population)
series.add()
# Add future phase with model and tau
series.add(end_date="01Sep2020", model=SIR, tau=360)
series.add(end_date="01Oct2020")
length = len(series)
assert series.to_dict()[Term.num2str(length - 2)][Term.ODE] == SIR.NAME
assert series.to_dict()[Term.num2str(length - 1)][Term.TAU] == 360
series.add(end_date="01Nov2020", rho=0.006)
series.add(end_date="01Dec2020", sigma=0.011)
assert series.to_dict()[Term.num2str(length + 1)][Term.RT] == 0.55
assert series.to_dict()[Term.num2str(length + 1)]["1/beta [day]"] == 41
def test_records(self, jhu_data, population_data, country):
warnings.simplefilter("ignore", category=UserWarning)
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01Aug2020"
# Test
df = snl.records(show_figure=False)
assert isinstance(df, pd.DataFrame)
assert set(df.columns) == set(Term.NLOC_COLUMNS)
dates = df[Term.DATE]
assert dates.min() == Term.date_obj(snl.first_date)
assert dates.max() == Term.date_obj(snl.last_date)
df2 = snl.records(show_figure=True)
assert isinstance(df2, pd.DataFrame)
assert set(df2.columns) == set(Term.NLOC_COLUMNS)
def test_records(self, jhu_data, population_data, country):
warnings.simplefilter("ignore", category=UserWarning)
# Setting
dhl = DataHandler(jhu_data, population_data, country)
dhl.init_records()
dhl.first_date = "01Apr2020"
dhl.last_date = "01Aug2020"
# Test
df = dhl.records(variables=None, show_figure=False)
assert isinstance(df, pd.DataFrame)
assert set(df.columns) == set([Term.DATE, Term.CI, Term.F, Term.R])
dates = df[Term.DATE]
assert dates.min() == Term.date_obj(dhl.first_date)
assert dates.max() == Term.date_obj(dhl.last_date)
df2 = dhl.records(variables=["Susceptible"], show_figure=True)
assert set(df2.columns) == set([Term.DATE, Term.S])
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_find_with_few_records(self, jhu_data, population_data):
population = population_data.value("Italy")
min_size = 7
df = jhu_data.subset(country="Italy")
start_date = df.loc[df.index[0], Term.DATE].strftime(Term.DATE_FORMAT)
end_date = Term.date_change(start_date, days=min_size - 2)
sr_df = jhu_data.to_sr(country="Italy",
population=population,
end_date=end_date)
with pytest.raises(ValueError):
change_finder = ChangeFinder(sr_df, min_size=min_size)
change_finder.run()
def test_start_record_range(self, jhu_data, population_data, country):
# Setting
snl = Scenario(jhu_data, population_data, country)
# Test
snl.first_date = "01Apr2020"
assert snl.first_date == "01Apr2020"
snl.last_date = "01May2020"
assert snl.last_date == "01May2020"
with pytest.raises(ValueError):
snl.first_date = "01Jan2019"
with pytest.raises(ValueError):
tomorrow = Term.tomorrow(datetime.now().strftime(Term.DATE_FORMAT))
snl.last_date = tomorrow
def test_start_record_range(self, jhu_data, population_data, country):
# Setting
dhl = DataHandler(jhu_data, population_data, country)
dhl.init_records()
# Test
dhl.first_date = "01Apr2020"
assert dhl.first_date == "01Apr2020"
dhl.last_date = "01May2020"
assert dhl.last_date == "01May2020"
with pytest.raises(ValueError):
dhl.first_date = "01Jan2019"
with pytest.raises(ValueError):
tomorrow = Term.tomorrow(datetime.now().strftime(Term.DATE_FORMAT))
dhl.last_date = tomorrow
def test_record_range(self, snl, first_date, last_date, today):
snl.timepoints()
snl.first_date = first_date
snl.last_date = last_date
snl.today = today
assert snl.first_date == first_date
assert snl.last_date == last_date
assert snl.today == today
with pytest.raises(ValueError):
snl.first_date = "01Jan2019"
with pytest.raises(ValueError):
snl.last_date = Term.tomorrow(datetime.now().strftime(Term.DATE_FORMAT))
# Add a phase to today (01Apr2020)
snl.add(name="Main")
assert snl.get(Term.END, phase="last", name="Main") == today
snl.clear(name="Main", include_past=True)
def test_score(self, snl, metrics):
try:
snl.delete(name="Score")
except KeyError:
pass
snl.clear(name="Score", template="Main")
assert isinstance(snl.score(metrics=metrics, name="Score"), float)
# Selected phases
df = snl.summary(name="Score")
all_phases = df.index.tolist()
sel_score = snl.score(phases=all_phases[-2:], name="Score")
# Selected past days (when the beginning date is a start date)
beginning_date = df.loc[df.index[-2], Term.START]
past_days = Term.steps(beginning_date, snl.today, tau=1440)
assert snl.score(past_days=past_days, name="Score") == sel_score
# Selected past days
snl.score(past_days=60, name="Score")
def test_score(self, jhu_data, population_data, country):
snl = Scenario(jhu_data, population_data, country, tau=360)
snl.trend(show_figure=False)
snl.estimate(SIRF, timeout=1, timeout_iteration=1)
assert isinstance(snl.score(metrics="RMSLE"), float)
# Selected phases
df = snl.summary()
all_phases = df.index.tolist()
sel_score = snl.score(phases=all_phases[-2:])
# Selected past days (when the begging date is a start date)
beginning_date = df.loc[df.index[-2], Term.START]
past_days = Term.steps(beginning_date, snl.last_date, tau=1440)
assert snl.score(past_days=past_days) == sel_score
# Selected past days
snl.score(past_days=60)
with pytest.raises(ValueError):
snl.score(phases=["1st"], past_days=60)
def test_score(self, jhu_data, population_data, country):
snl = Scenario(jhu_data, population_data, country, tau=360)
snl.trend(show_figure=False)
snl.estimate(SIRF, timeout=10)
metrics_list = ["MAE", "MSE", "MSLE", "RMSE", "RMSLE"]
for metrics in metrics_list:
score = snl.score(metrics=metrics)
assert isinstance(score, float)
# Selected phases
df = snl.summary()
all_phases = df.index.tolist()
sel_score = snl.score(phases=all_phases[-2:])
# Selected past days (when the begging date is a start date)
beginning_date = df.loc[df.index[-2], Term.START]
past_days = Term.steps(beginning_date, snl.last_date, tau=1440)
assert snl.score(past_days=past_days) == sel_score
# Selected past days
snl.score(past_days=60)