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_add_past_phases(self, jhu_data, population_data):
scenario = Scenario(jhu_data, population_data, country="India")
scenario.delete()
# Phase series
scenario.clear(name="Medicine")
scenario.add(days=100)
scenario.delete(name="Medicine")
with pytest.raises(TypeError):
scenario.delete(phase="0th")
with pytest.raises(TypeError):
scenario.summary(columns="Population")
with pytest.raises(KeyError):
scenario.summary(columns=["Value"])
# Range of past phases
scenario.first_date = "01Mar2020"
scenario.first_date
scenario.last_date = "16Jul2020"
scenario.last_date
with pytest.raises(ValueError):
scenario.first_date = "01Aug2020"
with pytest.raises(ValueError):
scenario.last_date = "01Feb2020"
# With trend analysis
scenario.trend(set_phases=True)
with pytest.raises(ValueError):
scenario.trend(set_phases=False, n_points=3)
scenario.combine(phases=["3rd", "4th"])
scenario.separate(date="30May2020", phase="1st")
scenario.delete(phases=["1st"])
scenario.trend(set_phases=False)
trend_df = scenario.summary()
assert len(trend_df) == 4
# add scenarios one by one
scenario.clear(include_past=True)
scenario.add(end_date="29May2020")
scenario.add(end_date="05Jun2020").delete(phases=["0th"])
scenario.add(end_date="15Jun2020")
scenario.add(end_date="04Jul2020")
scenario.add()
one_df = scenario.summary()
assert len(one_df) == 4
# With 0th phase
scenario.use_0th = True
scenario.trend(set_phases=False, include_init_phase=True)
scenario.use_0th = False
scenario.trend(set_phases=True, include_init_phase=True)
scenario.delete(phases=["0th"])
assert len(scenario.summary()) == 5
with pytest.raises(TypeError):
scenario.delete(phases="1st")
def test_edit_series(self, jhu_data, population_data, country):
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01Aug2020"
# Add and clear
assert snl.summary().empty
snl.add(end_date="05May2020")
snl.add(days=20)
snl.add()
snl.add(end_date="01Sep2020")
assert len(snl["Main"]) == 4
snl.clear(include_past=True)
snl.add(end_date="01Sep2020", name="New")
assert len(snl["New"]) == 2
# Delete
snl.delete(name="Main")
assert len(snl["Main"]) == 0
with pytest.raises(TypeError):
snl.delete(phases="1st", name="New")
snl.delete(phases=["1st"], name="New")
assert len(snl["New"]) == 1
snl.delete(name="New")
with pytest.raises(KeyError):
assert len(snl["New"]) == 1
def test_estimate(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"
with pytest.raises(ValueError):
snl.estimate(SIR)
snl.trend(include_init_phase=True, show_figure=False)
snl.disable(phases=["0th"])
with pytest.raises(AttributeError):
snl.estimate_history(phase="1th")
# Parameter estimation
with pytest.raises(KeyError):
snl.estimate(SIR, phases=["30th"])
with pytest.raises(ValueError):
snl.estimate(model=SIR, tau=1440)
snl.enable(phases=["0th"])
with pytest.raises(TypeError):
snl.estimate(model=SIR, phases="1st")
with pytest.raises(ValueError):
snl.estimate(model=SIR, phases=["0th"])
snl.clear(include_past=True)
snl.trend(show_figure=False)
snl.estimate(SIR)
# Estimation history
snl.estimate_history(phase="1st")
# Estimation accuracy
snl.estimate_accuracy(phase="1st")
# Get a value
snl.get(Term.RT)
with pytest.raises(KeyError):
snl.get("feeling")
def test_summary(self, jhu_data, population_data, country):
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01Aug2020"
snl.trend(show_figure=False)
# One scenario
assert set(snl.summary().columns) == set(
[Term.TENSE, Term.START, Term.END, Term.N])
# Show two scenarios
snl.clear(name="New")
cols = snl.summary().reset_index().columns
assert set([Term.SERIES, Term.PHASE]).issubset(set(cols))
# Show selected scenario
cols_sel = snl.summary(name="New").reset_index().columns
assert not set([Term.SERIES, Term.PHASE]).issubset(set(cols_sel))
# Columns to show
show_cols = [Term.N, Term.START]
assert set(snl.summary(columns=show_cols).columns) == set(show_cols)
with pytest.raises(TypeError):
snl.summary(columns=Term.N)
with pytest.raises(KeyError):
snl.summary(columns=[Term.N, "Temperature"])
# To markdown
snl.summary().to_markdown()
def test_estimate(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"
with pytest.raises(ValueError):
snl.estimate(SIR)
snl.trend(show_figure=False)
with pytest.raises(AttributeError):
snl.estimate_history(phase="last")
# Parameter estimation
with pytest.raises(KeyError):
snl.estimate(SIR, phases=["30th"])
with pytest.raises(ValueError):
snl.estimate(model=SIR, tau=1440)
snl.estimate(SIR, timeout=1, timeout_iteration=1)
# Estimation history
snl.estimate_history(phase="last")
# Estimation accuracy
snl.estimate_accuracy(phase="last")
# Get a value
snl.get(Term.RT)
with pytest.raises(KeyError):
snl.get("feeling")
def test_trend(self, jhu_data, population_data, country):
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01Aug2020"
# Deprecated
warnings.simplefilter("error")
with pytest.raises(DeprecationWarning):
snl.trend(include_init_phase=False, show_figure=False)
warnings.simplefilter("ignore")
snl.trend(include_init_phase=False, show_figure=False)
# S-R trend analysis
snl.trend(show_figure=False)
assert snl["Main"]
with pytest.raises(ValueError):
snl.trend(show_figure=False, n_points=3)
# Disable/enable
length = len(snl["Main"])
snl.disable(phases=["0th"], name="Main")
assert len(snl["Main"]) == length - 1
snl.enable(phases=["0th"], name="Main")
assert len(snl["Main"]) == length
with pytest.raises(TypeError):
snl.enable(phases="0th", name="Main")
with pytest.raises(TypeError):
snl.disable(phases="1st", name="Main")
def test_retrospective(self, jhu_data, population_data, country):
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "19Oct2020"
snl.trend(show_figure=False)
# Retrospective analysis
snl.retrospective(
"01Sep2020", model=SIR, control="Main", target="Retrospective")
def test_retrospective(self, jhu_data, population_data, country):
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01Jun2020"
snl.trend(show_figure=False)
# Retrospective analysis
snl.retrospective(
"01May2020", model=SIRF, control="Main", target="Retrospective",
timeout=1, timeout_iteration=1)
def test_add_phase_dep(self, jhu_data, population_data, country):
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01Aug2020"
# Test
warnings.simplefilter("error")
with pytest.raises(DeprecationWarning):
snl.add_phase(end_date="01May2020")
warnings.simplefilter("ignore")
snl.add_phase(end_date="01May2020")
def test_simulate(self, jhu_data, population_data, country):
warnings.simplefilter("ignore", category=UserWarning)
warnings.simplefilter("ignore", category=DeprecationWarning)
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01May2020"
with pytest.raises(ValueError):
snl.simulate()
with pytest.raises(ValueError):
snl.track()
snl.trend(show_figure=False)
# Parameter estimation
with pytest.raises(ValueError):
# Deprecated
snl.param_history(["rho"])
all_phases = snl.summary().index.tolist()
snl.disable(all_phases[:-2])
with pytest.raises(NameError):
snl.simulate()
snl.estimate(SIRF, timeout=5, timeout_iteration=5)
# Simulation
snl.simulate(variables=[Term.C, Term.CI, Term.F, Term.R])
snl.simulate(phases=all_phases[-2:])
# Parameter history (Deprecated)
snl.param_history([Term.RT], divide_by_first=False)
snl.param_history(["rho"])
snl.param_history(["rho"], show_figure=False)
snl.param_history(["rho"], show_box_plot=False)
with pytest.raises(KeyError):
snl.param_history(["feeling"])
# Comparison of scenarios
snl.describe()
snl.track()
snl.history(target="Rt")
snl.history(target="sigma")
snl.history(target="rho", show_figure=False)
snl.history(target="Infected", phases=all_phases[-2:])
with pytest.raises(KeyError):
snl.history(target="temperature")
# Change rate of parameters
snl.history_rate(name="Main")
snl.history_rate(
name="Main", params=["theta", "kappa"], show_figure=False)
with pytest.raises(TypeError):
snl.history_rate(params="", name="Main")
# Add new scenario
snl.add(end_date="01Sep2020", name="New")
snl.describe()
def test_edit(self, jhu_data, population_data, country):
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01Aug2020"
snl.trend(show_figure=False)
# Combine
length = len(snl["Main"])
snl.combine(["1st", "2nd"])
n_changed = int(population_data.value(country) * 0.98)
snl.combine(["2nd", "3rd"], population=n_changed)
assert len(snl["Main"]) == length - 2
# Separate
snl.separate(date="01May2020")
assert len(snl["Main"]) == length - 1
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_trend(self, jhu_data, population_data, country):
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01Aug2020"
snl.trend(show_figure=False)
assert snl["Main"]
with pytest.raises(ValueError):
snl.trend(show_figure=False, n_points=3)
# Disable/enable
length = len(snl["Main"])
snl.disable(phases=["0th"], name="Main")
assert len(snl["Main"]) == length - 1
snl.enable(phases=["0th"], name="Main")
assert len(snl["Main"]) == length
with pytest.raises(TypeError):
snl.enable(phases="0th", name="Main")
with pytest.raises(TypeError):
snl.disable(phases="1st", name="Main")
def test_simulate(self, jhu_data, population_data, country):
warnings.simplefilter("ignore", category=UserWarning)
warnings.simplefilter("ignore", category=DeprecationWarning)
# Setting
snl = Scenario(jhu_data, population_data, country)
snl.first_date = "01Apr2020"
snl.last_date = "01Aug2020"
snl.trend(show_figure=False)
# Parameter estimation
with pytest.raises(ValueError):
# Deprecated
snl.param_history(["rho"])
snl.estimate(SIR)
# Simulation
snl.simulate()
# Parameter history (Deprecated)
snl.param_history([Term.RT], divide_by_first=False)
snl.param_history(["rho"])
snl.param_history(["rho"], show_figure=False)
snl.param_history(["rho"], show_box_plot=False)
with pytest.raises(KeyError):
snl.param_history(["feeling"])
# Comparison of scenarios
snl.describe()
snl.history(target="Rt")
snl.history(target="sigma")
snl.history(target="Infected")
with pytest.raises(KeyError):
snl.history(target="temperature")
# Change rate of parameters
snl.history_rate(name="Main")
with pytest.raises(TypeError):
snl.history_rate(params="", name="Main")
# Add new scenario
snl.add(end_date="01Sep2020", name="New")
snl.describe()