def test_set_parameters_arrays_set_single_value(self):
p = Parameters(input_households="notset.csv", read_param_file=False, read_hospital_param_file=False)
assert (
p.get_param("population_40_49") == 0
), "Array memebers not intilialised to zero"
p.set_param("population_40_49", 400)
assert (
p.get_param("population_40_49") == 400
), "Did not set pop group to 400"
assert p.get_param("population_50_59") == 0
def test_update_fatality_fraction(self):
params = Parameters(
constant.TEST_DATA_TEMPLATE,
constant.PARAM_LINE_NUMBER,
constant.DATA_DIR_TEST,
constant.TEST_HOUSEHOLD_FILE,
constant.TEST_HOSPITAL_FILE,
)
params.set_param( "n_total", 50000 )
model = Model(params)
assert model.get_param("fatality_fraction_80") == 1.0
model.update_running_params("fatality_fraction_80", 0.6)
assert model.get_param("fatality_fraction_80") == 0.6
def test_model_total_infected_by_age(self):
params = Parameters(
constant.TEST_DATA_TEMPLATE,
constant.PARAM_LINE_NUMBER,
constant.DATA_DIR_TEST,
constant.TEST_HOUSEHOLD_FILE,
)
params.set_param( "app_users_fraction", 0.25)
model = Model(params)
for _ in range(30):
model.one_time_step()
res = model.one_time_step_results()
for age in AgeGroupEnum:
assert res.get(f"total_infected{age.name}", None) is not None, f"Could not get total_infected{age.name}"
assert res.get("total_infected") == sum([res.get(f"total_infected{age.name}") for age in AgeGroupEnum]), "Total infected does not equal sum of age groups"
def test_deaths(self):
params = Parameters(
constant.TEST_DATA_TEMPLATE,
constant.PARAM_LINE_NUMBER,
constant.DATA_DIR_TEST,
constant.TEST_HOUSEHOLD_FILE,
constant.TEST_HOSPITAL_FILE,
)
params.set_param( "n_total", 50000);
model = Model(params)
daily_deaths = []
for step in range(50):
model.one_time_step()
daily_death = model.one_time_step_results()["daily_death"]
daily_deaths.append(daily_death)
assert sum(daily_deaths) == model.one_time_step_results()["total_death"]
assert sum(daily_deaths) > 0
def test_icu_entry(self):
params = Parameters(
constant.TEST_DATA_TEMPLATE,
constant.PARAM_LINE_NUMBER,
constant.DATA_DIR_TEST,
constant.TEST_HOUSEHOLD_FILE,
constant.TEST_HOSPITAL_FILE,
)
params.set_param( "n_total", 50000 )
model = Model(params)
daily_critical = []
for step in range(50):
model.one_time_step()
daily_c = model.one_time_step_results()["hospital_to_critical_daily"]
daily_critical.append(daily_c)
assert sum(daily_critical) == model.one_time_step_results()["hospital_to_critical_total"]
assert sum(daily_critical) > 0
def test_hostpital_admissions(self):
params = Parameters(
constant.TEST_DATA_TEMPLATE,
constant.PARAM_LINE_NUMBER,
constant.DATA_DIR_TEST,
constant.TEST_HOUSEHOLD_FILE,
constant.TEST_HOSPITAL_FILE,
)
params.set_param( "n_total", 50000 )
model = Model(params)
daily_hospitalisations = []
for step in range(50):
model.one_time_step()
daily_h = model.one_time_step_results()["hospital_admissions"]
daily_hospitalisations.append(daily_h)
assert sum(daily_hospitalisations) == model.one_time_step_results()["hospital_admissions_total"]
assert sum(daily_hospitalisations) > 0
def basic_example_lockdown_infected_agent():
params = Parameters("../tests/data/baseline_parameters.csv", 1, ".",
"../tests/data/baseline_household_demographics.csv")
T = 50
params.set_param("end_time", T)
params.set_param("n_total", 10000)
model = simulation.COVID19IBM(model=Model(params))
agent = LockdownInfectedOnePercent()
sim = simulation.Simulation(env=model,
agent=agent,
end_time=T,
verbose=True)
# Run the model for 25 time steps, print output
sim.steps(25)
print(sim.results)
def basic_example_lockdown_agent():
params = Parameters("../tests/data/baseline_parameters.csv", 1, ".",
"../tests/data/baseline_household_demographics.csv")
T = 35
params.set_param("end_time", T)
model = simulation.COVID19IBM(model=Model(params))
agent = LockdownAt20()
sim = simulation.Simulation(env=model,
agent=agent,
end_time=T,
verbose=True)
# Run the model for 25 time steps, print output
sim.steps(25)
print(sim.results)
model.model.write_output_files()
def test_daily_deaths_by_age(self):
params = Parameters(
constant.TEST_DATA_TEMPLATE,
constant.PARAM_LINE_NUMBER,
constant.DATA_DIR_TEST,
constant.TEST_HOUSEHOLD_FILE,
constant.TEST_HOSPITAL_FILE,
)
params.set_param( "n_total", 50000 )
model = Model(params)
for step in range(50):
model.one_time_step()
daily_death = model.one_time_step_results()["daily_death"]
sum_daily_deaths_by_age = 0
for age in AgeGroupEnum:
sum_daily_deaths_by_age += model.one_time_step_results()[f"daily_death{age.name}"]
assert daily_death == sum_daily_deaths_by_age
assert model.one_time_step_results()[f"daily_death{age.name}"] > 0
def basic_example_dummy_agent():
params = Parameters("../tests/data/baseline_parameters.csv", 1, ".",
"../tests/data/baseline_household_demographics.csv")
T = 15
params.set_param("end_time", T)
model = simulation.COVID19IBM(model=Model(params))
agent = simulation.Agent() # Dummy agent
sim = simulation.Simulation(env=model,
agent=agent,
end_time=T,
verbose=True)
# Run the model for 3 time steps, print output
sim.steps(3)
print(sim.results)
# RUn for another 5 time steps, print output
sim.steps(5)
print(sim.results)
def test_set_lockdown_multiplier_params(self):
params = Parameters(
constant.TEST_DATA_TEMPLATE,
constant.PARAM_LINE_NUMBER,
constant.DATA_DIR_TEST,
constant.TEST_HOUSEHOLD_FILE,
constant.TEST_HOSPITAL_FILE,
constant.PARAM_LINE_NUMBER
)
params.set_param( "n_total", 50000 )
model = Model(params)
assert covid19.get_param_lockdown_on(model.c_params) == 0
for oc_net in OccupationNetworkEnum:
model.update_running_params(f"lockdown_occupation_multiplier{oc_net.name}", 0.4)
assert model.get_param(f"lockdown_occupation_multiplier{oc_net.name}") == 0.4
for oc_net in OccupationNetworkEnum:
model.update_running_params(f"lockdown_occupation_multiplier{oc_net.name}", 0.8)
assert model.get_param(f"lockdown_occupation_multiplier{oc_net.name}") == 0.8
model.update_running_params("lockdown_house_interaction_multiplier", 1.2)
assert model.get_param("lockdown_house_interaction_multiplier") == 1.2
model.update_running_params("lockdown_on", 1)
assert covid19.get_param_lockdown_on(model.c_params) == 1
for oc_net in OccupationNetworkEnum:
model.update_running_params(f"lockdown_occupation_multiplier{oc_net.name}", 0.5)
assert model.get_param(f"lockdown_occupation_multiplier{oc_net.name}") == 0.5
model.update_running_params("lockdown_random_network_multiplier", 0.9)
assert model.get_param("lockdown_random_network_multiplier") == 0.9
model.update_running_params("lockdown_house_interaction_multiplier", 1.3)
assert model.get_param("lockdown_house_interaction_multiplier") == 1.3
assert covid19.get_param_lockdown_on(model.c_params) == 1
def test_set_get_parameters(self):
"""
Test the a parameter can be changed in between step runs
"""
# Create model object
params = Parameters(
constant.TEST_DATA_TEMPLATE,
constant.PARAM_LINE_NUMBER,
constant.DATA_DIR_TEST,
constant.TEST_HOUSEHOLD_FILE,
)
params.set_param("app_users_fraction", 0.25)
model = Model(params)
STEPS = 2
# Run steps
for step in range(0, STEPS):
model.one_time_step()
res = model.one_time_step_results()
# Try to set valid parameters
model.update_running_params("test_on_symptoms", 1)
np.testing.assert_equal(model.get_param("test_on_symptoms"), 1)
model.update_running_params("test_on_traced", 1)
np.testing.assert_equal(model.get_param("test_on_traced"), 1)
model.update_running_params("quarantine_on_traced", 1)
np.testing.assert_equal(model.get_param("quarantine_on_traced"), 1)
model.update_running_params("traceable_interaction_fraction", 0.30)
np.testing.assert_equal(
model.get_param("traceable_interaction_fraction"), 0.30)
model.update_running_params("tracing_network_depth", 1)
np.testing.assert_equal(model.get_param("tracing_network_depth"),
1)
model.update_running_params("allow_clinical_diagnosis", 1)
np.testing.assert_equal(
model.get_param("allow_clinical_diagnosis"), 1)
model.update_running_params("quarantine_household_on_positive", 1)
np.testing.assert_equal(
model.get_param("quarantine_household_on_positive"), 1)
model.update_running_params("quarantine_household_on_symptoms", 1)
np.testing.assert_equal(
model.get_param("quarantine_household_on_symptoms"), 1)
model.update_running_params(
"quarantine_household_on_traced_positive", 1)
np.testing.assert_equal(
model.get_param("quarantine_household_on_traced_positive"), 1)
model.update_running_params(
"quarantine_household_contacts_on_positive", 1)
np.testing.assert_equal(
model.get_param("quarantine_household_contacts_on_positive"),
1,
)
model.update_running_params("quarantine_days", 1)
np.testing.assert_equal(model.get_param("quarantine_days"), 1)
model.update_running_params("test_order_wait", 1)
np.testing.assert_equal(model.get_param("test_order_wait"), 1)
model.update_running_params("test_result_wait", 1)
np.testing.assert_equal(model.get_param("test_result_wait"), 1)
model.update_running_params("self_quarantine_fraction", 1)
np.testing.assert_equal(
model.get_param("self_quarantine_fraction"), 1)
# Try to set/get invalid parameters
with pytest.raises(ModelParameterException):
model.update_running_params("wrong_parameter", 1)
with pytest.raises(ModelParameterException):
model.get_param("wrong_parameter")
def test_set_get_model_parameters(self):
"""
Test the a parameter can be changed in between step runs
"""
# Cr.eate model object
params = Parameters(
constant.TEST_DATA_TEMPLATE,
constant.PARAM_LINE_NUMBER,
constant.DATA_DIR_TEST,
constant.TEST_HOUSEHOLD_FILE,
constant.TEST_HOSPITAL_FILE,
constant.HOSPITAL_PARAM_LINE_NUMBER
)
params.set_param( "n_total", 50000 )
model = Model(params)
# Run steps
for step in range(0, STEPS):
model.one_time_step()
# Try to set valid model parameters
model.update_running_params("test_on_symptoms", 1)
np.testing.assert_equal(model.get_param("test_on_symptoms"), 1)
model.update_running_params("test_on_traced", 1)
np.testing.assert_equal(model.get_param("test_on_traced"), 1)
model.update_running_params("quarantine_on_traced", 1)
np.testing.assert_equal(model.get_param("quarantine_on_traced"), 1)
model.update_running_params("traceable_interaction_fraction", 0.30)
np.testing.assert_equal(
model.get_param("traceable_interaction_fraction"), 0.30
)
model.update_running_params("tracing_network_depth", 1)
np.testing.assert_equal(model.get_param("tracing_network_depth"), 1)
model.update_running_params("allow_clinical_diagnosis", 1)
np.testing.assert_equal(model.get_param("allow_clinical_diagnosis"), 1)
model.update_running_params("quarantine_household_on_positive", 1)
np.testing.assert_equal(
model.get_param("quarantine_household_on_positive"), 1
)
model.update_running_params("quarantine_household_on_symptoms", 1)
np.testing.assert_equal(
model.get_param("quarantine_household_on_symptoms"), 1
)
model.update_running_params("quarantine_household_on_traced_positive", 1)
np.testing.assert_equal(
model.get_param("quarantine_household_on_traced_positive"), 1
)
model.update_running_params("quarantine_household_contacts_on_positive", 1)
np.testing.assert_equal(
model.get_param("quarantine_household_contacts_on_positive"), 1,
)
model.update_running_params("quarantine_days", 1)
np.testing.assert_equal(model.get_param("quarantine_days"), 1)
model.update_running_params("test_order_wait", 1)
np.testing.assert_equal(model.get_param("test_order_wait"), 1)
model.update_running_params("test_result_wait", 1)
np.testing.assert_equal(model.get_param("test_result_wait"), 1)
model.update_running_params("self_quarantine_fraction", 1)
np.testing.assert_equal(model.get_param("self_quarantine_fraction"), 1)
# Try to set/get array model parameters
for age in AgeGroupEnum:
contacts = randrange(1, 10)
model.update_running_params(f"priority_test_contacts{age.name}", contacts)
assert model.get_param(f"priority_test_contacts{age.name}") == contacts
# Try to set/get invalid parameters
with pytest.raises(ModelParameterException):
model.update_running_params("wrong_parameter", 1)
with pytest.raises(ModelParameterException):
model.get_param("wrong_parameter")
def test_set_age_out_of_range(self):
p = Parameters(input_households="notset.csv", read_param_file=False, read_hospital_param_file=False)
with pytest.raises(ParameterException):
p.set_param("population_80_89", 5000)
