def test_basic_contact_trace():
tweaking = {
'n_days': 60,
'pop_size': 2000,
'pop_type': 'hybrid'
}
start_days = []
interventions = []
test_prob_start_day = 35
prob_test_perfect_symptomatic = test_prob(symp_prob=1.0, symp_quar_prob=1.0, asymp_quar_prob=1.0,
test_sensitivity=1.0, test_delay=1, start_day=test_prob_start_day)
start_days.append(test_prob_start_day)
interventions.append(prob_test_perfect_symptomatic)
contact_trace_start_day = 35
all_contacts = {
'h': 1.0,
'w': 1.0,
's': 1.0,
'c': 1.0
}
single_day_delays = {
'h': 1,
'w': 1,
's': 1,
'c': 1
}
brutal_contact_trace = contact_tracing(trace_probs=all_contacts,
trace_time=single_day_delays,
start_day=contact_trace_start_day)
start_days.append(contact_trace_start_day)
interventions.append(brutal_contact_trace)
tweaking['interventions'] = interventions
test_stuff_simulation = Sim(pars=tweaking)
test_stuff_simulation.run()
test_stuff_results = test_stuff_simulation.to_json(tostring=False)
with open("DEBUG_test_intervention_list_simulation.json","w") as outfile:
json.dump(test_stuff_results, outfile, indent=4, sort_keys=True)
pass
assert test_stuff_results["results"]["n_symptomatic"][test_prob_start_day] > 0 # If there are symptomatics
assert sum(test_stuff_results["results"]["new_tests"][test_prob_start_day:test_prob_start_day + 5]) > 0 # then there should be tests
assert sum(test_stuff_results["results"]["new_diagnoses"][test_prob_start_day + 1:test_prob_start_day + 6]) > 0 # and some diagnoses
assert sum(test_stuff_results["results"]["new_diagnoses"][test_prob_start_day + 2:test_prob_start_day + 7]) > 0 # and therefore some quarantined
pass
class CovaSimTest(unittest.TestCase):
def setUp(self):
self.is_debugging = False
self.simulation_parameters = None
self.sim = None
self.simulation_result = None
self.expected_result_filename = f"DEBUG_{self.id()}.json"
if os.path.isfile(self.expected_result_filename):
os.unlink(self.expected_result_filename)
pass
def tearDown(self):
if not self.is_debugging:
if os.path.isfile(self.expected_result_filename):
os.unlink(self.expected_result_filename)
pass
# region configuration methods
def set_simulation_parameters(self, params_dict=None):
"""
Overrides all of the default sim parameters
with the ones in the dictionary
Args:
params_dict: keys are param names, values are expected values to use
Returns:
None, sets self.simulation_params
"""
if not self.simulation_parameters:
self.simulation_parameters = parameters.make_pars(
set_prognoses=True, prog_by_age=True, use_layers=True)
if params_dict:
self.simulation_parameters.update(params_dict)
pass
def set_simulation_prognosis_probability(self, params_dict):
"""
Allows for testing prognoses probability as absolute rather than relative.
NOTE: You can only call this once per test or you will overwrite your stuff.
"""
ProbKeys = TestProperties.ParameterKeys.ProgressionKeys.ProbabilityKeys
supported_probabilities = [
ProbKeys.inf_to_symptomatic_probability,
ProbKeys.sym_to_severe_probability,
ProbKeys.sev_to_critical_probability,
ProbKeys.crt_to_death_probability
]
for k in params_dict:
if k not in supported_probabilities:
raise KeyError(
f"Key {k} not found in {supported_probabilities}.")
if not self.simulation_parameters:
self.set_simulation_parameters()
pass
for k in params_dict:
expected_prob = params_dict[k]
old_probs = self.simulation_parameters['prognoses'][k]
self.simulation_parameters['prognoses'][k] = np.array(
[expected_prob] * len(old_probs))
pass
pass
def set_duration_distribution_parameters(self, duration_in_question, par1,
par2):
if not self.simulation_parameters:
self.set_simulation_parameters()
pass
duration_node = self.simulation_parameters["dur"]
duration_node[duration_in_question] = {
"dist": "normal",
"par1": par1,
"par2": par2
}
params_dict = {"dur": duration_node}
self.set_simulation_parameters(params_dict=params_dict)
def run_sim(self, params_dict=None, write_results_json=False):
if not self.simulation_parameters or params_dict: # If we need one, or have one here
self.set_simulation_parameters(params_dict=params_dict)
pass
self.sim = Sim(pars=self.simulation_parameters, datafile=None)
self.sim.run(verbose=0)
self.simulation_result = self.sim.to_json(tostring=False)
if write_results_json:
with open(self.expected_result_filename, 'w') as outfile:
json.dump(self.simulation_result,
outfile,
indent=4,
sort_keys=True)
pass
# endregion
# region simulation results support
def get_full_result_channel(self, channel):
result_data = self.simulation_result["results"][channel]
return result_data
def get_day_zero_channel_value(
self,
channel=TestProperties.ResultsDataKeys.susceptible_at_timestep):
"""
Args:
channel: timeseries channel to report ('n_susceptible')
Returns: day zero value for channel
"""
result_data = self.get_full_result_channel(channel=channel)
return result_data[0]
def get_day_final_channel_value(self, channel):
channel = self.get_full_result_channel(channel=channel)
return channel[-1]
# endregion
# region specialized simulation methods
def set_microsim(self):
Simkeys = TestProperties.ParameterKeys.SimulationKeys
Micro = TestProperties.SpecializedSimulations.Microsim
microsim_parameters = {
Simkeys.number_agents: Micro.n,
Simkeys.initial_infected_count: Micro.pop_infected,
Simkeys.number_simulated_days: Micro.n_days
}
self.set_simulation_parameters(microsim_parameters)
pass
def set_everyone_infected(self, agent_count=1000):
Simkeys = TestProperties.ParameterKeys.SimulationKeys
everyone_infected = {
Simkeys.number_agents: agent_count,
Simkeys.initial_infected_count: agent_count
}
self.set_simulation_parameters(params_dict=everyone_infected)
pass
DurationKeys = TestProperties.ParameterKeys.ProgressionKeys.DurationKeys
def set_everyone_infectious_same_day(self,
num_agents,
days_to_infectious=1,
num_days=60):
"""
Args:
num_agents: number of agents to create and infect
days_to_infectious: days until all agents are infectious (1)
num_days: days to simulate (60)
"""
self.set_everyone_infected(agent_count=num_agents)
prob_dict = {
TestProperties.ParameterKeys.ProgressionKeys.ProbabilityKeys.inf_to_symptomatic_probability:
0
}
self.set_simulation_prognosis_probability(prob_dict)
test_config = {
TestProperties.ParameterKeys.SimulationKeys.number_simulated_days:
num_days
}
self.set_duration_distribution_parameters(
duration_in_question=DurationKeys.exposed_to_infectious,
par1=days_to_infectious,
par2=0)
self.set_simulation_parameters(params_dict=test_config)
pass
def set_everyone_symptomatic(self, num_agents, constant_delay: int = None):
"""
Cause all agents in the simulation to begin infected
And proceed to symptomatic (but not severe or death)
Args:
num_agents: Number of agents to begin with
"""
self.set_everyone_infectious_same_day(num_agents=num_agents,
days_to_infectious=0)
prob_dict = {
TestProperties.ParameterKeys.ProgressionKeys.ProbabilityKeys.inf_to_symptomatic_probability:
1.0,
TestProperties.ParameterKeys.ProgressionKeys.ProbabilityKeys.sym_to_severe_probability:
0
}
self.set_simulation_prognosis_probability(prob_dict)
if constant_delay is not None:
self.set_duration_distribution_parameters(
duration_in_question=DurationKeys.infectious_to_symptomatic,
par1=constant_delay,
par2=0)
pass
def set_everyone_is_going_to_die(self, num_agents):
"""
Cause all agents in the simulation to begin infected and die.
Args:
num_agents: Number of agents to simulate
"""
ProbKeys = TestProperties.ParameterKeys.ProgressionKeys.ProbabilityKeys
self.set_everyone_infectious_same_day(num_agents=num_agents)
prob_dict = {
ProbKeys.inf_to_symptomatic_probability: 1,
ProbKeys.sym_to_severe_probability: 1,
ProbKeys.sev_to_critical_probability: 1,
ProbKeys.crt_to_death_probability: 1
}
self.set_simulation_prognosis_probability(prob_dict)
pass
def set_everyone_severe(self, num_agents, constant_delay: int = None):
self.set_everyone_symptomatic(num_agents=num_agents,
constant_delay=constant_delay)
prob_dict = {
TestProperties.ParameterKeys.ProgressionKeys.ProbabilityKeys.sym_to_severe_probability:
1.0,
TestProperties.ParameterKeys.ProgressionKeys.ProbabilityKeys.sev_to_critical_probability:
0.0
}
self.set_simulation_prognosis_probability(prob_dict)
if constant_delay is not None:
self.set_duration_distribution_parameters(
duration_in_question=DurationKeys.symptomatic_to_severe,
par1=constant_delay,
par2=0)
pass
def set_everyone_critical(self, num_agents, constant_delay: int = None):
"""
Causes all agents to become critically ill day 1
"""
self.set_everyone_severe(num_agents=num_agents,
constant_delay=constant_delay)
prob_dict = {
TestProperties.ParameterKeys.ProgressionKeys.ProbabilityKeys.sev_to_critical_probability:
1.0,
TestProperties.ParameterKeys.ProgressionKeys.ProbabilityKeys.crt_to_death_probability:
0.0
}
self.set_simulation_prognosis_probability(prob_dict)
if constant_delay is not None:
self.set_duration_distribution_parameters(
duration_in_question=DurationKeys.severe_to_critical,
par1=constant_delay,
par2=0)
pass
def set_smallpop_hightransmission(self):
"""
Creates a small population with lots of transmission
"""
Simkeys = TestProperties.ParameterKeys.SimulationKeys
Transkeys = TestProperties.ParameterKeys.TransmissionKeys
Progkeys = TestProperties.ParameterKeys.ProgressionKeys
Hightrans = TestProperties.SpecializedSimulations.Hightransmission
hightrans_parameters = {
Simkeys.number_agents: Hightrans.n,
Simkeys.initial_infected_count: Hightrans.pop_infected,
Simkeys.number_simulated_days: Hightrans.n_days,
Transkeys.beta: Hightrans.beta
}
self.set_simulation_parameters(hightrans_parameters)
pass
# endregion
pass
class CovaSimTest(unittest.TestCase):
def setUp(self):
self.is_debugging = False
self.simulation_parameters = None
self.sim = None
self.simulation_result = None
self.expected_result_filename = f"DEBUG_{self.id()}.json"
if os.path.isfile(self.expected_result_filename):
os.unlink(self.expected_result_filename)
pass
def tearDown(self):
if not self.is_debugging:
if os.path.isfile(self.expected_result_filename):
os.unlink(self.expected_result_filename)
pass
# region configuration methods
def set_simulation_parameters(self, params_dict=None):
"""
Overrides all of the default sim parameters
with the ones in the dictionary
Args:
params_dict: keys are param names, values are expected values to use
Returns:
None, sets self.simulation_params
"""
if not self.simulation_parameters:
self.simulation_parameters = parameters.make_pars()
if params_dict:
self.simulation_parameters.update(params_dict)
pass
def run_sim(self, params_dict=None, write_results_json=True):
if not self.simulation_parameters or params_dict: # If we need one, or have one here
self.set_simulation_parameters(params_dict=params_dict)
pass
self.sim = Sim(pars=self.simulation_parameters, datafile=None)
self.sim.run(verbose=0)
self.simulation_result = self.sim.to_json(tostring=False)
if write_results_json:
with open(self.expected_result_filename, 'w') as outfile:
json.dump(self.simulation_result,
outfile,
indent=4,
sort_keys=True)
pass
# endregion
# region simulation results support
def get_full_result_channel(self, channel):
result_data = self.simulation_result["results"][channel]
return result_data
def get_day_zero_channel_value(
self,
channel=TestProperties.ResultsDataKeys.susceptible_at_timestep):
"""
Args:
channel: timeseries channel to report ('n_susceptible')
Returns: day zero value for channel
"""
result_data = self.get_full_result_channel(channel=channel)
return result_data[0]
def get_day_final_channel_value(self, channel):
channel = self.get_full_result_channel(channel=channel)
return channel[-1]
# endregion
# region specialized simulation methods
def set_microsim(self):
Simkeys = TestProperties.ParameterKeys.SimulationKeys
Transkeys = TestProperties.ParameterKeys.TransmissionKeys
Micro = TestProperties.SpecializedSimulations.Microsim
microsim_parameters = {
Simkeys.number_agents: Micro.n,
Simkeys.initial_infected_count: Micro.n_infected,
Simkeys.number_simulated_days: Micro.n_days,
Transkeys.contacts_per_agent: Micro.contacts
}
self.set_simulation_parameters(microsim_parameters)
pass
def set_smallpop_hightransmission(self):
"""
Creates a small population with lots of transmission
"""
Simkeys = TestProperties.ParameterKeys.SimulationKeys
Transkeys = TestProperties.ParameterKeys.TransmissionKeys
Progkeys = TestProperties.ParameterKeys.ProgressionKeys
Hightrans = TestProperties.SpecializedSimulations.Hightransmission
hightrans_parameters = {
Simkeys.number_agents: Hightrans.n,
Simkeys.initial_infected_count: Hightrans.n_infected,
Simkeys.number_simulated_days: Hightrans.n_days,
Transkeys.contacts_per_agent: Hightrans.contacts,
Transkeys.beta: Hightrans.beta,
Progkeys.exposed_to_infectious: Hightrans.serial,
Progkeys.exposed_to_infectious_std: Hightrans.serial_std,
Progkeys.infectiousness_duration: Hightrans.dur
}
self.set_simulation_parameters(hightrans_parameters)
pass
def set_superhigh_mortality(self):
"""
builds on high transmission with high mortality
"""
Simkeys = TestProperties.ParameterKeys.SimulationKeys
MortKeys = TestProperties.ParameterKeys.MortalityKeys
MortalityTestKeys = TestProperties.SpecializedSimulations.HighMortality
self.set_smallpop_hightransmission()
more_people_high_mortality = {
Simkeys.number_agents: MortalityTestKeys.n,
MortKeys.use_cfr_by_age: MortalityTestKeys.cfr_by_age,
MortKeys.default_cfr: MortalityTestKeys.default_cfr,
MortKeys.time_to_death: MortalityTestKeys.timetodie,
MortKeys.time_to_death_std: MortalityTestKeys.timetodie_std
}
self.set_simulation_parameters(params_dict=more_people_high_mortality)
pass
# endregion
pass
class CovaSimTest(unittest.TestCase):
def setUp(self):
self.is_debugging = False
self.simulation_parameters = None
self.sim = None
self.simulation_result = None
self.expected_result_filename = f"DEBUG_{self.id()}.json"
if os.path.isfile(self.expected_result_filename):
os.unlink(self.expected_result_filename)
pass
def tearDown(self):
if not self.is_debugging:
if os.path.isfile(self.expected_result_filename):
os.unlink(self.expected_result_filename)
pass
# region configuration methods
def set_simulation_parameters(self, params_dict=None):
"""
Overrides all of the default sim parameters
with the ones in the dictionary
Args:
params_dict: keys are param names, values are expected values to use
Returns:
None, sets self.simulation_params
"""
if not self.simulation_parameters:
self.simulation_parameters = parameters.make_pars()
if params_dict:
self.simulation_parameters.update(params_dict)
pass
def run_sim(self, params_dict=None, write_results_json=True):
if not self.simulation_parameters or params_dict: # If we need one, or have one here
self.set_simulation_parameters(params_dict=params_dict)
pass
self.sim = Sim(pars=self.simulation_parameters,
datafile=None)
self.sim.run(verbose=0)
self.simulation_result = self.sim.to_json(tostring=False)
if write_results_json:
with open(self.expected_result_filename, 'w') as outfile:
json.dump(self.simulation_result, outfile, indent=4, sort_keys=True)
pass
# endregion
# region simulation results support
def get_full_result_channel(self, channel):
result_data = self.simulation_result["results"][channel]
return result_data
def get_day_zero_channel_value(self, channel=TestProperties.ResultsDataKeys.susceptible_at_timestep):
"""
Args:
channel: timeseries channel to report ('n_susceptible')
Returns: day zero value for channel
"""
result_data = self.get_full_result_channel(channel=channel)
return result_data[0]
def get_day_final_channel_value(self, channel):
channel = self.get_full_result_channel(channel=channel)
return channel[-1]
# endregion
# region specialized simulation methods
def set_microsim(self):
Simkeys = TestProperties.ParameterKeys.SimulationKeys
Transkeys = TestProperties.ParameterKeys.TransmissionKeys
Micro = TestProperties.SpecializedSimulations.Microsim
microsim_parameters = {
Simkeys.number_agents : Micro.n,
Simkeys.initial_infected_count: Micro.n_infected,
Simkeys.number_simulated_days: Micro.n_days,
Transkeys.contacts_per_agent: Micro.contacts
}
self.set_simulation_parameters(microsim_parameters)
pass
def set_everyone_infected(self, agent_count=1000):
Simkeys = TestProperties.ParameterKeys.SimulationKeys
everyone_infected = {
Simkeys.number_agents: agent_count,
Simkeys.initial_infected_count: agent_count
}
self.set_simulation_parameters(params_dict=everyone_infected)
pass
def set_everyone_infectious_same_day(self, num_agents, days_to_infectious=1, num_days=60):
"""
Args:
num_agents: number of agents to create and infect
days_to_infectious: days until all agents are infectious (1)
num_days: days to simulate (60)
"""
self.set_everyone_infected(agent_count=num_agents)
test_config = {
TestProperties.ParameterKeys.SimulationKeys.number_simulated_days: num_days,
TestProperties.ParameterKeys.ProgressionKeys.exposed_to_infectious: days_to_infectious,
TestProperties.ParameterKeys.ProgressionKeys.exposed_to_infectious_std: 0,
TestProperties.ParameterKeys.MortalityKeys.use_cfr_by_age: False,
TestProperties.ParameterKeys.MortalityKeys.prob_infected_symptomatic: 0
}
self.set_simulation_parameters(params_dict=test_config)
pass
def set_everyone_symptomatic(self, num_agents):
"""
Cause all agents in the simulation to begin infected
And proceed to symptomatic (but not severe or death)
Args:
num_agents: Number of agents to begin with
"""
self.set_everyone_infectious_same_day(num_agents=num_agents,
days_to_infectious=0)
everyone_symptomatic_config = {
TestProperties.ParameterKeys.MortalityKeys.prob_infected_symptomatic: 1.0,
TestProperties.ParameterKeys.MortalityKeys.prob_symptomatic_severe: 0
}
self.set_simulation_parameters(params_dict=everyone_symptomatic_config)
pass
def set_everyone_is_going_to_die(self, num_agents):
"""
Cause all agents in the simulation to begin infected and die.
Args:
num_agents: Number of agents to simulate
"""
self.set_everyone_infectious_same_day(num_agents=num_agents)
everyone_dying_config = {
TestProperties.ParameterKeys.MortalityKeys.use_cfr_by_age: False,
TestProperties.ParameterKeys.MortalityKeys.prob_infected_symptomatic: 1, # Uh oh
TestProperties.ParameterKeys.MortalityKeys.prob_symptomatic_severe: 1, # Oh no
TestProperties.ParameterKeys.MortalityKeys.prob_severe_death: 1, # No recoveries
}
self.set_simulation_parameters(params_dict=everyone_dying_config)
pass
def set_smallpop_hightransmission(self):
"""
Creates a small population with lots of transmission
"""
Simkeys = TestProperties.ParameterKeys.SimulationKeys
Transkeys = TestProperties.ParameterKeys.TransmissionKeys
Progkeys = TestProperties.ParameterKeys.ProgressionKeys
Hightrans = TestProperties.SpecializedSimulations.Hightransmission
hightrans_parameters = {
Simkeys.number_agents : Hightrans.n,
Simkeys.initial_infected_count: Hightrans.n_infected,
Simkeys.number_simulated_days: Hightrans.n_days,
Transkeys.contacts_per_agent: Hightrans.contacts,
Transkeys.beta : Hightrans.beta,
Progkeys.exposed_to_infectious: Hightrans.serial,
Progkeys.exposed_to_infectious_std: Hightrans.serial_std,
Progkeys.infectiousness_duration: Hightrans.dur
}
self.set_simulation_parameters(hightrans_parameters)
pass
# endregion
pass
