def transmission_success(self, person, contact_strength):
days_infected = self.day - self.infection_start_date[person]
likelihood = self.serial_interval_distribution[days_infected]
if person in self.symptomatic_infecteds:
likelihood *= 1.6
else:
likelihood *= 0.8
return probtools.random_event(1 - (1 - likelihood)**contact_strength)
def event(self,etype,person,**kwargs):
if etype == 'quarantined':
self.quarantined[person] = True
self.quarantine_end_day[person] = self.quarantine_days + self.day
self.quarantine_start_day[person] = self.day
self.registrar.register_departure(person)
self._record_state_change(person,'quarantined')
return
elif etype == 'dequarantined':
del self.quarantined[person]
self.registrar.register_return(person)
self._record_state_change(person,'dequarantined')
return
elif etype == 'removed':
self.removed[person] = True
if person in self.symptomatic_infecteds:
del self.symptomatic_infecteds[person]
del self.infected[person]
del self.infection_start_date[person]
if 'artificial' not in kwargs:
self.average_transmissions *= self.completed_infections
self.completed_infections += 1
self.average_transmissions += self.infection_transmissions[person]
self.average_transmissions /= self.completed_infections
self._record_state_change(person,'removed')
return
elif etype == 'infected':
del self.susceptible[person]
self.infected[person] = True
self.infection_start_date[person] = self.day
self.infection_detectable_day[person] = self.day + self.days_indetectable
self.infection_transmissions[person] = 0
if probtools.random_event(self.symptomatic_fraction):
self.symptomatic_infecteds[person] = True
self.symptomatic_day[person] = self.day + self.incubation_picker.draw()
self.infection_end_day[person] = self.day + self.recovery_days
self._record_state_change(person,'infected')
return
elif etype == 'new person':
if person in self.registrar.student_data:
pstring = 'student ' + str(self.registrar.student_data[person]['cohort'])
else:
pstring = 'instructor'
self.susceptible[person] = True
self.person_state[person] = ('nonquarantined','susceptible',pstring)
self.all_individuals[person] = True
self._record_state_change(person,None)
if 'infected' in kwargs and kwargs['infected'] == True:
self.event('infected',person,infected_by=None,message='Initially Infected')
elif 'removed' in kwargs and kwargs['removed'] == True:
self.event('infected',person,infected_by=None,artificial=True,message='Infection-Pending Initial Removal')
self.event('removed',person,artificial=True,message='Initially Removed')
return
raise Exception('Unknown event',etype)
def execute_main_step(self):
self.day += 1
self.registrar.update_query_system()
self.tests_performed_today = 0
self.contact_traces_performed_today = 0
self.positive_tests_today = 0
if self.quarantining:
for person in self.all_individuals:
if probtools.random_event(self.daily_testing_fraction):
result = self.testing_queue.add(person,
abort_if=self.quarantined)
for person in self.testing_queue:
test_result = self.get_test_result(
person) # Need to change so that all tests are forced
if test_result > 0 and person not in self.quarantined:
self.event('quarantined',
person,
message='Quarantined on Positive Test Result')
if test_result > 0 and self.contact_tracing:
self.contact_tracing_queue.add(person)
for person in self.symptomatic_infecteds:
if self.day == self.symptomatic_day[person]:
if person not in self.quarantined:
self.event('quarantined',
person,
message='Quarantined on Reported Symptoms')
if self.contact_tracing:
self.contact_tracing_queue.add(person)
to_be_released = {}
for person in self.quarantined:
if self.day == self.quarantine_end_day[person]:
to_be_released[person] = True
for person in to_be_released:
self.event('dequarantined',
person,
message='Released from Quarantine today')
to_be_removed = {}
for person in self.infected:
if self.day == self.infection_end_day[person]:
to_be_removed[person] = True
for person in to_be_removed:
self.event('removed', person, message='Removed from infection')
if self.contact_tracing:
for person in self.contact_tracing_queue:
self.contact_traces_performed_today += 1
first_trace_day = self.day - self.contact_tracing_days
post_trace_day = self.day
if person in self.quarantined:
post_trace_day = min(post_trace_day,
self.quarantine_start_day[person] + 1)
for trace_day in range(first_trace_day, post_trace_day):
identified_contacts = self.registrar.query_contacts(
person, trace_day - self.day)
for found_individual in identified_contacts:
if found_individual in self.all_individuals and found_individual not in self.quarantined:
actions = probtools.random_threshold({
'test':
self.contact_tracing_testing_rate,
'quarantine':
self.contact_tracing_quarantine_rate
})
if 'test' in actions:
self.testing_queue.add(
found_individual,
abort_if=self.quarantined)
if 'quarantine' in actions and found_individual not in self.quarantined:
self.event(
'quarantined',
found_individual,
message='Quarantined on Contact Trace')
to_be_infected = {}
for person in self.infected:
if person not in self.quarantined:
contact_information = self.registrar.query_transmit(person)
for potential_infected in contact_information:
if potential_infected in self.susceptible and potential_infected not in self.quarantined and potential_infected not in to_be_infected and self.transmission_success(
person, contact_information[potential_infected]):
to_be_infected[potential_infected] = person
self.infection_transmissions[person] += 1
for person in to_be_infected:
self.event('infected',
person,
infected_by=to_be_infected[person],
message='Infection by transmission')
new_cases_to_create = self.daily_outside_cases
if type(new_cases_to_create) == list:
new_cases_to_create = probtools.list_select(new_cases_to_create)
for index in range(new_cases_to_create):
person = probtools.list_select(list(self.susceptible.keys()))
if person is not None and person not in self.quarantined:
self.event('infected',
person,
infected_by=None,
message='infected by outside source')
self.recorded_info[
'tests_performed_today'] = self.tests_performed_today
self.recorded_info[
'contact_traces_performed_today'] = self.contact_traces_performed_today
self.recorded_info['positive_tests_today'] = self.positive_tests_today
self.recorded_info['day'] = self.day
self.recorded_info['R'] = self.average_transmissions
for key, value in self.registrar.get_attendance().items():
self.recorded_info[key] = value