def test__symptoms_progression(self):
selector = infect.InfectionSelector.from_file(transmission_config_path=paths.configs_path / 'defaults/transmission/TransmissionConstant.yaml')
dummy = Person(sex='f', age=65)
infection = selector.make_infection(person=dummy, time=0.1)
fixed_severity = 0.97
infection.symptoms.max_severity = fixed_severity
max_tag = infection.symptoms.max_tag()
assert max_tag == june.infection.symptom_tag.SymptomTag.hospitalised
infection.symptoms.trajectory = selector.trajectory_maker[max_tag]
print(infection.symptoms.trajectory)
assert infection.symptoms.trajectory == [
(0.0, june.infection.symptom_tag.SymptomTag.exposed),
(pytest.approx(5, 2.5), june.infection.symptom_tag.SymptomTag.mild),
(pytest.approx(5, rel=5), june.infection.symptom_tag.SymptomTag.hospitalised),
(pytest.approx(13, rel=5), june.infection.symptom_tag.SymptomTag.mild),
(pytest.approx(30, rel=5), june.infection.symptom_tag.SymptomTag.recovered),
]
hospitalised_time = infection.symptoms.trajectory[2][0]
infection.update_at_time(float(1.))
assert infection.symptoms.tag == june.infection.symptom_tag.SymptomTag.exposed
infection.update_at_time(float(1.))
assert infection.symptoms.tag == june.infection.symptom_tag.SymptomTag.exposed
infection.update_at_time(float(6.))
assert infection.symptoms.tag == june.infection.symptom_tag.SymptomTag.mild
infection.update_at_time(hospitalised_time + 8.)
assert infection.symptoms.tag == june.infection.symptom_tag.SymptomTag.hospitalised
infection.update_at_time(float(40.))
assert infection.symptoms.tag == june.infection.symptom_tag.SymptomTag.mild
infection.update_at_time(float(50.))
assert infection.symptoms.tag == june.infection.symptom_tag.SymptomTag.recovered
def missing_workforce_nr(self):
"""
Estimate missing workforce in simulated region.
This will establish the number of workers recruited
from the boundary.
"""
self.ADULT_THRESHOLD = self.world.config["people"]["adult_threshold"]
self.OLD_THRESHOLD = self.world.config["people"]["old_threshold"]
self._init_frequencies()
for company in self.world.companies.members:
# nr. of missing workforce
# TODO companies shouldn always be completely full
n_residents = (company.n_employees_max - company.n_employees)
(sex_rnd_arr, nomis_bin_rnd_arr,
age_rnd_arr) = self.init_random_variables(n_residents,
company.industry)
for i in range(n_residents):
# create new person
person = Person(
self.world,
(i + self.n_residents),
'boundary',
company.msoa,
age_rnd_arr[i],
nomis_bin_rnd_arr[i],
sex_rnd_arr[i],
econ_index=0,
mode_of_transport=None,
)
person.industry = company.industry
# Inform groups about new person
self.people.append(person)
self.world.people.members.append(person)
company.people.append(person)
idx = [
idx for idx, msoa in enumerate(self.world.msoareas.members)
if msoa.name == company.msoa
][0]
self.world.msoareas.members[idx].work_people.append(person)
self.n_residents += n_residents
def test_group_types(self):
group = Household()
group.add(Person(), Household.SubgroupType.adults)
assert group[Household.SubgroupType.adults].size == 1