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updated deposited_exposure method and infection probability tests

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This commit is contained in:
Luis Aleixo 2023-05-30 16:54:10 +02:00
parent e8cf3d160a
commit a16957d319
2 changed files with 30 additions and 23 deletions
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23
caimira/models.py
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@ -1638,17 +1638,7 @@ class ExposureModel:
return deposited_exposure
def deposited_exposure(self) -> _VectorisedFloat:
"""
The number of virus per m^3 deposited on the respiratory tract.
"""
deposited_exposure: _VectorisedFloat = 0.0
for start, stop in self.exposed.presence_interval().boundaries():
deposited_exposure += (self.deposited_exposure_between_bounds(start, stop))
return deposited_exposure * self.repeats
def deposited_exposure_list(self):
def _deposited_exposure_list(self):
"""
The number of virus per m^3 deposited on the respiratory tract.
"""
@ -1658,11 +1648,17 @@ class ExposureModel:
for start, stop in zip(population_change_times[:-1], population_change_times[1:]):
deposited_exposure.append(self.deposited_exposure_between_bounds(start, stop))
return deposited_exposure * self.repeats
return deposited_exposure
def deposited_exposure(self) -> _VectorisedFloat:
"""
The number of virus per m^3 deposited on the respiratory tract.
"""
return np.sum(self._deposited_exposure_list(), axis=0) * self.repeats
def infection_probability_list(self):
# Viral dose (vD)
vD_list = self.deposited_exposure_list()
vD_list = self._deposited_exposure_list()
# oneoverln2 multiplied by ID_50 corresponds to ID_63.
infectious_dose = oneoverln2 * self.concentration_model.virus.infectious_dose
@ -1709,7 +1705,6 @@ class ExposureModel:
total_probability_rule_list = []
population_change_times = self.population_state_change_times()
for start, stop in zip(population_change_times[:-1], population_change_times[1:]):
sum_probability = 0.0
exposed_present = self.exposed.people_present(stop)
infected_present = self.concentration_model.infected.people_present(stop)

30
caimira/tests/models/test_dynamic_population.py
View file

@ -149,7 +149,7 @@ def test_linearity_with_number_of_infected(full_exposure_model: models.ExposureM
@pytest.mark.parametrize(
"time", (8., 9., 10., 11., 12., 13., 14.),
)
def test_dynamic_dose(full_exposure_model, time):
def test_dynamic_dose(full_exposure_model: models.ExposureModel, time: float):
dynamic_infected: models.ExposureModel = dc_utils.nested_replace(
full_exposure_model,
@ -201,19 +201,31 @@ def test_dynamic_dose(full_exposure_model, time):
npt.assert_almost_equal(dynamic_exposure, np.sum(static_exposure))
def test_dynamic_total_probability_rule(
def test_infection_probability(
full_exposure_model: models.ExposureModel,
dynamic_infected_single_exposure_model: models.ExposureModel,
dynamic_exposed_single_exposure_model: models.ExposureModel,
dynamic_population_exposure_model: models.ExposureModel):
base_infection_probability = full_exposure_model.infection_probability()
npt.assert_almost_equal(base_infection_probability, dynamic_infected_single_exposure_model.infection_probability())
npt.assert_almost_equal(base_infection_probability, dynamic_exposed_single_exposure_model.infection_probability())
npt.assert_almost_equal(base_infection_probability, dynamic_population_exposure_model.infection_probability())
full_model_total_prob_rule = full_exposure_model.total_probability_rule()
npt.assert_almost_equal(full_model_total_prob_rule,
dynamic_population_exposure_model.dynamic_total_probability_rule())
# def test_dynamic_total_probability_rule(
# full_exposure_model: models.ExposureModel,
# dynamic_infected_single_exposure_model: models.ExposureModel,
# dynamic_exposed_single_exposure_model: models.ExposureModel,
# dynamic_population_exposure_model: models.ExposureModel):
# full_model_total_prob_rule = full_exposure_model.total_probability_rule()
# npt.assert_almost_equal(full_model_total_prob_rule,
# dynamic_population_exposure_model.dynamic_total_probability_rule())
npt.assert_almost_equal(full_model_total_prob_rule,
dynamic_infected_single_exposure_model.dynamic_total_probability_rule())
# npt.assert_almost_equal(full_model_total_prob_rule,
# dynamic_infected_single_exposure_model.dynamic_total_probability_rule())
npt.assert_almost_equal(full_model_total_prob_rule,
dynamic_exposed_single_exposure_model.dynamic_total_probability_rule())
# npt.assert_almost_equal(full_model_total_prob_rule,
# dynamic_exposed_single_exposure_model.dynamic_total_probability_rule())