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fix to model_start_end and reproduction number methods

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lrdossan 2024-12-19 16:46:19 +00:00
parent cd3df90c4c
commit d46b5846a1
2 changed files with 9 additions and 38 deletions
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22
caimira/src/caimira/calculator/models/models.py
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@ -1944,24 +1944,6 @@ class ExposureModelGroup:
def reproduction_number(self) -> _VectorisedFloat:
"""
Reproduction number considering the contribution
of each individual probability of infection and
a single infected occupant.
Expected number of cases when there is only one infected case.
"""
single_exposure_models = []
for model in self.exposure_models:
if model.concentration_model.infected.number != 1:
model = nested_replace(
self, {
'model.concentration_model.infected.number': 1
}
)
single_exposure_models.append(model)
single_exposure_model_group = nested_replace(
self, {
'exposure_models': single_exposure_models,
}
)
return single_exposure_model_group.expected_new_cases()
return np.sum([model.reproduction_number() for model in self.exposure_models], axis=0) # type: ignore

25
caimira/src/caimira/calculator/report/virus_report_data.py
View file

@ -11,22 +11,7 @@ from caimira.calculator.models.enums import ViralLoads
from caimira.calculator.validators.virus.virus_validator import VirusFormData
def model_start_end(model: models.ExposureModel):
"""
Calculates the start and end times for a single ExposureModel.
Determines the boundary times of an ExposureModel by comparing
the presence intervals of both the exposed and the infected people.
"""
t_start = min(model.exposed.presence_interval().boundaries()[0][0],
model.concentration_model.infected.presence_interval().boundaries()[0][0])
t_end = max(model.exposed.presence_interval().boundaries()[-1][1],
model.concentration_model.infected.presence_interval().boundaries()[-1][1])
return t_start, t_end
def model_boundary_times(model: typing.Union[models.ExposureModelGroup, models.ExposureModel]):
def model_start_end(model: typing.Union[models.ExposureModelGroup, models.ExposureModel]):
"""
Calculates the boundary times for an ExposureModel or ExposureModelGroup.
@ -40,7 +25,11 @@ def model_boundary_times(model: typing.Union[models.ExposureModelGroup, models.E
t_end = max((model_start_end(nth_model)[1] for nth_model in model.exposure_models))
return t_start, t_end
else:
return model_start_end(model)
t_start = min(model.exposed.presence_interval().boundaries()[0][0],
model.concentration_model.infected.presence_interval().boundaries()[0][0])
t_end = max(model.exposed.presence_interval().boundaries()[-1][1],
model.concentration_model.infected.presence_interval().boundaries()[-1][1])
return t_start, t_end
def fill_big_gaps(array, gap_size):
@ -84,7 +73,7 @@ def non_temp_transition_times(model: typing.Union[models.ExposureModelGroup, mod
else:
yield name, obj
t_start, t_end = model_boundary_times(model)
t_start, t_end = model_start_end(model)
change_times = {t_start, t_end}
for _, obj in walk_model(model, name="exposure"):