diff --git a/caimira/tests/test_full_algorithm.py b/caimira/tests/test_full_algorithm.py index 77aa3646..0ce0fa0d 100644 --- a/caimira/tests/test_full_algorithm.py +++ b/caimira/tests/test_full_algorithm.py @@ -15,6 +15,8 @@ from caimira.models import _VectorisedFloat,Interval,SpecificInterval from caimira.monte_carlo.data import (expiration_distributions, expiration_BLO_factors,short_range_expiration_distributions, short_range_distances,virus_distributions,activity_distributions) +import caimira.dataclass_utils as dc_utils + SAMPLE_SIZE = 1_000_000 TOLERANCE = 0.04 @@ -849,3 +851,119 @@ def test_exposure_with_shortrange_and_distributions(expo_sr_model_distr, rtol=0.03 ) + +def exposure_model_from_parameter(data_registry, short_range_models, f_inf=0.5, viral_load=1e9, BR=1.25): + virus: models.SARSCoV2 = models.SARSCoV2( + viral_load_in_sputum=viral_load, + infectious_dose=50, + viable_to_RNA_ratio=f_inf, + transmissibility_factor=0.51, + ) + c_model = mc.ConcentrationModel( + data_registry=data_registry, + room=models.Room(volume=50, humidity=0.3), + ventilation=models.AirChange(active=models.PeriodicInterval(period=120, duration=120), + air_exch=10_000_000), + infected=mc.InfectedPopulation( + data_registry=data_registry, + number=1, + presence=models.SpecificInterval(present_times=((8.5, 12.5), (13.5, 17.5))), + virus=virus, + mask=models.Mask.types['No mask'], + activity=models.Activity.types['Seated'], + expiration=expiration_distributions(data_registry)['Breathing'], + host_immunity=0., + ), + evaporation_factor=0.3, + ) + return mc.ExposureModel( + data_registry=data_registry, + concentration_model=c_model, + short_range=short_range_models, + exposed=mc.Population( + number=1, + presence=models.SpecificInterval(present_times=((8.5, 12.5), (13.5, 17.5))), + mask=models.Mask.types['No mask'], + activity=models.Activity(inhalation_rate=BR, exhalation_rate=1.25), + host_immunity=0., + ), + geographical_data=models.Cases(), + ).build_model(SAMPLE_SIZE) + + +@retry(tries=10) +def test_exposure_scale_with_f_inf(data_registry, sr_models): + """ + Exposure scaling test for the fraction of infectious virus. + """ + e_model_1: models.ExposureModel = exposure_model_from_parameter(data_registry=data_registry, short_range_models=sr_models, f_inf=0.5) + e_model_2: models.ExposureModel = exposure_model_from_parameter(data_registry=data_registry, short_range_models=sr_models, f_inf=1) + np.testing.assert_allclose( + 2*e_model_1.deposited_exposure().mean(), + e_model_2.deposited_exposure().mean(), rtol=0.02 + ) + + +@retry(tries=10) +def test_exposure_scale_with_viral_load(data_registry, sr_models): + """ + Exposure scaling test for the viral load. + """ + e_model_1: models.ExposureModel = exposure_model_from_parameter(data_registry=data_registry, short_range_models=sr_models, viral_load=1e9) + e_model_2: models.ExposureModel = exposure_model_from_parameter(data_registry=data_registry, short_range_models=sr_models, viral_load=2e9) + np.testing.assert_allclose( + 2*e_model_1.deposited_exposure().mean(), + e_model_2.deposited_exposure().mean(), rtol=0.02 + ) + + +@retry(tries=10) +def test_lr_exposure_scale_with_breathing_rate(data_registry): + """ + Exposure scaling test for the breathing rate when there are only long-range + interactions defined. Only the inhalation rate of the infected takes place + at the deposited exposure level. + """ + e_model_1: models.ExposureModel = exposure_model_from_parameter(data_registry=data_registry, short_range_models=(), BR=1.25) + e_model_2: models.ExposureModel = exposure_model_from_parameter(data_registry=data_registry, short_range_models=(), BR=2.5) + np.testing.assert_allclose( + 2*e_model_1.deposited_exposure().mean(), + e_model_2.deposited_exposure().mean(), rtol=0.02 + ) + + +@retry(tries=10) +def test_exposure_scale_with_breathing_rate(data_registry, sr_models): + """ + Exposure scaling test for the breathing rate when long- and short-range + interactions are defined. We need to apply the multiplication factor + to the inhalation rate of the infected (long-range), but also for + each short-range interaction + """ + e_model_1: models.ExposureModel = exposure_model_from_parameter(data_registry=data_registry, short_range_models=sr_models, BR=1.25) + + seated_act = models.Activity.types['Seated'] + heavy_exercise_act = models.Activity.types['Heavy exercise'] + sr_models_activity = ( + mc.ShortRangeModel( + data_registry = data_registry, + expiration = short_range_expiration_distributions(data_registry)['Speaking'], + activity = models.Activity(inhalation_rate=seated_act.inhalation_rate * 2, + exhalation_rate=seated_act.exhalation_rate), + presence = interaction_intervals[0], + distance = 0.854, + ), + mc.ShortRangeModel( + data_registry = data_registry, + expiration = short_range_expiration_distributions(data_registry)['Breathing'], + activity = models.Activity(inhalation_rate=heavy_exercise_act.inhalation_rate * 2, + exhalation_rate=heavy_exercise_act.inhalation_rate), + presence = interaction_intervals[1], + distance = 0.854, + ), + ) + e_model_2: models.ExposureModel = exposure_model_from_parameter(data_registry=data_registry, short_range_models=sr_models_activity, BR=2.5) + np.testing.assert_allclose( + 2*e_model_1.deposited_exposure().mean(), + e_model_2.deposited_exposure().mean(), rtol=0.02 + )