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Fit ventilation and exhalation rates on CO2 sensor data
Default form values:
NO_DEFAULT = object()
DEFAULT_MC_SAMPLE_SIZE = config.monte_carlo_sample_size
DEFAULTS = {
'activity_type': 'office',
'air_changes': 0.,
'air_supply': 0.,
'arve_sensors_option': False,
'specific_breaks': '{}',
'precise_activity': '{}',
'calculator_version': NO_DEFAULT,
'ceiling_height': 0.,
'conditional_probability_plot': False,
'conditional_probability_viral_loads': False,
'CO2_fitting_result': '{}',
'exposed_coffee_break_option': 'coffee_break_0',
'exposed_coffee_duration': 5,
'exposed_finish': '17:30',
'exposed_lunch_finish': '13:30',
'exposed_lunch_option': True,
'exposed_lunch_start': '12:30',
'exposed_start': '08:30',
'event_month': 'January',
'floor_area': 0.,
'hepa_amount': 0.,
'hepa_option': False,
'humidity': '',
'infected_coffee_break_option': 'coffee_break_0',
'infected_coffee_duration': 5,
'infected_dont_have_breaks_with_exposed': False,
'infected_finish': '17:30',
'infected_lunch_finish': '13:30',
'infected_lunch_option': True,
'infected_lunch_start': '12:30',
'infected_people': 1,
'infected_start': '08:30',
'inside_temp': NO_DEFAULT,
'location_latitude': NO_DEFAULT,
'location_longitude': NO_DEFAULT,
'location_name': NO_DEFAULT,
'geographic_population': 0,
'geographic_cases': 0,
'ascertainment_bias': 'confidence_low',
'exposure_option': 'p_deterministic_exposure',
'mask_type': 'Type I',
'mask_wearing_option': 'mask_off',
'mechanical_ventilation_type': 'not-applicable',
'opening_distance': 0.,
'room_heating_option': False,
'room_number': NO_DEFAULT,
'room_volume': 0.,
'simulation_name': NO_DEFAULT,
'total_people': NO_DEFAULT,
'vaccine_option': False,
'vaccine_booster_option': False,
'vaccine_type': 'AZD1222_(AstraZeneca)',
'vaccine_booster_type': 'AZD1222_(AstraZeneca)',
'ventilation_type': 'no_ventilation',
'virus_type': 'SARS_CoV_2',
'volume_type': NO_DEFAULT,
'window_type': 'window_sliding',
'window_height': 0.,
'window_width': 0.,
'windows_duration': 10.,
'windows_frequency': 60.,
'windows_number': 0,
'window_opening_regime': 'windows_open_permanently',
'sensor_in_use': '',
'short_range_option': 'short_range_no',
'short_range_interactions': '[]',
}
ACTIVITIES: typing.Dict[str, typing.Dict] = config.population_scenario_activity
ACTIVITY_TYPES: typing.List[str] = list(ACTIVITIES.keys())
COFFEE_OPTIONS_INT = {'coffee_break_0': 0, 'coffee_break_1': 1,
'coffee_break_2': 2, 'coffee_break_4': 4}
CONFIDENCE_LEVEL_OPTIONS = {'confidence_low': 10,
'confidence_medium': 5, 'confidence_high': 2}
MECHANICAL_VENTILATION_TYPES = {
'mech_type_air_changes', 'mech_type_air_supply', 'not-applicable'}
MASK_TYPES: typing.List[str] = list(config.mask_distributions.keys())
MASK_WEARING_OPTIONS = {'mask_on', 'mask_off'}
MONTH_NAMES = [
'January', 'February', 'March', 'April', 'May', 'June', 'July',
'August', 'September', 'October', 'November', 'December',
]
VACCINE_BOOSTER_TYPE = ['AZD1222_(AstraZeneca)', 'Ad26.COV2.S_(Janssen)', 'BNT162b2_(Pfizer)', 'BNT162b2_(Pfizer)_(4th_dose)', 'BNT162b2_(Pfizer)_and_mRNA-1273_(Moderna)',
'BNT162b2_(Pfizer)_or_mRNA-1273_(Moderna)', 'BNT162b2_(Pfizer)_or_mRNA-1273_(Moderna)_(4th_dose)', 'CoronaVac_(Sinovac)', 'Coronavac_(Sinovac)', 'Sinopharm',
'mRNA-1273_(Moderna)', 'mRNA-1273_(Moderna)_(4th_dose)', 'Other']
VACCINE_TYPE = ['Ad26.COV2.S_(Janssen)', 'Any_mRNA_-_heterologous', 'AZD1222_(AstraZeneca)', 'AZD1222_(AstraZeneca)_and_any_mRNA_-_heterologous', 'AZD1222_(AstraZeneca)_and_BNT162b2_(Pfizer)',
'BBIBP-CorV_(Beijing_CNBG)', 'BNT162b2_(Pfizer)', 'BNT162b2_(Pfizer)_and_mRNA-1273_(Moderna)', 'CoronaVac_(Sinovac)', 'CoronaVac_(Sinovac)_and_AZD1222_(AstraZeneca)', 'Covishield',
'mRNA-1273_(Moderna)', 'Sputnik_V_(Gamaleya)', 'CoronaVac_(Sinovac)_and_BNT162b2_(Pfizer)']
VENTILATION_TYPES = {'natural_ventilation', 'mechanical_ventilation',
'no_ventilation', 'from_fitting'}
VIRUS_TYPES: typing.List[str] = list(config.virus_distributions)
VOLUME_TYPES = {'room_volume_explicit', 'room_volume_from_dimensions'}
WINDOWS_OPENING_REGIMES = {'windows_open_permanently',
'windows_open_periodically', 'not-applicable'}
WINDOWS_TYPES = {'window_sliding', 'window_hinged', 'not-applicable'}
Configuration:
BLOmodel = {
"cn": {
"B": 0.06,
"L": 0.2,
"O": 0.0010008,
},
"mu": {
"B": 0.989541,
"L": 1.38629,
"O": 4.97673,
},
"sigma": {
"B": 0.262364,
"L": 0.506818,
"O": 0.585005,
},
}
activity_distributions = {
"Seated": {
"inhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": -0.6872121723362303,
"standard_deviation_gaussian": 0.10498338229297108,
},
},
"exhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": -0.6872121723362303,
"standard_deviation_gaussian": 0.10498338229297108,
},
},
},
"Standing": {
"inhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": -0.5742377578494785,
"standard_deviation_gaussian": 0.09373162411398223,
},
},
"exhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": -0.5742377578494785,
"standard_deviation_gaussian": 0.09373162411398223,
},
},
},
"Light activity": {
"inhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": 0.21380242785625422,
"standard_deviation_gaussian": 0.09435378091059601,
},
},
"exhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": 0.21380242785625422,
"standard_deviation_gaussian": 0.09435378091059601,
},
},
},
"Moderate activity": {
"inhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": 0.551771330362601,
"standard_deviation_gaussian": 0.1894616357138137,
},
},
"exhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": 0.551771330362601,
"standard_deviation_gaussian": 0.1894616357138137,
},
},
},
"Heavy exercise": {
"inhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": 1.1644665696723049,
"standard_deviation_gaussian": 0.21744554768657565,
},
},
"exhalation_rate": {
"associated_distribution": "Numpy Log-normal Distribution (random.lognormal)",
"parameters": {
"mean_gaussian": 1.1644665696723049,
"standard_deviation_gaussian": 0.21744554768657565,
},
},
},
}
symptomatic_vl_frequencies = {
"log_variable": [
2.46032,
2.67431,
2.85434,
3.06155,
3.25856,
3.47256,
3.66957,
3.85979,
4.09927,
4.27081,
4.47631,
4.66653,
4.87204,
5.10302,
5.27456,
5.46478,
5.6533,
5.88428,
6.07281,
6.30549,
6.48552,
6.64856,
6.85407,
7.10373,
7.30075,
7.47229,
7.66081,
7.85782,
8.05653,
8.27053,
8.48453,
8.65607,
8.90573,
9.06878,
9.27429,
9.473,
9.66152,
9.87552,
],
"frequencies": [
0.001206885,
0.007851618,
0.008078144,
0.01502491,
0.013258014,
0.018528495,
0.020053765,
0.021896167,
0.022047184,
0.018604005,
0.01547796,
0.018075445,
0.021503523,
0.022349217,
0.025097721,
0.032875078,
0.030594727,
0.032573045,
0.034717482,
0.034792991,
0.033267721,
0.042887485,
0.036846816,
0.03876473,
0.045016819,
0.040063473,
0.04883754,
0.043944602,
0.048142864,
0.041588741,
0.048762031,
0.027921732,
0.033871788,
0.022122693,
0.016927718,
0.008833228,
0.00478598,
0.002807662,
],
"kernel_bandwidth": 0.1,
}
covid_overal_vl_data = {
"shape_factor": 3.47,
"scale_factor": 7.01,
"start": 0.01,
"stop": 0.99,
"num": 30.0,
"min_bound": 2,
"max_bound": 10,
"interpolation_fp_left": 0,
"interpolation_fp_right": 0,
"max_function": 0.2,
}
viable_to_RNA_ratio_distribution = {
"low": 0.01,
"high": 0.6,
}
infectious_dose_distribution = {
"low": 10,
"high": 100,
}
virus_distributions = {
"SARS_CoV_2": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"transmissibility_factor": 1,
"infectiousness_days": 14,
},
"SARS_CoV_2_ALPHA": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"transmissibility_factor": 0.78,
"infectiousness_days": 14,
},
"SARS_CoV_2_BETA": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"transmissibility_factor": 0.8,
"infectiousness_days": 14,
},
"SARS_CoV_2_GAMMA": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"transmissibility_factor": 0.72,
"infectiousness_days": 14,
},
"SARS_CoV_2_DELTA": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"transmissibility_factor": 0.51,
"infectiousness_days": 14,
},
"SARS_CoV_2_OMICRON": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"transmissibility_factor": 0.2,
"infectiousness_days": 14,
},
"SARS_CoV_2_Other": {
"viral_load_in_sputum": "Ref: Viral load - covid_overal_vl_data",
"infectious_dose": "Ref: Infectious dose - infectious_dose_distribution",
"viable_to_RNA_ratio": "Ref: Viable to RNA ratio - viable_to_RNA_ratio_distribution",
"transmissibility_factor": 0.1,
"infectiousness_days": 14,
},
}
mask_distributions = {
"Type I": {
"η_inhale": {
"associated_distribution": "Numpy Uniform Distribution (random.uniform)",
"parameters": {
"low": 0.25,
"high": 0.80,
},
},
"Known filtration efficiency of masks when exhaling?": "No",
"factor_exhale": 1,
},
"FFP2": {
"η_inhale": {
"associated_distribution": "Numpy Uniform Distribution (random.uniform)",
"parameters": {
"low": 0.83,
"high": 0.91,
},
},
"Known filtration efficiency of masks when exhaling?": "No",
"factor_exhale": 1,
},
"Cloth": {
"η_inhale": {
"associated_distribution": "Numpy Uniform Distribution (random.uniform)",
"parameters": {
"low": 0.05,
"high": 0.40,
},
},
"Known filtration efficiency of masks when exhaling?": "Yes",
"η_exhale": {
"associated_distribution": "Numpy Uniform Distribution (random.uniform)",
"parameters": {
"low": 0.20,
"high": 0.50,
},
},
"factor_exhale": 1,
},
}
expiration_BLO_factors = {
"Breathing": {
"B": 1.0,
"L": 0.0,
"O": 0.0,
},
"Speaking": {
"B": 1.0,
"L": 1.0,
"O": 1.0,
},
"Singing": {
"B": 1.0,
"L": 5.0,
"O": 5.0,
},
"Shouting": {
"B": 1.0,
"L": 5.0,
"O": 5.0,
},
}
long_range_expiration_distributions = {
"minimum_diameter": 0.1,
"maximum_diameter": 30,
}
short_range_expiration_distributions = {
"minimum_diameter": 0.1,
"maximum_diameter": 100,
}
short_range_distances = {
"minimum_distance": 0.5,
"maximum_distance": 2.0,
}
####################################
room = {
"defaults": {
"inside_temp": 293,
"humidity_with_heating": 0.3,
"humidity_without_heating": 0.5,
},
}
ventilation = {
"natural": {
"discharge_factor": {
"sliding": 0.6,
},
},
"infiltration_ventilation": 0.25,
}
particle = {
"evaporation_factor": 0.3,
}
population_with_virus = {
"fraction_of_infectious_virus": 1,
}
concentration_model = {
"min_background_concentration": 0.0,
"CO2_concentration_model": {
"CO2_atmosphere_concentration": 440.44,
"CO2_fraction_exhaled": 0.042,
},
}
short_range_model = {
"dilution_factor": {
"mouth_diameter": 0.02,
"exhalation_coefficient": 2,
"tstar": 2,
"penetration_coefficients": {
"𝛽r1": 0.18,
"𝛽r2": 0.2,
"𝛽x1": 2.4,
},
},
}
exposure_model = {
"repeats": 1,
}
conditional_prob_inf_given_viral_load = {
"lower_percentile": 0.05,
"upper_percentile": 0.95,
"min_vl": 2,
"max_vl": 10,
}
monte_carlo_sample_size = 250000
population_scenario_activity = {
"office": {"activity": "Seated", "expiration": {"Speaking": 1, "Breathing": 2}},
"smallmeeting": {
"activity": "Seated",
"expiration": {"Speaking": 1, "Breathing": None},
},
"largemeeting": {
"activity": "Standing",
"expiration": {"Speaking": 1, "Breathing": 2},
},
"callcenter": {"activity": "Seated", "expiration": {"Speaking": 1}},
"controlroom-day": {
"activity": "Seated",
"expiration": {"Speaking": 1, "Breathing": 1},
},
"controlroom-night": {
"activity": "Seated",
"expiration": {"Speaking": 1, "Breathing": 9},
},
"library": {"activity": "Seated", "expiration": {"Breathing": 1}},
"lab": {
"activity": "Light activity",
"expiration": {"Speaking": 1, "Breathing": 1},
},
"workshop": {
"activity": "Moderate activity",
"expiration": {"Speaking": 1, "Breathing": 1},
},
"training": {"activity": "Standing", "expiration": {"Speaking": 1}},
"training_attendee": {"activity": "Seated", "expiration": {"Breathing": 1}},
"gym": {"activity": "Heavy exercise", "expiration": {"Breathing": 1}},
"household-day": {
"activity": "Light activity",
"expiration": {"Breathing": 5, "Speaking": 5},
},
"household-night": {
"activity": "Seated",
"expiration": {"Breathing": 7, "Speaking": 3},
},
"primary-school": {
"activity": "Light activity",
"expiration": {"Breathing": 5, "Speaking": 5},
},
"secondary-school": {
"activity": "Light activity",
"expiration": {"Breathing": 7, "Speaking": 3},
},
"university": {
"activity": "Seated",
"expiration": {"Breathing": 9, "Speaking": 1},
},
"restaurant": {
"activity": "Seated",
"expiration": {"Breathing": 1, "Speaking": 9},
},
"precise": {"activity": "", "expiration": {}},
}
