455 lines
14 KiB
Python
455 lines
14 KiB
Python
from caimira.enums import ViralLoads, InfectiousDoses, ViableToRNARatios
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class DataRegistry:
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"""Registry to hold data values."""
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version = None
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BLOmodel = {
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"cn": {
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"B": 0.06,
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"L": 0.2,
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"O": 0.0010008,
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},
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"mu": {
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"B": 0.989541,
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"L": 1.38629,
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"O": 4.97673,
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},
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"sigma": {
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"B": 0.262364,
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"L": 0.506818,
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"O": 0.585005,
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},
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}
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activity_distributions = {
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"Seated": {
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"inhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": -0.6872121723362303,
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"lognormal_standard_deviation_gaussian": 0.10498338229297108,
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},
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},
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"exhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": -0.6872121723362303,
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"lognormal_standard_deviation_gaussian": 0.10498338229297108,
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},
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},
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},
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"Standing": {
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"inhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": -0.5742377578494785,
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"lognormal_standard_deviation_gaussian": 0.09373162411398223,
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},
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},
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"exhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": -0.5742377578494785,
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"lognormal_standard_deviation_gaussian": 0.09373162411398223,
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},
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},
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},
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"Light activity": {
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"inhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": 0.21380242785625422,
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"lognormal_standard_deviation_gaussian": 0.09435378091059601,
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},
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},
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"exhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": 0.21380242785625422,
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"lognormal_standard_deviation_gaussian": 0.09435378091059601,
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},
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},
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},
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"Moderate activity": {
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"inhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": 0.551771330362601,
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"lognormal_standard_deviation_gaussian": 0.1894616357138137,
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},
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},
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"exhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": 0.551771330362601,
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"lognormal_standard_deviation_gaussian": 0.1894616357138137,
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},
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},
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},
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"Heavy exercise": {
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"inhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": 1.1644665696723049,
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"lognormal_standard_deviation_gaussian": 0.21744554768657565,
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},
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},
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"exhalation_rate": {
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"associated_distribution": "Log-normal",
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"parameters": {
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"lognormal_mean_gaussian": 1.1644665696723049,
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"lognormal_standard_deviation_gaussian": 0.21744554768657565,
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},
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},
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},
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}
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symptomatic_vl_frequencies = {
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"log_variable": [
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2.46032,
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2.67431,
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2.85434,
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3.06155,
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3.25856,
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3.47256,
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3.66957,
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3.85979,
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4.09927,
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4.27081,
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4.47631,
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4.66653,
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4.87204,
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5.10302,
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5.27456,
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5.46478,
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5.6533,
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5.88428,
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6.07281,
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6.30549,
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6.48552,
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6.64856,
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6.85407,
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7.10373,
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7.30075,
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7.47229,
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7.66081,
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7.85782,
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8.05653,
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8.27053,
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8.48453,
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8.65607,
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8.90573,
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9.06878,
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9.27429,
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9.473,
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9.66152,
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9.87552,
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],
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"frequencies": [
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0.001206885,
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0.007851618,
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0.008078144,
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0.01502491,
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0.013258014,
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0.018528495,
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0.020053765,
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0.021896167,
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0.022047184,
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0.018604005,
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0.01547796,
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0.018075445,
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0.021503523,
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0.022349217,
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0.025097721,
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0.032875078,
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0.030594727,
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0.032573045,
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0.034717482,
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0.034792991,
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0.033267721,
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0.042887485,
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0.036846816,
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0.03876473,
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0.045016819,
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0.040063473,
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0.04883754,
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0.043944602,
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0.048142864,
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0.041588741,
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0.048762031,
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0.027921732,
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0.033871788,
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0.022122693,
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0.016927718,
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0.008833228,
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0.00478598,
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0.002807662,
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],
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"kernel_bandwidth": 0.1,
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}
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covid_overal_vl_data = {
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"shape_factor": 3.47,
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"scale_factor": 7.01,
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"start": 0.01,
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"stop": 0.99,
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"num": 30.0,
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"min_bound": 2,
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"max_bound": 10,
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"interpolation_fp_left": 0,
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"interpolation_fp_right": 0,
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"max_function": 0.2,
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}
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viable_to_RNA_ratio_distribution = {
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"low": 0.01,
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"high": 0.6,
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}
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infectious_dose_distribution = {
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"low": 10,
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"high": 100,
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}
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virus_distributions = {
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"SARS_CoV_2": {
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"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
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"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
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"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
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"transmissibility_factor": 1,
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"infectiousness_days": 14,
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},
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"SARS_CoV_2_ALPHA": {
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"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
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"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
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"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
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"transmissibility_factor": 0.78,
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"infectiousness_days": 14,
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},
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"SARS_CoV_2_BETA": {
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"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
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"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
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"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
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"transmissibility_factor": 0.8,
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"infectiousness_days": 14,
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},
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"SARS_CoV_2_GAMMA": {
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"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
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"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
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"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
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"transmissibility_factor": 0.72,
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"infectiousness_days": 14,
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},
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"SARS_CoV_2_DELTA": {
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"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
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"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
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"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
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"transmissibility_factor": 0.51,
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"infectiousness_days": 14,
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},
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"SARS_CoV_2_OMICRON": {
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"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
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"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
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"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
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"transmissibility_factor": 0.2,
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"infectiousness_days": 14,
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},
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"SARS_CoV_2_Other": {
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"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
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"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
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"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
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"transmissibility_factor": 0.1,
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"infectiousness_days": 14,
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},
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}
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mask_distributions = {
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"Type I": {
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"η_inhale": {
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"associated_distribution": "Uniform",
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"parameters": {
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"low": 0.25,
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"high": 0.80,
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},
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},
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"Known filtration efficiency of masks when exhaling?": "No",
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"factor_exhale": 1,
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},
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"FFP2": {
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"η_inhale": {
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"associated_distribution": "Uniform",
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"parameters": {
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"low": 0.83,
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"high": 0.91,
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},
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},
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"Known filtration efficiency of masks when exhaling?": "No",
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"factor_exhale": 1,
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},
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"Cloth": {
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"η_inhale": {
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"associated_distribution": "Uniform",
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"parameters": {
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"low": 0.05,
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"high": 0.40,
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},
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},
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"Known filtration efficiency of masks when exhaling?": "Yes",
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"η_exhale": {
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"associated_distribution": "Uniform",
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"parameters": {
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"low": 0.20,
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"high": 0.50,
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},
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},
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"factor_exhale": 1,
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},
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}
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expiration_BLO_factors = {
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"Breathing": {
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"B": 1.0,
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"L": 0.0,
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"O": 0.0,
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},
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"Speaking": {
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"B": 1.0,
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"L": 1.0,
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"O": 1.0,
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},
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"Singing": {
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"B": 1.0,
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"L": 5.0,
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"O": 5.0,
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},
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"Shouting": {
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"B": 1.0,
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"L": 5.0,
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"O": 5.0,
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},
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}
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long_range_expiration_distributions = {
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"minimum_diameter": 0.1,
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"maximum_diameter": 30,
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}
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short_range_expiration_distributions = {
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"minimum_diameter": 0.1,
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"maximum_diameter": 100,
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}
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short_range_distances = {
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"minimum_distance": 0.5,
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"maximum_distance": 2.0,
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}
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####################################
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room = {
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"defaults": {
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"inside_temp": 293,
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"humidity_with_heating": 0.3,
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"humidity_without_heating": 0.5,
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},
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}
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ventilation = {
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"natural": {
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"discharge_factor": {
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"sliding": 0.6,
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},
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},
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"infiltration_ventilation": 0.25,
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}
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particle = {
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"evaporation_factor": 0.3,
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}
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population_with_virus = {
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"fraction_of_infectious_virus": 1,
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}
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concentration_model = {
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"min_background_concentration": 0.0,
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"CO2_concentration_model": {
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"CO2_atmosphere_concentration": 440.44,
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"CO2_fraction_exhaled": 0.042,
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},
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}
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short_range_model = {
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"dilution_factor": {
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"mouth_diameter": 0.02,
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"exhalation_coefficient": 2,
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"tstar": 2,
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"penetration_coefficients": {
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"𝛽r1": 0.18,
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"𝛽r2": 0.2,
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"𝛽x1": 2.4,
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},
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},
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}
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exposure_model = {
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"repeats": 1,
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}
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conditional_prob_inf_given_viral_load = {
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"lower_percentile": 0.05,
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"upper_percentile": 0.95,
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"min_vl": 2,
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"max_vl": 10,
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}
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monte_carlo_sample_size = 250000
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population_scenario_activity = {
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"office": {"activity": "Seated", "expiration": {"Speaking": 1, "Breathing": 2}},
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"smallmeeting": {
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"activity": "Seated",
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"expiration": {"Speaking": 1},
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},
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"largemeeting": {
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"activity": "Standing",
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"expiration": {"Speaking": 1, "Breathing": 2},
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},
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"callcenter": {"activity": "Seated", "expiration": {"Speaking": 1}},
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"controlroom-day": {
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"activity": "Seated",
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"expiration": {"Speaking": 1, "Breathing": 1},
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},
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"controlroom-night": {
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"activity": "Seated",
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"expiration": {"Speaking": 1, "Breathing": 9},
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},
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"library": {"activity": "Seated", "expiration": {"Breathing": 1}},
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"lab": {
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"activity": "Light activity",
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"expiration": {"Speaking": 1, "Breathing": 1},
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},
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"workshop": {
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"activity": "Moderate activity",
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"expiration": {"Speaking": 1, "Breathing": 1},
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},
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"training": {"activity": "Standing", "expiration": {"Speaking": 1}},
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"training_attendee": {"activity": "Seated", "expiration": {"Breathing": 1}},
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"gym": {"activity": "Heavy exercise", "expiration": {"Breathing": 1}},
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"household-day": {
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"activity": "Light activity",
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"expiration": {"Breathing": 5, "Speaking": 5},
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},
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"household-night": {
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"activity": "Seated",
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"expiration": {"Breathing": 7, "Speaking": 3},
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},
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"primary-school": {
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"activity": "Light activity",
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"expiration": {"Breathing": 5, "Speaking": 5},
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},
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"secondary-school": {
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"activity": "Light activity",
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"expiration": {"Breathing": 7, "Speaking": 3},
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},
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"university": {
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"activity": "Seated",
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"expiration": {"Breathing": 9, "Speaking": 1},
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},
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"restaurant": {
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"activity": "Seated",
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"expiration": {"Breathing": 1, "Speaking": 9},
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},
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"precise": {"activity": "", "expiration": {}},
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}
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def update(self, data, version=None):
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"""Update local cache with data provided as argument."""
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for attr_name, value in data.items():
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setattr(self, attr_name, value)
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if version:
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self.version = version
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