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Adding data.py with pre-defined distributions for breathing rates and viral loads

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Nicolas Mounet 2021-06-03 10:35:17 +02:00
parent cc628cd1e6
commit d246530704
1 changed files with 56 additions and 0 deletions
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cara/monte_carlo/data.py Normal file
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import numpy as np
import cara.monte_carlo as mc
from cara.monte_carlo.sampleable import Normal,LogNormal,LogCustomKernel
# From CERN-OPEN-2021-04 and refererences therein
activity_distributions = {
'Seated': mc.Activity(LogNormal(-0.6872121723362303, 0.10498338229297108),
LogNormal(-0.6872121723362303, 0.10498338229297108)),
'Standing': mc.Activity(LogNormal(-0.5742377578494785, 0.09373162411398223),
LogNormal(-0.5742377578494785, 0.09373162411398223)),
'Light activity': mc.Activity(LogNormal(0.21380242785625422,0.09435378091059601),
LogNormal(0.21380242785625422,0.09435378091059601)),
'Moderate activity': mc.Activity(LogNormal(0.551771330362601, 0.1894616357138137),
LogNormal(0.551771330362601, 0.1894616357138137)),
'Heavy exercise': mc.Activity(LogNormal(1.1644665696723049, 0.21744554768657565),
LogNormal(1.1644665696723049, 0.21744554768657565)),
}
# From CERN-OPEN-2021-04 and refererences therein
log_symptomatic_vl_frequencies = LogCustomKernel(
np.array((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)),
np.array((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
)
# From CERN-OPEN-2021-04 and refererences therein
virus_distributions = {
'SARS_CoV_2': mc.SARSCoV2(
viral_load_in_sputum=log_symptomatic_vl_frequencies,
quantum_infectious_dose=100,
),
'SARS_CoV_2_B117': mc.SARSCoV2(
viral_load_in_sputum=log_symptomatic_vl_frequencies,
quantum_infectious_dose=60,
),
'SARS_CoV_2_P1': mc.SARSCoV2(
viral_load_in_sputum=log_symptomatic_vl_frequencies,
quantum_infectious_dose=100/2.25,
),
}