Added uniform distribution to the infectious_dose
This commit is contained in:
Luis Aleixo
parent
f50ce6d15b
commit
29f191dd2a
3 changed files with 26 additions and 21 deletions
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@ -1,5 +1,5 @@
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from cara import models
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from cara.monte_carlo.data import activity_distributions, symptomatic_vl_frequencies, infectious_virus_distribution
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from cara.monte_carlo.data import activity_distributions, symptomatic_vl_frequencies, infectious_virus_distribution, infectious_dose_distribution
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import cara.monte_carlo as mc
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import numpy as np
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@ -41,7 +41,7 @@ def breathing_exposure(activity: str, mask: str):
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -72,7 +72,7 @@ def speaking_exposure(activity: str, mask: str):
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -103,7 +103,7 @@ def shouting_exposure(activity: str, mask: str):
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -134,7 +134,7 @@ def breathing_exposure_vl(vl):
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number=1,
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virus=models.Virus(
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viral_load_in_sputum=10**vl,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -165,7 +165,7 @@ def talking_exposure_vl(vl):
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number=1,
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virus=models.Virus(
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viral_load_in_sputum=10**vl,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -196,7 +196,7 @@ def shouting_exposure_vl(vl):
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=10**vl,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -228,7 +228,7 @@ def breathing_seated_exposure():
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -258,7 +258,7 @@ def breathing_light_activity_exposure():
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -288,7 +288,7 @@ def breathing_heavy_exercise_exposure():
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -319,7 +319,7 @@ def speaking_seated_exposure():
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -349,7 +349,7 @@ def speaking_light_activity_exposure():
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -379,7 +379,7 @@ def speaking_heavy_exercise_exposure():
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -410,7 +410,7 @@ def shouting_seated_exposure():
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -440,7 +440,7 @@ def shouting_light_activity_exposure():
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -470,7 +470,7 @@ def shouting_heavy_exercise_exposure():
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number=1,
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virus=mc.Virus(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=50.,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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presence=mc.SpecificInterval(((0, 2),)),
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@ -915,7 +915,11 @@ class ExposureModel:
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repeats: int = 1
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#: The fraction of viruses actually deposited in the respiratory tract
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d = 1.37 # To be updated in the future.
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"""
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To be updated in the future.
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The diameter value of 1.37 is the correspondent to a fraction_deposited of 0.6
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"""
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d = 1.37
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IF = 1 - 0.5 * (1 - (1 / (1 + (0.00076*(d**2.8)))))
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DF = IF * (0.0587 + (0.911/(1 + np.exp(4.77 + 1.485 * np.log(d)))) + (0.943/(1 + np.exp(0.508 - 2.58 * np.log(d)))))
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fraction_deposited: _VectorisedFloat = DF
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@ -40,27 +40,28 @@ symptomatic_vl_frequencies = LogCustomKernel(
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# From https://doi.org/10.1093/cid/ciaa1579
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infectious_virus_distribution = Uniform(0.15, 0.45)
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infectious_dose_distribution = Uniform(10., 100.)
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# From CERN-OPEN-2021-04 and refererences therein
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virus_distributions = {
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'SARS_CoV_2': mc.SARSCoV2(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=100,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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'SARS_CoV_2_B117': mc.SARSCoV2(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=60,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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'SARS_CoV_2_P1': mc.SARSCoV2(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=100/2.25,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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'SARS_CoV_2_B16172': mc.SARSCoV2(
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viral_load_in_sputum=symptomatic_vl_frequencies,
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infectious_dose=60/1.6,
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infectious_dose=infectious_dose_distribution,
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viable_to_RNA=infectious_virus_distribution,
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),
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}
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