From 8c1ab2f5049f8c5b06e01e130279d4bebcd0c10c Mon Sep 17 00:00:00 2001 From: Luis Aleixo Date: Wed, 8 Sep 2021 15:46:19 +0200 Subject: [PATCH] Added viable_to_RNA variable to each virus in model --- cara/model_scenarios_paper.py | 16 +++++++++++++++- cara/monte_carlo/data.py | 2 ++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/cara/model_scenarios_paper.py b/cara/model_scenarios_paper.py index c449dfa9..901db116 100644 --- a/cara/model_scenarios_paper.py +++ b/cara/model_scenarios_paper.py @@ -1,5 +1,5 @@ from cara import models -from cara.monte_carlo.data import activity_distributions, symptomatic_vl_frequencies +from cara.monte_carlo.data import activity_distributions, symptomatic_vl_frequencies, infectious_virus_distribution import cara.monte_carlo as mc import numpy as np @@ -42,6 +42,7 @@ def breathing_exposure(activity: str, mask: str): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types[mask], @@ -72,6 +73,7 @@ def speaking_exposure(activity: str, mask: str): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types[mask], @@ -102,6 +104,7 @@ def shouting_exposure(activity: str, mask: str): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types[mask], @@ -132,6 +135,7 @@ def breathing_exposure_vl(vl): virus=models.Virus( viral_load_in_sputum=10**vl, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -162,6 +166,7 @@ def talking_exposure_vl(vl): virus=models.Virus( viral_load_in_sputum=10**vl, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -193,6 +198,7 @@ def breathing_seated_exposure(): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -222,6 +228,7 @@ def breathing_light_activity_exposure(): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -251,6 +258,7 @@ def breathing_heavy_exercise_exposure(): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -281,6 +289,7 @@ def speaking_seated_exposure(): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -310,6 +319,7 @@ def speaking_light_activity_exposure(): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -339,6 +349,7 @@ def speaking_heavy_exercise_exposure(): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -369,6 +380,7 @@ def shouting_seated_exposure(): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -398,6 +410,7 @@ def shouting_light_activity_exposure(): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], @@ -427,6 +440,7 @@ def shouting_heavy_exercise_exposure(): virus=mc.Virus( viral_load_in_sputum=symptomatic_vl_frequencies, infectious_dose=50., + viable_to_RNA=infectious_virus_distribution, ), presence=mc.SpecificInterval(((0, 2),)), mask=models.Mask.types["No mask"], diff --git a/cara/monte_carlo/data.py b/cara/monte_carlo/data.py index 7547877a..b3724524 100644 --- a/cara/monte_carlo/data.py +++ b/cara/monte_carlo/data.py @@ -72,3 +72,5 @@ mask_distributions = { 'Type I': mc.Mask(Uniform(0.25, 0.80)), 'FFP2': mc.Mask(Uniform(0.83, 0.91)), } + +infectious_virus_distribution = Uniform(0.15, 0.45)