pingu_98/cara
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

twinks in the generated scenarios

Browse source
This commit is contained in:
Luis Aleixo 2021-09-22 16:37:47 +02:00
parent c114eaa794
commit cf966b427a
1 changed files with 26 additions and 31 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

57
cara/model_scenarios_paper.py
View file

@ -1,5 +1,5 @@
from cara import models, data from cara import models, data
from cara.monte_carlo.data import activity_distributions, symptomatic_vl_frequencies, viable_to_RNA_ratio_distribution, infectious_dose_distribution, expiration_distributions from cara.monte_carlo.data import activity_distributions, symptomatic_vl_frequencies, viable_to_RNA_ratio_distribution, infectious_dose_distribution, expiration_distributions, mask_distributions, virus_distributions
import cara.monte_carlo as mc import cara.monte_carlo as mc
import numpy as np import numpy as np
from cara.monte_carlo.sampleable import Normal,LogNormal,LogCustomKernel,CustomKernel,Uniform from cara.monte_carlo.sampleable import Normal,LogNormal,LogCustomKernel,CustomKernel,Uniform
@ -54,6 +54,11 @@ expiration_BLO_factors = {
######### Standard exposure models ########### ######### Standard exposure models ###########
def exposure_module(activity: str, expiration: str, mask: str): def exposure_module(activity: str, expiration: str, mask: str):
if mask == 'No mask':
exposure_mask = models.Mask.types['No mask']
else:
exposure_mask = mask_distributions[mask]
exposure_mc = mc.ExposureModel( exposure_mc = mc.ExposureModel(
concentration_model=mc.ConcentrationModel( concentration_model=mc.ConcentrationModel(
room=models.Room(volume=100, humidity=0.5), room=models.Room(volume=100, humidity=0.5),
@ -63,14 +68,9 @@ def exposure_module(activity: str, expiration: str, mask: str):
), ),
infected=mc.InfectedPopulation( infected=mc.InfectedPopulation(
number=1, number=1,
virus=mc.SARSCoV2( virus=virus_distributions['SARS_CoV_2'],
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=infectious_dose_distribution,
viable_to_RNA_ratio=viable_to_RNA_ratio_distribution,
transmissibility_factor=1.,
),
presence=mc.SpecificInterval(((0, 2),)), presence=mc.SpecificInterval(((0, 2),)),
mask=models.Mask.types[mask], mask=exposure_mask,
activity=activity_distributions[activity], activity=activity_distributions[activity],
expiration=expiration_distributions[expiration], expiration=expiration_distributions[expiration],
host_immunity=0., host_immunity=0.,
@ -80,7 +80,7 @@ def exposure_module(activity: str, expiration: str, mask: str):
number=14, number=14,
presence=mc.SpecificInterval(((0, 2),)), presence=mc.SpecificInterval(((0, 2),)),
activity=activity_distributions[activity], activity=activity_distributions[activity],
mask=models.Mask.types[mask], mask=exposure_mask,
host_immunity=0., host_immunity=0.,
), ),
) )
@ -88,6 +88,11 @@ def exposure_module(activity: str, expiration: str, mask: str):
######### Exposure model for specific viral load ########### ######### Exposure model for specific viral load ###########
def exposure_vl(activity: str, expiration: str, mask: str, vl: float): def exposure_vl(activity: str, expiration: str, mask: str, vl: float):
if mask == 'No mask':
exposure_mask = models.Mask.types['No mask']
else:
exposure_mask = mask_distributions[mask]
exposure_mc = mc.ExposureModel( exposure_mc = mc.ExposureModel(
concentration_model=mc.ConcentrationModel( concentration_model=mc.ConcentrationModel(
room=models.Room(volume=100, humidity=0.5), room=models.Room(volume=100, humidity=0.5),
@ -104,7 +109,7 @@ def exposure_vl(activity: str, expiration: str, mask: str, vl: float):
transmissibility_factor=1., transmissibility_factor=1.,
), ),
presence=mc.SpecificInterval(((0, 2),)), presence=mc.SpecificInterval(((0, 2),)),
mask=models.Mask.types[mask], mask=exposure_mask,
activity=activity_distributions[activity], activity=activity_distributions[activity],
expiration=expiration_distributions[expiration], expiration=expiration_distributions[expiration],
host_immunity=0., host_immunity=0.,
@ -114,7 +119,7 @@ def exposure_vl(activity: str, expiration: str, mask: str, vl: float):
number=14, number=14,
presence=mc.SpecificInterval(((0, 2),)), presence=mc.SpecificInterval(((0, 2),)),
activity=activity_distributions[activity], activity=activity_distributions[activity],
mask=models.Mask.types[mask], mask=exposure_mask,
host_immunity=0., host_immunity=0.,
), ),
) )
@ -122,6 +127,11 @@ def exposure_vl(activity: str, expiration: str, mask: str, vl: float):
######### Exposure model for specific viral load ########### ######### Exposure model for specific viral load ###########
def exposure_vl_cn(activity: str, expiration: str, mask: str, vl: float, cn: typing.Tuple[float, float, float]): def exposure_vl_cn(activity: str, expiration: str, mask: str, vl: float, cn: typing.Tuple[float, float, float]):
if mask == 'No mask':
exposure_mask = models.Mask.types['No mask']
else:
exposure_mask = mask_distributions[mask]
exposure_mc = mc.ExposureModel( exposure_mc = mc.ExposureModel(
concentration_model=mc.ConcentrationModel( concentration_model=mc.ConcentrationModel(
room=models.Room(volume=100, humidity=0.5), room=models.Room(volume=100, humidity=0.5),
@ -138,7 +148,7 @@ def exposure_vl_cn(activity: str, expiration: str, mask: str, vl: float, cn: typ
transmissibility_factor=1., transmissibility_factor=1.,
), ),
presence=mc.SpecificInterval(((0, 2),)), presence=mc.SpecificInterval(((0, 2),)),
mask=models.Mask.types[mask], mask=exposure_mask,
activity=activity_distributions[activity], activity=activity_distributions[activity],
expiration=cn_expiration_distribution(expiration_BLO_factors[expiration], cn), expiration=cn_expiration_distribution(expiration_BLO_factors[expiration], cn),
host_immunity=0., host_immunity=0.,
@ -148,7 +158,7 @@ def exposure_vl_cn(activity: str, expiration: str, mask: str, vl: float, cn: typ
number=14, number=14,
presence=mc.SpecificInterval(((0, 2),)), presence=mc.SpecificInterval(((0, 2),)),
activity=activity_distributions[activity], activity=activity_distributions[activity],
mask=models.Mask.types[mask], mask=exposure_mask,
host_immunity=0., host_immunity=0.,
), ),
) )
@ -165,12 +175,7 @@ def office_model_no_mask_windows_closed():
infected=mc.InfectedPopulation( infected=mc.InfectedPopulation(
number=1, number=1,
presence=mc.SpecificInterval(present_times = ((0, 1.5), (2, 3.5), (4.5, 6), (6.5, 8))), presence=mc.SpecificInterval(present_times = ((0, 1.5), (2, 3.5), (4.5, 6), (6.5, 8))),
virus=mc.SARSCoV2( virus=virus_distributions['SARS_CoV_2'],
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=infectious_dose_distribution,
viable_to_RNA_ratio=viable_to_RNA_ratio_distribution,
transmissibility_factor=1.,
),
mask=models.Mask.types["No mask"], mask=models.Mask.types["No mask"],
activity=activity_distributions['Light activity'], activity=activity_distributions['Light activity'],
expiration=build_expiration({'Talking': 0.33, 'Breathing': 0.67}), expiration=build_expiration({'Talking': 0.33, 'Breathing': 0.67}),
@ -206,12 +211,7 @@ def office_model_no_mask_windows_open_breaks():
infected=mc.InfectedPopulation( infected=mc.InfectedPopulation(
number=1, number=1,
presence=mc.SpecificInterval(present_times=((0, 1.5), (2, 3.5), (4.5, 6), (6.5, 8))), presence=mc.SpecificInterval(present_times=((0, 1.5), (2, 3.5), (4.5, 6), (6.5, 8))),
virus=mc.SARSCoV2( virus=virus_distributions['SARS_CoV_2'],
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=infectious_dose_distribution,
viable_to_RNA_ratio=viable_to_RNA_ratio_distribution,
transmissibility_factor=1.,
),
mask=models.Mask.types["No mask"], mask=models.Mask.types["No mask"],
activity=activity_distributions['Light activity'], activity=activity_distributions['Light activity'],
expiration=build_expiration({'Talking': 0.33, 'Breathing': 0.67}), expiration=build_expiration({'Talking': 0.33, 'Breathing': 0.67}),
@ -246,12 +246,7 @@ def office_model_no_mask_windows_open_alltimes():
infected=mc.InfectedPopulation( infected=mc.InfectedPopulation(
number=1, number=1,
presence=mc.SpecificInterval(present_times=((0, 1.5), (2, 3.5), (4.5, 6), (6.5, 8))), presence=mc.SpecificInterval(present_times=((0, 1.5), (2, 3.5), (4.5, 6), (6.5, 8))),
virus=mc.SARSCoV2( virus=virus_distributions['SARS_CoV_2'],
viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=infectious_dose_distribution,
viable_to_RNA_ratio=viable_to_RNA_ratio_distribution,
transmissibility_factor=1.,
),
mask=models.Mask.types["No mask"], mask=models.Mask.types["No mask"],
activity=activity_distributions['Light activity'], activity=activity_distributions['Light activity'],
expiration=build_expiration({'Talking': 0.33, 'Breathing': 0.67}), expiration=build_expiration({'Talking': 0.33, 'Breathing': 0.67}),