files division
This commit is contained in:
Luis Aleixo
parent
90040a62a2
commit
2988f2085b
3 changed files with 61 additions and 51 deletions
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@ -19,6 +19,8 @@ import jinja2
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import matplotlib
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matplotlib.use('agg')
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from cara.monte_carlo.data import activity_distributions, virus_distributions
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def model_start_end(model: models.ExposureModel):
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t_start = min(model.exposed.presence.boundaries()[0][0],
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@ -119,50 +121,54 @@ def plot(times, concentrations, model: models.ExposureModel):
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upper_percentiles = []
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for vl in viral_loads:
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exposure_model = models.ExposureModel(
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concentration_model=models.ConcentrationModel(
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room=models.Room(volume=45, humidity=0.5),
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ventilation=models.SlidingWindow(
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active=models.PeriodicInterval(period=120, duration=120),
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inside_temp=models.PiecewiseConstant((0, 24), (293, )),
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outside_temp=models.PiecewiseConstant((0, 24), (283,)),
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window_height=1.6, opening_length=0.2,
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exposure_mc = mc.ExposureModel(
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concentration_model=mc.ConcentrationModel(
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room=models.Room(volume=100, humidity=0.5),
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ventilation=models.AirChange(
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active=models.SpecificInterval(((0, 24),)),
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air_exch=0.25,
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),
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infected=models.InfectedPopulation(
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infected=mc.InfectedPopulation(
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number=1,
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presence=models.SpecificInterval(((0, 4), (5, 9))),
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mask=models.Mask.types['No mask'],
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activity=models.Activity.types['Seated'],
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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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virus=mc.Virus(
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viral_load_in_sputum = 10**vl,
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infectious_dose = 50.,
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),
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expiration=models.Expiration.types['Breathing']
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)
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presence=mc.SpecificInterval(((0, 2),)),
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mask=models.Mask.types["No mask"],
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activity=activity_distributions['Seated'],
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expiration=models.MultipleExpiration(
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expirations=(models.Expiration.types['Talking'],
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models.Expiration.types['Breathing']),
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weights=(0.3, 0.7)),
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),
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),
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exposed=models.Population(
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number=2,
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presence=models.SpecificInterval(((0, 4), (5, 9))),
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exposed=mc.Population(
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number=14,
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presence=mc.SpecificInterval(((0, 2),)),
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activity=models.Activity.types['Seated'],
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mask=models.Mask.types['No mask']
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mask=models.Mask.types["No mask"],
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),
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)
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)
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exposure_model = exposure_mc.build_model(size=_DEFAULT_MC_SAMPLE_SIZE)
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emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present()
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er_means.append(np.mean(emission_rate))
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er_medians.append(np.median(emission_rate))
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lower_percentiles.append(np.quantile(emission_rate, 0.25))
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upper_percentiles.append(np.quantile(emission_rate, 0.75))
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lower_percentiles.append(np.quantile(emission_rate, 0.01))
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upper_percentiles.append(np.quantile(emission_rate, 0.99))
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ax.plot(viral_loads, er_means)
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ax.fill_between(viral_loads, lower_percentiles, upper_percentiles, alpha=0.2)
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ax.fill_between(viral_loads, lower_percentiles,
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upper_percentiles, alpha=0.2)
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ax.set_yscale('log')
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plt.title('Emission rate vs Viral Load')
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plt.ylabel('ER (Virions/h)', fontsize=14)
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plt.xticks(ticks=[i for i in range(2, 13)], labels=['$10^{' + str(i) + '}$' for i in range(2, 13)])
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plt.xticks(ticks=[i for i in range(2, 13)], labels=[
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'$10^{' + str(i) + '}$' for i in range(2, 13)])
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plt.xlabel('Viral load (RNA copies mL$^{-1}$)', fontsize=14)
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return fig
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@ -1,29 +1,34 @@
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from cara import models
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import monte_carlo as mc
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from cara.monte_carlo.data import activity_distributions
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exposure_models = models.ExposureModel(
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concentration_model=models.ConcentrationModel(
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room=models.Room(volume=45, humidity=0.5),
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ventilation=models.SlidingWindow(
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active=models.PeriodicInterval(period=120, duration=120),
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inside_temp=models.PiecewiseConstant((0, 24), (293, )),
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outside_temp=models.PiecewiseConstant((0, 24), (283,)),
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window_height=1.6, opening_length=0.2,
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exposure_mc = mc.ExposureModel(
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concentration_model=mc.ConcentrationModel(
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room=models.Room(volume=100, humidity=0.5),
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ventilation=models.AirChange(
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active=models.SpecificInterval(((0, 24),)),
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air_exch=0.25,
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),
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infected=models.InfectedPopulation(
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infected=mc.InfectedPopulation(
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number=1,
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presence=models.SpecificInterval(((0, 4), (5, 9))),
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mask=False,
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mask=models.Mask.types['Type I'],
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activity=models.Activity.types['Seated'],
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virus=models.Virus.types['SARS_CoV_2_B117'],
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expiration=models.Expiration.types['Breathing']
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)
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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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),
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presence=mc.SpecificInterval(((0, 2),)),
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mask=models.Mask.types["No mask"],
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activity=activity_distributions['Seated'],
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expiration=models.MultipleExpiration(
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expirations=(models.Expiration.types['Talking'],
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models.Expiration.types['Breathing']),
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weights=(0.3, 0.7)),
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),
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),
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exposed=models.Population(
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number=2,
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presence=models.SpecificInterval(((0, 4), (5, 9))),
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exposed=mc.Population(
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number=14,
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presence=mc.SpecificInterval(((0, 2),)),
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activity=models.Activity.types['Seated'],
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mask=models.Mask.types['Type I']
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mask=models.Mask.types["No mask"],
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),
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)
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)
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exposure_model = exposure_mc.build_model(size=50000)
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@ -1,3 +1,2 @@
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from cara import *
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