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variables renaming (removal of quantum)

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This commit is contained in:
Luis Aleixo 2021-08-03 11:10:57 +02:00
parent 2645ff2a43
commit ae4db5a4b0
4 changed files with 25 additions and 26 deletions
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31
cara/models.py
View file

@ -420,8 +420,8 @@ class Virus:
#: RNA copies / mL
viral_load_in_sputum: _VectorisedFloat
#: RNA-copies per quantum
quantum_infectious_dose: _VectorisedFloat
#: RNA-copies
infectious_dose: _VectorisedFloat
#: Pre-populated examples of Viruses.
types: typing.ClassVar[typing.Dict[str, "Virus"]]
@ -458,20 +458,20 @@ Virus.types = {
# It is somewhere between 1000 or 10 SARS-CoV viruses,
# as per https://www.dhs.gov/publication/st-master-question-list-covid-19
# 50 comes from Buonanno et al.
quantum_infectious_dose=50.,
infectious_dose=50.,
),
'SARS_CoV_2_B117': SARSCoV2(
# also called VOC-202012/01
viral_load_in_sputum=1e9,
quantum_infectious_dose=30.,
infectious_dose=30.,
),
'SARS_CoV_2_P1': SARSCoV2(
viral_load_in_sputum=1e9,
quantum_infectious_dose=1/0.045,
infectious_dose=1/0.045,
),
'SARS_CoV_2_B16172': SARSCoV2(
viral_load_in_sputum=1e9,
quantum_infectious_dose=30/1.6,
infectious_dose=30/1.6,
),
}
@ -677,7 +677,7 @@ class InfectedPopulation(Population):
Note that the rate is not currently time-dependent.
"""
# Emission Rate (infectious quantum / h)
# Emission Rate (infectious dose / h)
# Note on units: exhalation rate is in m^3/h, aerosols in mL/cm^3
# and viral load in virus/mL -> 1e6 conversion factor
aerosols = self.expiration.aerosols(self.mask)
@ -685,15 +685,14 @@ class InfectedPopulation(Population):
ER = (self.virus.viral_load_in_sputum *
self.activity.exhalation_rate *
10 ** 6 *
aerosols /
self.virus.quantum_infectious_dose)
aerosols)
# For superspreading event, where ejection_factor is infinite we fix the ER
# based on Miller et al. (2020).
if isinstance(aerosols, np.ndarray):
ER[np.isinf(aerosols)] = 970
ER[np.isinf(aerosols)] = 970 * self.virus.infectious_dose
elif np.isinf(aerosols):
ER = 970
ER = 970 * self.virus.infectious_dose
return ER
@ -804,7 +803,7 @@ class ConcentrationModel:
def concentration(self, time: float) -> _VectorisedFloat:
"""
Virus quanta concentration, as a function of time.
Virus concentration, as a function of time.
The formulas used here assume that all parameters (ventilation,
emission rate) are constant between two state changes - only
the value of these parameters at the next state change, are used.
@ -867,8 +866,8 @@ class ExposureModel:
#: The fraction of viruses actually deposited in the respiratory tract
fraction_deposited: _VectorisedFloat = 0.6
def quanta_exposure(self) -> _VectorisedFloat:
"""The number of virus quanta per meter^3."""
def exposure(self) -> _VectorisedFloat:
"""The number of virus per meter^3."""
exposure = 0.0
for start, stop in self.exposed.presence.boundaries():
@ -877,7 +876,7 @@ class ExposureModel:
return exposure * self.repeats
def infection_probability(self) -> _VectorisedFloat:
exposure = self.quanta_exposure()
exposure = self.exposure()
inf_aero = (
self.exposed.activity.inhalation_rate *
@ -886,7 +885,7 @@ class ExposureModel:
)
# Probability of infection.
return (1 - np.exp(-inf_aero)) * 100
return (1 - np.exp(-inf_aero / self.concentration_model.virus.infectious_dose)) * 100
def expected_new_cases(self) -> _VectorisedFloat:
prob = self.infection_probability()

8
cara/monte_carlo/data.py
View file

@ -43,18 +43,18 @@ symptomatic_vl_frequencies = LogCustomKernel(
virus_distributions = {
'SARS_CoV_2': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
quantum_infectious_dose=100,
infectious_dose=100,
),
'SARS_CoV_2_B117': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
quantum_infectious_dose=60,
infectious_dose=60,
),
'SARS_CoV_2_P1': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
quantum_infectious_dose=100/2.25,
infectious_dose=100/2.25,
),
'SARS_CoV_2_B16172': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,
quantum_infectious_dose=60/1.6,
infectious_dose=60/1.6,
),
}

6
cara/tests/models/test_concentration_model.py
View file

@ -13,7 +13,7 @@ from cara import models
{'humidity': np.array([0.5, 0.4])},
{'air_change': np.array([100, 120])},
{'viral_load_in_sputum': np.array([5e8, 1e9])},
{'quantum_infectious_dose': np.array([50, 20])},
{'infectious_dose': np.array([50, 20])},
]
)
def test_concentration_model_vectorisation(override_params):
@ -22,7 +22,7 @@ def test_concentration_model_vectorisation(override_params):
'humidity': 0.5,
'air_change': 100,
'viral_load_in_sputum': 1e9,
'quantum_infectious_dose': 50,
'infectious_dose': 50,
}
defaults.update(override_params)
@ -43,7 +43,7 @@ def test_concentration_model_vectorisation(override_params):
),
virus=models.SARSCoV2(
viral_load_in_sputum=defaults['viral_load_in_sputum'],
quantum_infectious_dose=defaults['quantum_infectious_dose'],
infectious_dose=defaults['infectious_dose'],
),
expiration=models.Expiration((1., 0., 0.)),
)

6
cara/tests/test_infected_population.py
View file

@ -7,14 +7,14 @@ import cara.models
@pytest.mark.parametrize(
"override_params", [
{'viral_load_in_sputum': np.array([5e8, 1e9])},
{'quantum_infectious_dose': np.array([50, 20])},
{'infectious_dose': np.array([50, 20])},
{'exhalation_rate': np.array([0.75, 0.81])},
]
)
def test_infected_population_vectorisation(override_params):
defaults = {
'viral_load_in_sputum': 1e9,
'quantum_infectious_dose': 50,
'infectious_dose': 50,
'exhalation_rate': 0.75,
}
defaults.update(override_params)
@ -33,7 +33,7 @@ def test_infected_population_vectorisation(override_params):
),
virus=cara.models.Virus(
viral_load_in_sputum=defaults['viral_load_in_sputum'],
quantum_infectious_dose=defaults['quantum_infectious_dose'],
infectious_dose=defaults['infectious_dose'],
),
expiration=cara.models.Expiration((1., 0., 0.)),
)