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Revert "variables renaming (removal of quantum)"

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This reverts commit ae4db5a4b0.
This commit is contained in:
Luis Aleixo 2021-08-03 11:18:44 +02:00
parent ae4db5a4b0
commit 52c4eb7c2c
4 changed files with 26 additions and 25 deletions
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31
cara/models.py
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@ -420,8 +420,8 @@ class Virus:
#: RNA copies / mL #: RNA copies / mL
viral_load_in_sputum: _VectorisedFloat viral_load_in_sputum: _VectorisedFloat
#: RNA-copies #: RNA-copies per quantum
infectious_dose: _VectorisedFloat quantum_infectious_dose: _VectorisedFloat
#: Pre-populated examples of Viruses. #: Pre-populated examples of Viruses.
types: typing.ClassVar[typing.Dict[str, "Virus"]] types: typing.ClassVar[typing.Dict[str, "Virus"]]
@ -458,20 +458,20 @@ Virus.types = {
# It is somewhere between 1000 or 10 SARS-CoV viruses, # It is somewhere between 1000 or 10 SARS-CoV viruses,
# as per https://www.dhs.gov/publication/st-master-question-list-covid-19 # as per https://www.dhs.gov/publication/st-master-question-list-covid-19
# 50 comes from Buonanno et al. # 50 comes from Buonanno et al.
infectious_dose=50., quantum_infectious_dose=50.,
), ),
'SARS_CoV_2_B117': SARSCoV2( 'SARS_CoV_2_B117': SARSCoV2(
# also called VOC-202012/01 # also called VOC-202012/01
viral_load_in_sputum=1e9, viral_load_in_sputum=1e9,
infectious_dose=30., quantum_infectious_dose=30.,
), ),
'SARS_CoV_2_P1': SARSCoV2( 'SARS_CoV_2_P1': SARSCoV2(
viral_load_in_sputum=1e9, viral_load_in_sputum=1e9,
infectious_dose=1/0.045, quantum_infectious_dose=1/0.045,
), ),
'SARS_CoV_2_B16172': SARSCoV2( 'SARS_CoV_2_B16172': SARSCoV2(
viral_load_in_sputum=1e9, viral_load_in_sputum=1e9,
infectious_dose=30/1.6, quantum_infectious_dose=30/1.6,
), ),
} }
@ -677,7 +677,7 @@ class InfectedPopulation(Population):
Note that the rate is not currently time-dependent. Note that the rate is not currently time-dependent.
""" """
# Emission Rate (infectious dose / h) # Emission Rate (infectious quantum / h)
# Note on units: exhalation rate is in m^3/h, aerosols in mL/cm^3 # Note on units: exhalation rate is in m^3/h, aerosols in mL/cm^3
# and viral load in virus/mL -> 1e6 conversion factor # and viral load in virus/mL -> 1e6 conversion factor
aerosols = self.expiration.aerosols(self.mask) aerosols = self.expiration.aerosols(self.mask)
@ -685,14 +685,15 @@ class InfectedPopulation(Population):
ER = (self.virus.viral_load_in_sputum * ER = (self.virus.viral_load_in_sputum *
self.activity.exhalation_rate * self.activity.exhalation_rate *
10 ** 6 * 10 ** 6 *
aerosols) aerosols /
self.virus.quantum_infectious_dose)
# For superspreading event, where ejection_factor is infinite we fix the ER # For superspreading event, where ejection_factor is infinite we fix the ER
# based on Miller et al. (2020). # based on Miller et al. (2020).
if isinstance(aerosols, np.ndarray): if isinstance(aerosols, np.ndarray):
ER[np.isinf(aerosols)] = 970 * self.virus.infectious_dose ER[np.isinf(aerosols)] = 970
elif np.isinf(aerosols): elif np.isinf(aerosols):
ER = 970 * self.virus.infectious_dose ER = 970
return ER return ER
@ -803,7 +804,7 @@ class ConcentrationModel:
def concentration(self, time: float) -> _VectorisedFloat: def concentration(self, time: float) -> _VectorisedFloat:
""" """
Virus concentration, as a function of time. Virus quanta concentration, as a function of time.
The formulas used here assume that all parameters (ventilation, The formulas used here assume that all parameters (ventilation,
emission rate) are constant between two state changes - only emission rate) are constant between two state changes - only
the value of these parameters at the next state change, are used. the value of these parameters at the next state change, are used.
@ -866,8 +867,8 @@ class ExposureModel:
#: The fraction of viruses actually deposited in the respiratory tract #: The fraction of viruses actually deposited in the respiratory tract
fraction_deposited: _VectorisedFloat = 0.6 fraction_deposited: _VectorisedFloat = 0.6
def exposure(self) -> _VectorisedFloat: def quanta_exposure(self) -> _VectorisedFloat:
"""The number of virus per meter^3.""" """The number of virus quanta per meter^3."""
exposure = 0.0 exposure = 0.0
for start, stop in self.exposed.presence.boundaries(): for start, stop in self.exposed.presence.boundaries():
@ -876,7 +877,7 @@ class ExposureModel:
return exposure * self.repeats return exposure * self.repeats
def infection_probability(self) -> _VectorisedFloat: def infection_probability(self) -> _VectorisedFloat:
exposure = self.exposure() exposure = self.quanta_exposure()
inf_aero = ( inf_aero = (
self.exposed.activity.inhalation_rate * self.exposed.activity.inhalation_rate *
@ -885,7 +886,7 @@ class ExposureModel:
) )
# Probability of infection. # Probability of infection.
return (1 - np.exp(-inf_aero / self.concentration_model.virus.infectious_dose)) * 100 return (1 - np.exp(-inf_aero)) * 100
def expected_new_cases(self) -> _VectorisedFloat: def expected_new_cases(self) -> _VectorisedFloat:
prob = self.infection_probability() prob = self.infection_probability()

8
cara/monte_carlo/data.py
View file

@ -43,18 +43,18 @@ symptomatic_vl_frequencies = LogCustomKernel(
virus_distributions = { virus_distributions = {
'SARS_CoV_2': mc.SARSCoV2( 'SARS_CoV_2': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies, viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=100, quantum_infectious_dose=100,
), ),
'SARS_CoV_2_B117': mc.SARSCoV2( 'SARS_CoV_2_B117': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies, viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=60, quantum_infectious_dose=60,
), ),
'SARS_CoV_2_P1': mc.SARSCoV2( 'SARS_CoV_2_P1': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies, viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=100/2.25, quantum_infectious_dose=100/2.25,
), ),
'SARS_CoV_2_B16172': mc.SARSCoV2( 'SARS_CoV_2_B16172': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies, viral_load_in_sputum=symptomatic_vl_frequencies,
infectious_dose=60/1.6, quantum_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])}, {'humidity': np.array([0.5, 0.4])},
{'air_change': np.array([100, 120])}, {'air_change': np.array([100, 120])},
{'viral_load_in_sputum': np.array([5e8, 1e9])}, {'viral_load_in_sputum': np.array([5e8, 1e9])},
{'infectious_dose': np.array([50, 20])}, {'quantum_infectious_dose': np.array([50, 20])},
] ]
) )
def test_concentration_model_vectorisation(override_params): def test_concentration_model_vectorisation(override_params):
@ -22,7 +22,7 @@ def test_concentration_model_vectorisation(override_params):
'humidity': 0.5, 'humidity': 0.5,
'air_change': 100, 'air_change': 100,
'viral_load_in_sputum': 1e9, 'viral_load_in_sputum': 1e9,
'infectious_dose': 50, 'quantum_infectious_dose': 50,
} }
defaults.update(override_params) defaults.update(override_params)
@ -43,7 +43,7 @@ def test_concentration_model_vectorisation(override_params):
), ),
virus=models.SARSCoV2( virus=models.SARSCoV2(
viral_load_in_sputum=defaults['viral_load_in_sputum'], viral_load_in_sputum=defaults['viral_load_in_sputum'],
infectious_dose=defaults['infectious_dose'], quantum_infectious_dose=defaults['quantum_infectious_dose'],
), ),
expiration=models.Expiration((1., 0., 0.)), 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( @pytest.mark.parametrize(
"override_params", [ "override_params", [
{'viral_load_in_sputum': np.array([5e8, 1e9])}, {'viral_load_in_sputum': np.array([5e8, 1e9])},
{'infectious_dose': np.array([50, 20])}, {'quantum_infectious_dose': np.array([50, 20])},
{'exhalation_rate': np.array([0.75, 0.81])}, {'exhalation_rate': np.array([0.75, 0.81])},
] ]
) )
def test_infected_population_vectorisation(override_params): def test_infected_population_vectorisation(override_params):
defaults = { defaults = {
'viral_load_in_sputum': 1e9, 'viral_load_in_sputum': 1e9,
'infectious_dose': 50, 'quantum_infectious_dose': 50,
'exhalation_rate': 0.75, 'exhalation_rate': 0.75,
} }
defaults.update(override_params) defaults.update(override_params)
@ -33,7 +33,7 @@ def test_infected_population_vectorisation(override_params):
), ),
virus=cara.models.Virus( virus=cara.models.Virus(
viral_load_in_sputum=defaults['viral_load_in_sputum'], viral_load_in_sputum=defaults['viral_load_in_sputum'],
infectious_dose=defaults['infectious_dose'], quantum_infectious_dose=defaults['quantum_infectious_dose'],
), ),
expiration=cara.models.Expiration((1., 0., 0.)), expiration=cara.models.Expiration((1., 0., 0.)),
) )