From ae4db5a4b0801659bdd679156ec7c020712a1c31 Mon Sep 17 00:00:00 2001 From: Luis Aleixo Date: Tue, 3 Aug 2021 11:10:57 +0200 Subject: [PATCH] variables renaming (removal of quantum) --- cara/models.py | 31 +++++++++---------- cara/monte_carlo/data.py | 8 ++--- cara/tests/models/test_concentration_model.py | 6 ++-- cara/tests/test_infected_population.py | 6 ++-- 4 files changed, 25 insertions(+), 26 deletions(-) diff --git a/cara/models.py b/cara/models.py index 585fb824..38e40bcf 100644 --- a/cara/models.py +++ b/cara/models.py @@ -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() diff --git a/cara/monte_carlo/data.py b/cara/monte_carlo/data.py index 57c7ebba..613b830c 100644 --- a/cara/monte_carlo/data.py +++ b/cara/monte_carlo/data.py @@ -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, ), } diff --git a/cara/tests/models/test_concentration_model.py b/cara/tests/models/test_concentration_model.py index 26707236..bfbc88bb 100644 --- a/cara/tests/models/test_concentration_model.py +++ b/cara/tests/models/test_concentration_model.py @@ -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.)), ) diff --git a/cara/tests/test_infected_population.py b/cara/tests/test_infected_population.py index 7acef7f7..3b607feb 100644 --- a/cara/tests/test_infected_population.py +++ b/cara/tests/test_infected_population.py @@ -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.)), )