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Replacing qID by quantum_infectious_dose

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This commit is contained in:
Nicolas Mounet 2021-05-26 08:55:38 +02:00
parent 3e9652d012
commit ca1440bf5c
3 changed files with 11 additions and 11 deletions
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10
cara/models.py
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@ -420,7 +420,7 @@ class Virus:
viral_load_in_sputum: _VectorisedFloat
#: RNA-copies per quantum
qID: _VectorisedFloat
quantum_infectious_dose: _VectorisedFloat
#: Pre-populated examples of Viruses.
types: typing.ClassVar[typing.Dict[str, "Virus"]]
@ -438,18 +438,18 @@ Virus.types = {
# No data on coefficient for SARS-CoV-2 yet.
# It is somewhere between 1000 or 100 SARS-CoV viruses to have
# a 50% chance to cause infection.
qID=50.,
quantum_infectious_dose=50.,
),
'SARS_CoV_2_B117': Virus(
# also called VOC-202012/01
halflife=1.1,
viral_load_in_sputum=1e9,
qID=30.,
quantum_infectious_dose=30.,
),
'SARS_CoV_2_P1': Virus(
halflife=1.1,
viral_load_in_sputum=1e9,
qID=1/0.045,
quantum_infectious_dose=1/0.045,
),
}
@ -587,7 +587,7 @@ class InfectedPopulation(Population):
self.activity.exhalation_rate *
10 ** 6 *
aerosols /
self.virus.qID)
self.virus.quantum_infectious_dose)
# For superspreading event, where ejection_factor is infinite we fix the ER
# based on Miller et al. (2020).

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

@ -12,7 +12,7 @@ from cara import models
{'air_change': np.array([100, 120])},
{'virus_halflife': np.array([1.1, 1.5])},
{'viral_load_in_sputum': np.array([5e8, 1e9])},
{'qID': np.array([50, 20])},
{'quantum_infectious_dose': np.array([50, 20])},
{'η_exhale': np.array([0.92, 0.95])},
{'η_leaks': np.array([0.15, 0.20])},
]
@ -23,7 +23,7 @@ def test_concentration_model_vectorisation(override_params):
'air_change': 100,
'virus_halflife': 1.1,
'viral_load_in_sputum': 1e9,
'qID': 50,
'quantum_infectious_dose': 50,
'η_exhale': 0.95,
'η_leaks': 0.15,
}
@ -48,7 +48,7 @@ def test_concentration_model_vectorisation(override_params):
virus=models.Virus(
halflife=defaults['virus_halflife'],
viral_load_in_sputum=defaults['viral_load_in_sputum'],
qID=defaults['qID'],
quantum_infectious_dose=defaults['quantum_infectious_dose'],
),
expiration=models.Expiration(
ejection_factor=(0.084, 0.009, 0.003, 0.002),

6
cara/tests/test_infected_population.py
View file

@ -7,7 +7,7 @@ import cara.models
@pytest.mark.parametrize(
"override_params", [
{'viral_load_in_sputum': np.array([5e8, 1e9])},
{'qID': np.array([50, 20])},
{'quantum_infectious_dose': np.array([50, 20])},
{'η_exhale': np.array([0.92, 0.95])},
{'η_leaks': np.array([0.15, 0.20])},
{'exhalation_rate': np.array([0.75, 0.81])},
@ -17,7 +17,7 @@ def test_infected_population_vectorisation(override_params):
defaults = {
'virus_halflife': 1.1,
'viral_load_in_sputum': 1e9,
'qID': 50,
'quantum_infectious_dose': 50,
'η_exhale': 0.95,
'η_leaks': 0.15,
'exhalation_rate': 0.75,
@ -40,7 +40,7 @@ def test_infected_population_vectorisation(override_params):
virus=cara.models.Virus(
halflife=defaults['virus_halflife'],
viral_load_in_sputum=defaults['viral_load_in_sputum'],
qID=defaults['qID'],
quantum_infectious_dose=defaults['quantum_infectious_dose'],
),
expiration=cara.models.Expiration(
ejection_factor=(0.084, 0.009, 0.003, 0.002),