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Virus class: input is now qID instead of coefficient_of_infectivity (which remains as a property), as in the CERN note

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This commit is contained in:
Nicolas Mounet 2021-05-14 09:15:08 +02:00
parent f07bffaa4a
commit d5dcfa5a40
1 changed files with 12 additions and 7 deletions
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19
cara/models.py
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@ -432,8 +432,8 @@ class Virus:
#: RNA copies / mL
viral_load_in_sputum: _VectorisedFloat
#: Ratio between infectious aerosols and dose to cause infection.
coefficient_of_infectivity: _VectorisedFloat
#: RNA-copies per quantum
qID: _VectorisedFloat
#: Pre-populated examples of Viruses.
types: typing.ClassVar[typing.Dict[str, "Virus"]]
@ -443,26 +443,31 @@ class Virus:
# Viral inactivation per hour (h^-1)
return np.log(2) / self.halflife
@property
def coefficient_of_infectivity(self) -> _VectorisedFloat:
# Ratio between infectious aerosols and dose to cause infection.
return 1/self.qID
Virus.types = {
'SARS_CoV_2': Virus(
halflife=1.1,
viral_load_in_sputum=1e9,
# No data on coefficient for SARS-CoV-2 yet.
# It is somewhere between 0.001 and 0.01 to have a 50% chance
# to cause infection. i.e. 1000 or 100 SARS-CoV viruses to cause infection.
coefficient_of_infectivity=0.02,
# It is somewhere between 1000 or 100 SARS-CoV viruses to have
# a 50% chance to cause infection.
qID=50.,
),
'SARS_CoV_2_B117': Virus(
# also called VOC-202012/01
halflife=1.1,
viral_load_in_sputum=1e9,
coefficient_of_infectivity=1/30.,
qID=30.,
),
'SARS_CoV_2_P1': Virus(
halflife=1.1,
viral_load_in_sputum=1e9,
coefficient_of_infectivity=0.045,
qID=1/0.045,
),
}