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added the fraction of infectious virus method in the test full algorithm file

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This commit is contained in:
lrdossan 2024-06-20 15:51:17 +02:00
parent 7924af041f
commit ddaa77b1c9
1 changed files with 12 additions and 6 deletions
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18
caimira/tests/test_full_algorithm.py
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@ -55,7 +55,7 @@ class SimpleConcentrationModel:
#: Number of infected people
num_infected: int = 1
#: Fraction of infected viruses (viable to RNA ratio)
#: Viable to RNA ratio
viable_to_RNA: _VectorisedFloat = 0.5
#: Host immunity factor (0. for not immune)
@ -97,6 +97,12 @@ class SimpleConcentrationModel:
return (self.lambda_ventilation
+ ln2/(np.where(hl_calc <= 0, 6.43, np.minimum(6.43, hl_calc))))
def fraction_of_infectious_virus(self) -> _VectorisedFloat:
"""
The fraction of infectious virus.
"""
return self.viable_to_RNA * (1 - self.HI)
@method_cache
def deposition_removal_coefficient(self) -> float:
"""
@ -181,8 +187,8 @@ class SimpleConcentrationModel:
return ( ( (0 if not self.infected_presence.triggered(t)
else self.f(lambda_rate,0))
+ result * np.exp(-lambda_rate*(t-ti)) )
* self.num_infected * self.viable_to_RNA
* (1. - self.HI) / self.room_volume)
* self.num_infected * self.fraction_of_infectious_virus()
/ self.room_volume)
@dataclass(frozen=True)
@ -411,8 +417,8 @@ class SimpleExposureModel(SimpleConcentrationModel):
else self.f_with_fdep(lambda_rate,0,evaporation)*(t2-t1))
+ (primitive(t2) * np.exp(-lambda_rate*(t2-ti)) -
primitive(t1) * np.exp(-lambda_rate*(t1-ti)) ) )
* self.num_infected * self.viable_to_RNA
* (1. - self.HI) / self.room_volume)
* self.num_infected * self.fraction_of_infectious_virus()
/ self.room_volume)
@method_cache
def integrated_shortrange_concentration(self) -> _VectorisedFloat:
@ -431,7 +437,7 @@ class SimpleExposureModel(SimpleConcentrationModel):
res = (quad(integrand,
sr_model.diameter_min,sr_model.diameter_max,
epsabs=0.,limit=500)[0]
* self.viral_load * self.viable_to_RNA * 1e-6 * (t2-t1) )
* self.viral_load * self.fraction_of_infectious_virus() * 1e-6 * (t2-t1) )
result += sr_model.breathing_rate * (
res-self.integrated_longrange_concentration(t1,t2,evaporation)
)/sr_model.dilution_factor()