updated docstrings for virions vs. IRP
This commit is contained in:
lrdossan
parent
e0fa8fd0d2
commit
56550c4406
1 changed files with 22 additions and 20 deletions
|
|
@ -877,9 +877,9 @@ class _PopulationWithVirus(Population):
|
|||
|
||||
def emission_rate_per_aerosol_per_person_when_present(self) -> _VectorisedFloat:
|
||||
"""
|
||||
The emission rate of virions in the expired air per mL of respiratory fluid,
|
||||
per person, if the infected population is present, in (virion.cm^3)/(mL.h).
|
||||
This method includes only the diameter-independent variables within the emission rate.
|
||||
The emission rate of infectious respiratory particles (IRP) in the expired air per
|
||||
mL of respiratory fluid, if the infected population is present, in (IRP.cm^3)/(mL.h).
|
||||
This method returns only the diameter-independent variables within the emission rate.
|
||||
It should not be a function of time.
|
||||
"""
|
||||
raise NotImplementedError("Subclass must implement")
|
||||
|
|
@ -888,7 +888,7 @@ class _PopulationWithVirus(Population):
|
|||
def emission_rate_per_person_when_present(self) -> _VectorisedFloat:
|
||||
"""
|
||||
The emission rate if the infected population is present, per person
|
||||
(in virions / h).
|
||||
(in IRP/h).
|
||||
"""
|
||||
return (self.emission_rate_per_aerosol_per_person_when_present() *
|
||||
self.aerosols())
|
||||
|
|
@ -920,7 +920,7 @@ class _PopulationWithVirus(Population):
|
|||
|
||||
@dataclass(frozen=True)
|
||||
class EmittingPopulation(_PopulationWithVirus):
|
||||
#: The emission rate of a single individual, in virions / h.
|
||||
#: The emission rate of a single individual, in IRP / h.
|
||||
known_individual_emission_rate: float
|
||||
|
||||
def aerosols(self):
|
||||
|
|
@ -933,9 +933,9 @@ class EmittingPopulation(_PopulationWithVirus):
|
|||
@method_cache
|
||||
def emission_rate_per_aerosol_per_person_when_present(self) -> _VectorisedFloat:
|
||||
"""
|
||||
The emission rate of virions in the expired air per mL of respiratory fluid,
|
||||
per person, if the infected population is present, in (virion.cm^3)/(mL.h).
|
||||
This method includes only the diameter-independent variables within the emission rate.
|
||||
The emission rate of infectious respiratory particles (IRP) in the expired air per
|
||||
mL of respiratory fluid, if the infected population is present, in (IRP.cm^3)/(mL.h).
|
||||
This method returns only the diameter-independent variables within the emission rate.
|
||||
It should not be a function of time.
|
||||
"""
|
||||
return self.known_individual_emission_rate
|
||||
|
|
@ -962,14 +962,14 @@ class InfectedPopulation(_PopulationWithVirus):
|
|||
@method_cache
|
||||
def emission_rate_per_aerosol_per_person_when_present(self) -> _VectorisedFloat:
|
||||
"""
|
||||
The emission rate of virions in the expired air per mL of respiratory fluid,
|
||||
if the infected population is present, in (virion.cm^3)/(mL.h).
|
||||
The emission rate of infectious respiratory particles (IRP) in the expired air per
|
||||
mL of respiratory fluid, if the infected population is present, in (IRP.cm^3)/(mL.h).
|
||||
This method returns only the diameter-independent variables within the emission rate.
|
||||
It should not be a function of time.
|
||||
"""
|
||||
# Conversion factor explanation:
|
||||
# The exhalation rate is in m^3/h, therefore the 1e6 conversion factor
|
||||
# is to convert m^3/h into cm^3/h to return (virions.cm^3)/(mL.h),
|
||||
# is to convert m^3/h into cm^3/h to return (IRP.cm^3)/(mL.h),
|
||||
# so that we can then multiply by aerosols (mL/cm^3).
|
||||
ER = (self.virus.viral_load_in_sputum *
|
||||
self.activity.exhalation_rate *
|
||||
|
|
@ -1426,7 +1426,7 @@ class ShortRangeModel:
|
|||
"""
|
||||
The normalization factor applied to the short-range results. It refers to the emission
|
||||
rate per aerosol without accounting for the exhalation rate (viral load and f_inf).
|
||||
Result in (virions.cm^3)/(mL.m^3).
|
||||
Result in (IRP.cm^3)/(mL.m^3).
|
||||
"""
|
||||
# Re-use the emission rate method divided by the BR contribution.
|
||||
return infected.emission_rate_per_aerosol_per_person_when_present() / infected.activity.exhalation_rate
|
||||
|
|
@ -1434,14 +1434,14 @@ class ShortRangeModel:
|
|||
def jet_origin_concentration(self, infected: InfectedPopulation) -> _VectorisedFloat:
|
||||
"""
|
||||
The initial jet concentration at the source origin (mouth/nose).
|
||||
Returns the full result with the diameter dependent and independent variables, in virions/m^3.
|
||||
Returns the full result with the diameter dependent and independent variables, in IRP/m^3.
|
||||
"""
|
||||
return self._normed_jet_origin_concentration() * self.normalization_factor(infected)
|
||||
|
||||
def short_range_concentration(self, concentration_model: ConcentrationModel, time: float) -> _VectorisedFloat:
|
||||
"""
|
||||
Virus short-range exposure concentration, as a function of time.
|
||||
Factor of normalization applied back here. Results in virions/m^3.
|
||||
Factor of normalization applied back here. Results in IRP/m^3.
|
||||
"""
|
||||
return (self._normed_concentration(concentration_model, time) *
|
||||
self.normalization_factor(concentration_model.infected))
|
||||
|
|
@ -1499,16 +1499,16 @@ class ShortRangeModel:
|
|||
together with breathing rate, and without dilution.
|
||||
One needs to interpolate the integrated long-range concentration
|
||||
for the particle diameters defined here.
|
||||
TODO: make sure any potential extrapolation has a
|
||||
negligible effect.
|
||||
"""
|
||||
start, stop = self.extract_between_bounds(time1, time2)
|
||||
if stop<=start:
|
||||
return 0.
|
||||
|
||||
# Note that the emission_rate_per_aerosol_per_person_when_present method
|
||||
# is not used here due to the influence that the conversion factor (10**6)
|
||||
# could have in the interpolation.
|
||||
# Note that for the correct interpolation one needs to isolate those parameters
|
||||
# that are diameter-dependent from those that are diameter independent.
|
||||
# Therefore, the diameter-independent parameters (viral load, f_ind and BR)
|
||||
# are removed for the interpolation, and added back once the integration over
|
||||
# the new aerosol diameters (done with the mean) is completed.
|
||||
normed_int_concentration = (
|
||||
concentration_model.integrated_concentration(start, stop)
|
||||
/concentration_model.virus.viral_load_in_sputum
|
||||
|
|
@ -1586,7 +1586,8 @@ class CO2DataModel:
|
|||
@dataclass(frozen=True)
|
||||
class ExposureModel:
|
||||
"""
|
||||
Represents the exposure to a concentration of virions in the air.
|
||||
Represents the exposure to a concentration of
|
||||
infectious respiratory particles (IRP) in the air.
|
||||
"""
|
||||
data_registry: DataRegistry
|
||||
|
||||
|
|
@ -1726,6 +1727,7 @@ class ExposureModel:
|
|||
initial deposited exposure.
|
||||
"""
|
||||
deposited_exposure: _VectorisedFloat = 0.
|
||||
emission_rate_per_aerosol_per_person = self.concentration_model.normalization_factor()
|
||||
for interaction in self.short_range:
|
||||
start, stop = interaction.extract_between_bounds(time1, time2)
|
||||
short_range_jet_exposure = interaction._normed_jet_exposure_between_bounds(start, stop)
|
||||
|
|
|
|||
Loading…
Reference in a new issue