pingu_98/cara
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Merge branch 'feature/update_docstring_ER' into 'master'

Browse source 
update docstring of `emission_rate_per_aerosol_when_present` and `aerosol`

See merge request cara/cara!365
This commit is contained in:
Andre Henriques 2022-06-10 11:40:24 +02:00
commit 0898964333
2 changed files with 20 additions and 11 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

29
cara/models.py
View file

@ -635,7 +635,7 @@ class _ExpirationBase:
def aerosols(self, mask: Mask):
"""
Total volume of aerosols expired per volume of air (mL/cm^3).
Total volume of aerosols expired per volume of exhaled air (mL/cm^3).
"""
raise NotImplementedError("Subclass must implement")
@ -670,7 +670,10 @@ class Expiration(_ExpirationBase):
@cached()
def aerosols(self, mask: Mask):
""" Result is in mL.cm^-3 """
"""
Total volume of aerosols expired per volume of exhaled air.
Result is in mL.cm^-3
"""
def volume(d):
return (np.pi * d**3) / 6.
@ -791,14 +794,15 @@ class _PopulationWithVirus(Population):
def aerosols(self):
"""
Total volume of aerosols expired per volume of air (mL/cm^3).
Total volume of aerosols expired per volume of exhaled air (mL/cm^3).
"""
raise NotImplementedError("Subclass must implement")
def emission_rate_per_aerosol_when_present(self) -> _VectorisedFloat:
"""
The emission rate of virions per fraction of aerosol volume in
the expired air, if the infected population is present, in cm^3/(mL.h).
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).
This method includes only the diameter-independent variables within the emission rate.
It should not be a function of time.
"""
raise NotImplementedError("Subclass must implement")
@ -845,7 +849,7 @@ class EmittingPopulation(_PopulationWithVirus):
def aerosols(self):
"""
Total volume of aerosols expired per volume of air (mL/cm^3).
Total volume of aerosols expired per volume of exhaled air (mL/cm^3).
Here arbitrarily set to 1 as the full emission rate is known.
"""
return 1.
@ -853,8 +857,9 @@ class EmittingPopulation(_PopulationWithVirus):
@method_cache
def emission_rate_per_aerosol_when_present(self) -> _VectorisedFloat:
"""
The emission rate of virions per fraction of aerosol volume in
the expired air, if the infected population is present, in cm^3/(mL.h).
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).
This method includes only the diameter-independent variables within the emission rate.
It should not be a function of time.
"""
return self.known_individual_emission_rate * self.number
@ -874,18 +879,20 @@ class InfectedPopulation(_PopulationWithVirus):
def aerosols(self):
"""
Total volume of aerosols expired per volume of air (mL/cm^3).
Total volume of aerosols expired per volume of exhaled air (mL/cm^3).
"""
return self.expiration.aerosols(self.mask)
@method_cache
def emission_rate_per_aerosol_when_present(self) -> _VectorisedFloat:
"""
The emission rate of virions per fraction of aerosol volume in
the expired air, if the infected population is present, in cm^3/(mL.h).
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).
This method includes only the diameter-independent variables within the emission rate.
It should not be a function of time.
"""
# Note on units: exhalation rate is in m^3/h -> 1e6 conversion factor
# Returns the emission rate times the number of infected hosts in the room
ER = (self.virus.viral_load_in_sputum *
self.activity.exhalation_rate *

2
cara/tests/test_sampleable_distribution.py
View file

@ -1,10 +1,12 @@
import numpy as np
import numpy.testing as npt
import pytest
from retry import retry
from cara.monte_carlo import sampleable
@retry(tries=10)
@pytest.mark.parametrize(
"mean, std",[
[1., 0.5],