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Updated references throughout the code

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This commit is contained in:
Luis Aleixo 2021-11-10 16:59:02 +01:00
parent bf58d529a6
commit d966e91153
3 changed files with 11 additions and 9 deletions
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8
cara/models.py
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@ -788,14 +788,16 @@ class ConcentrationModel:
if (isinstance(self.infected, InfectedPopulation)
and isinstance(self.infected.expiration, Expiration)):
d = self.infected.expiration.diameter * self.evaporation_factor
vg = 1.88e-4 * (d / 2.5)**2 # see CERN-OPEN-2021-04
vg = 1.88e-4 * (d / 2.5)**2
# see https://doi.org/10.1101/2021.10.14.21264988
# (velocity of 1.88e-4 corresponds to diameter of 2.5 microns)
else:
# model is not evaluated for specific values of aerosol
# diameters - we choose a single velocity value
# corresponding to that obtained with a diameter of 2.5 microns
# (geometric average of the breathing expiration distribution,
# taking evaporation into account, see CERN-OPEN-2021-04)
# taking evaporation into account, see
# https://doi.org/10.1101/2021.10.14.21264988)
vg = 1.88e-4
# Height of the emission source to the floor - i.e. mouth/nose (m)
h = 1.5
@ -983,7 +985,7 @@ class ExposureModel:
and isinstance(self.concentration_model.infected.expiration,Expiration)):
# model is not evaluated for specific values of aerosol
# diameters - we choose a single "average" deposition factor,
# as in CERN-OPEN-2021-04.
# as in https://doi.org/10.1101/2021.10.14.21264988.
fdep = 0.6
else:
# deposition factor depends on aerosol particle diameter.

6
cara/monte_carlo/data.py
View file

@ -65,7 +65,7 @@ class BLOmodel:
return result
# From CERN-OPEN-2021-04 and refererences therein
# From https://doi.org/10.1101/2021.10.14.21264988 and refererences therein
activity_distributions = {
'Seated': mc.Activity(LogNormal(-0.6872121723362303, 0.10498338229297108),
LogNormal(-0.6872121723362303, 0.10498338229297108)),
@ -84,7 +84,7 @@ activity_distributions = {
}
# From CERN-OPEN-2021-04 and refererences therein
# From https://doi.org/10.1101/2021.10.14.21264988 and refererences therein
symptomatic_vl_frequencies = LogCustomKernel(
np.array((2.46032, 2.67431, 2.85434, 3.06155, 3.25856, 3.47256, 3.66957, 3.85979, 4.09927, 4.27081,
4.47631, 4.66653, 4.87204, 5.10302, 5.27456, 5.46478, 5.6533, 5.88428, 6.07281, 6.30549,
@ -105,7 +105,7 @@ viable_to_RNA_ratio_distribution = Uniform(0.15, 0.45)
# From discussion with virologists
infectious_dose_distribution = Uniform(10., 100.)
# From CERN-OPEN-2021-04 and refererences therein
# From https://doi.org/10.1101/2021.10.14.21264988 and refererences therein
virus_distributions = {
'SARS_CoV_2': mc.SARSCoV2(
viral_load_in_sputum=symptomatic_vl_frequencies,

6
cara/tests/test_predefined_distributions.py
View file

@ -8,7 +8,7 @@ from cara.monte_carlo.data import activity_distributions, virus_distributions
np.random.seed(2000)
# mean & std deviations from CERN-OPEN-2021-04 (Table 4)
# mean & std deviations from https://doi.org/10.1101/2021.10.14.21264988 (Table 3)
# NOTE: a mistake was corrected for the std deviation of the
# "Moderate exercise" case (0.37 in the report, but should be 0.34)
@pytest.mark.parametrize(
@ -30,8 +30,8 @@ def test_activity_distributions(distribution, mean, std):
npt.assert_allclose(activity.inhalation_rate.std(), std, atol=0.01)
# mean & std deviations from CERN-OPEN-2021-04 (Table 4) - with a refined
# precision on the values
# mean & std deviations from https://doi.org/10.1101/2021.10.14.21264988 (Table 3)
# - with a refined precision on the values
@pytest.mark.parametrize(
"distribution, mean, std",[
['SARS_CoV_2', 6.59, 1.74],