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add _generate_viral_loads

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markus 2021-01-25 13:20:08 +01:00
parent 487f01b0f8
commit 3a16b683f3
1 changed files with 20 additions and 0 deletions
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cara/montecarlo.py
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@ -5,6 +5,7 @@ import numpy as np
import scipy.stats as sct
import typing
import matplotlib.pyplot as plt
from sklearn.neighbors import KernelDensity
# The (k, lambda) parameters for the weibull-distributions corresponding to each quantity
@ -16,6 +17,18 @@ weibull_parameters = [((0.5951563631241763, 0.027071715346754264), # em
(7.348365409721486, 1.1158159287760463 * 3.33))] # particle_diameter_speaking_loudly
log_viral_load_frequencies = ((1.880302953, 2.958422139, 3.308759599, 3.676921581, 4.036604757, 4.383770594,
4.743136608, 5.094658141, 5.45613857, 5.812946142, 6.160090835, 6.518505362,
6.866918705, 7.225333232, 7.574148314, 7.923640008, 8.283027166, 8.641758855,
9.000448256, 9.35956054, 9.707720153, 10.06554264, 10.41435773, 10.76304594,
11.12198907, 11.47118475),
(0.001694915, 0.00720339, 0.027966102, 0.205932203, 0.213983051, 0.171186441,
0.172881356, 0.217372881, 0.261440678, 0.211864407, 0.168644068, 0.151271186,
0.133474576, 0.116101695, 0.106355932, 0.110169492, 0.112288136, 0.101271186,
0.08940678, 0.086016949, 0.063135593, 0.033898305, 0.024152542, 0.011864407,
0.005084746, 0.002966102))
@dataclass(frozen=True)
class MCVirus:
#: Biological decay (inactivation of the virus in air)
@ -47,6 +60,13 @@ class MCInfectedPopulation(models.Population):
viral_load: typing.Optional[float] = None
def _generate_viral_loads(self):
kde_model = KernelDensity(kernel='gaussian', bandwidth=0.1)
kde_model.fit(np.asarray(log_viral_load_frequencies)[0, :][:, np.newaxis],
sample_weight=np.asarray(log_viral_load_frequencies)[1, :])
return kde_model.sample(n_samples=self.samples)[:, 0]
def emission_rate_when_present(self) -> np.ndarray:
"""
Randomly samples values for the quantum generation rate