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

rearrange code in file to group talking together

Browse source
This commit is contained in:
Andrejh 2021-09-03 17:11:24 +02:00
parent 38b48d3341
commit 3ea400af2a
1 changed files with 43 additions and 46 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

89
cara/montecarlo.py
View file

@ -21,52 +21,6 @@ viral_loads = np.linspace(2, 12, 600)
markers = [5, 'd', 4]
""" Exhaled virions from exposure models """
######### Talking #########
def exposure_model_from_vl_talking():
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
er_means = []
er_medians = []
lower_percentiles = []
upper_percentiles = []
for vl in tqdm(viral_loads):
exposure_mc = talking_exposure_vl(vl)
exposure_model = exposure_mc.build_model(size=SAMPLE_SIZE)
# divide by 4 to have in 15min (quarter of an hour)
emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present(cn_B=0.06, cn_L=0.2)/4
er_means.append(np.mean(emission_rate))
er_medians.append(np.median(emission_rate))
lower_percentiles.append(np.quantile(emission_rate, 0.01))
upper_percentiles.append(np.quantile(emission_rate, 0.99))
# divide by 4 to have in 15min (quarter of an hour)
coleman_etal_er_talking_2 = [x/4 for x in coleman_etal_er_talking]
ax.plot(viral_loads, er_means)
ax.fill_between(viral_loads, lower_percentiles,
upper_percentiles, alpha=0.2)
ax.set_yscale('log')
############# Coleman #############
scatter_coleman_data(coleman_etal_vl_talking, coleman_etal_er_talking_2)
############ Legend ############
build_talking_legend(fig)
############ Plot ############
plt.title('Exhaled virions while talking for 15min',
fontsize=16, fontweight="bold")
plt.ylabel(
'Aerosol viral load, $\mathrm{vl_{out}}$\n(RNA copies)', fontsize=14)
plt.xticks(ticks=[i for i in range(2, 13)], labels=[
'$10^{' + str(i) + '}$' for i in range(2, 13)])
plt.xlabel('NP viral load, $\mathrm{vl_{in}}$\n(RNA copies)', fontsize=14)
plt.show()
######### Breathing #########
@ -198,6 +152,49 @@ def exposure_model_from_vl_breathing_cn():
############ Talking ############
def exposure_model_from_vl_talking():
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
er_means = []
er_medians = []
lower_percentiles = []
upper_percentiles = []
for vl in tqdm(viral_loads):
exposure_mc = talking_exposure_vl(vl)
exposure_model = exposure_mc.build_model(size=SAMPLE_SIZE)
# divide by 4 to have in 15min (quarter of an hour)
emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present(cn_B=0.06, cn_L=0.2)/4
er_means.append(np.mean(emission_rate))
er_medians.append(np.median(emission_rate))
lower_percentiles.append(np.quantile(emission_rate, 0.01))
upper_percentiles.append(np.quantile(emission_rate, 0.99))
# divide by 4 to have in 15min (quarter of an hour)
coleman_etal_er_talking_2 = [x/4 for x in coleman_etal_er_talking]
ax.plot(viral_loads, er_means)
ax.fill_between(viral_loads, lower_percentiles,
upper_percentiles, alpha=0.2)
ax.set_yscale('log')
############# Coleman #############
scatter_coleman_data(coleman_etal_vl_talking, coleman_etal_er_talking_2)
############ Legend ############
build_talking_legend(fig)
############ Plot ############
plt.title('Exhaled virions while talking for 15min',
fontsize=16, fontweight="bold")
plt.ylabel(
'Aerosol viral load, $\mathrm{vl_{out}}$\n(RNA copies)', fontsize=14)
plt.xticks(ticks=[i for i in range(2, 13)], labels=[
'$10^{' + str(i) + '}$' for i in range(2, 13)])
plt.xlabel('NP viral load, $\mathrm{vl_{in}}$\n(RNA copies)', fontsize=14)
plt.show()
def exposure_model_from_vl_talking_cn():
fig = plt.figure()