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Merge remote-tracking branch 'origin/feature/mc' into feature/mc

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markus 2021-03-02 16:22:31 +01:00
commit d4a48da49a
1 changed files with 9 additions and 9 deletions
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18
cara/montecarlo.py
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@ -558,9 +558,9 @@ def plot_pi_vs_viral_load(baselines: typing.Union[MCExposureModel, typing.List[M
plt.fill_between(viral_loads, lower_percentiles, upper_percentiles, alpha=0.2)
plt.title(title)
plt.ylabel('Probability of infection (%)\n$P(I|qID=60)$')
plt.ylabel('Probability of infection (%)', fontsize=14)
plt.xticks(ticks=[i for i in range(3, 13)], labels=['$10^{' + str(i) + '}$' for i in range(3, 13)])
plt.xlabel('Viral load (RNA copies mL$^{-1}$)\n$vl$')
plt.xlabel('Viral load (RNA copies mL$^{-1}$)', fontsize=14)
# add vertical lines for the critical viral loads for which pi= 5 or 95
if len(baselines) == 1:
@ -579,8 +579,8 @@ def plot_pi_vs_viral_load(baselines: typing.Union[MCExposureModel, typing.List[M
plt.vlines(x=(left, right), ymin=0, ymax=1,
colors=('grey', 'grey'), linestyles='dotted')
plt.text(left - 1.1, 0.80, '$vl_{0.05}$', fontsize=12,color='black')
plt.text(right + 0.1, 0.80, '$vl_{0.95}$', fontsize=12,color='black')
plt.text(left - 1.1, 0.80, '$vl_{0.05}$', fontsize=14,color='black')
plt.text(right + 0.1, 0.80, '$vl_{0.95}$', fontsize=14,color='black')
# add 3 shaded areas
plt.axvspan(3, left, alpha=0.1, color='limegreen')
plt.axvspan(left, right, alpha=0.1, color='orange')
@ -687,9 +687,9 @@ def composite_plot_pi_vs_viral_load(baselines: typing.List[MCExposureModel], lab
axs[1, 0].set_xticks([i for i in range(2, 13, 2)])
axs[1, 0].set_xticklabels(['$10^{' + str(i) + '}$' for i in range(2, 13, 2)])
axs[1, 0].set_xlim(2, 12)
axs[1, 0].set_xlabel('Viral load (RNA copies mL$^{-1}$)\n$vl$')
axs[0, 0].set_ylabel('Probability of infection (%)\n$P(I|qID=60)$')
plt.suptitle(title)
axs[1, 0].set_xlabel('Viral load (RNA copies mL$^{-1}$)', fontsize=12)
axs[0, 0].set_ylabel('Probability of infection (%)\n$P(I|qID=60)$', fontsize=12)
plt.suptitle(title, fontsize=12)
axs[0, 0].text(11, -0.01, '$(i)$')
axs[1, 0].text(11, axs[1, 0].get_ylim()[1] * 0.8, '$(ii)$')
@ -704,12 +704,12 @@ def composite_plot_pi_vs_viral_load(baselines: typing.List[MCExposureModel], lab
break
for i, (crit, color) in enumerate(zip(crits, colors)):
axs[0, 0].text(2.5, 0.4 - i * 0.1, f'x $vl_{"{0.95}"}=' + '10^{' + str(np.round(crits[i], 1)) + '}$', fontsize=10, color=color)
axs[0, 0].text(2.5, 0.45 - i * 0.1, f'x $vl_{"{0.95}"}=' + '10^{' + str(np.round(crits[i], 1)) + '}$', fontsize=10, color=color)
axs[0, 0].plot(crits[i], 0.95, 'x', color=color)
if show_lines:
axs[0, 0].hlines([0.5], colors=['lightgrey'], linestyles=['dashed'], xmin=2, xmax=12)
axs[0, 0].text(9.7, 0.52, "$P(I) = 0.5$", color='lightgrey')
axs[0, 0].text(9.7, 0.52, "$P(I) = 0.5$", color='grey')
middle_positions = []
for line in lines:
for i, point in enumerate(line):