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added results with different viral load values

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This commit is contained in:
Luis Aleixo 2023-05-30 11:04:38 +02:00
parent 3c139fb62d
commit ca786d7e7f
2 changed files with 62 additions and 0 deletions
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43
caimira/apps/calculator/report_generator.py
View file

@ -139,6 +139,7 @@ def calculate_report_data(form: FormData, model: models.ExposureModel) -> typing
expected_new_cases = np.array(model.expected_new_cases()).mean()
uncertainties_plot_src = img2base64(_figure2bytes(uncertainties_plot(model))) if form.conditional_probability_plot else None
exposed_presence_intervals = [list(interval) for interval in model.exposed.presence_interval().boundaries()]
manufacture_viral_load_scenarios(model)
return {
"model_repr": repr(model),
@ -302,6 +303,18 @@ def non_zero_percentage(percentage: int) -> str:
return "99.9%"
else:
return "{:0.1f}%".format(percentage)
def manufacture_viral_load_scenarios(model: mc.ExposureModel) -> typing.Dict[str, mc.ExposureModel]:
viral_load = model.concentration_model.infected.virus.viral_load_in_sputum
viral_load_values = [np.quantile(viral_load, percentil) for percentil in (0.05, 0.5, 0.95)]
scenarios = {}
for vl in viral_load_values:
specific_vl_scenario = dataclass_utils.nested_replace(model,
{'concentration_model.infected.virus.viral_load_in_sputum': vl}
)
scenarios[str(round(np.log10(vl), 1))] = specific_vl_scenario
return scenarios
def manufacture_alternative_scenarios(form: FormData) -> typing.Dict[str, mc.ExposureModel]:
@ -374,6 +387,32 @@ def scenario_statistics(mc_model: mc.ExposureModel, sample_times: typing.List[fl
}
def comparison_report_viral_load(
report_data: typing.Dict[str, typing.Any],
scenarios: typing.Dict[str, mc.ExposureModel],
):
statistics = {
# 'Current scenario' : {
# 'probability_of_infection': report_data['prob_inf'],
# 'expected_new_cases': report_data['expected_new_cases'],
# }
}
results = []
for mc_model in scenarios.values():
results.append({
'probability_of_infection': np.mean(mc_model.infection_probability()),
'expected_new_cases': np.mean(mc_model.expected_new_cases()),
})
for (name, model), model_stats in zip(scenarios.items(), results):
statistics[name] = model_stats
return {
'stats': statistics,
}
def comparison_report(
form: FormData,
report_data: typing.Dict[str, typing.Any],
@ -449,7 +488,11 @@ class ReportGenerator:
scenario_sample_times = interesting_times(model)
report_data = calculate_report_data(form, model)
context.update(report_data)
alternative_viral_loads = manufacture_viral_load_scenarios(model)
alternative_scenarios = manufacture_alternative_scenarios(form)
context['alternative_viral_load'] = comparison_report_viral_load(
report_data, alternative_viral_loads
)
context['alternative_scenarios'] = comparison_report(
form, report_data, alternative_scenarios, scenario_sample_times, executor_factory=executor_factory,
)

19
caimira/apps/templates/base/calculator.report.html.j2
View file

@ -161,6 +161,25 @@
{% block report_summary_footnote %}
{% endblock report_summary_footnote %}
</div>
<br>
<table class="table w-auto">
<thead class="thead-light">
<tr>
<th>Scenario</th>
<th>P(I)</th>
<th>Expected new cases</th>
</tr>
</thead>
<tbody>
{% for scenario_name, scenario_stats in alternative_viral_load.stats.items() %}
<tr>
<td> Viral load: 10<sup>{{ scenario_name }}</sup></td>
<td> {{ scenario_stats.probability_of_infection | non_zero_percentage }}</td>
<td style="text-align:right">{{ scenario_stats.expected_new_cases | float_format }}</td>
</tr>
{% endfor %}
</tbody>
</table>
<br><p id="section1">* The results are based on the parameters and assumptions published in the CARA publication: <a href="https://doi.org/10.1098/rsfs.2021.0076"> doi.org/10.1098/rsfs.2021.0076</a>.</p><br>
{% if form.short_range_option == "short_range_yes" %}
{% if 'Speaking' in form.short_range_interactions|string or 'Shouting' in form.short_range_interactions|string %}