- Taking into account the uncertainties tied to the model variables, in this scenario and assuming all occupants are exposed equally (i.e. without short-range interactions), the probability of one exposed occupant getting infected is {{ long_range_prob_inf | non_zero_percentage }} and the expected number of new cases is {{ expected_new_cases | float_format }}*.
+ Taking into account the uncertainties tied to the model variables, in this scenario and assuming all occupants are exposed equally (i.e. without short-range interactions), the probability of one exposed occupant getting infected is {{ long_range_prob_inf | non_zero_percentage }} and the expected number of new cases is {{ long_range_expected_cases | float_format }}*.
{% if form.short_range_option == "short_range_yes" %}
- In this scenario, assuming short-range interactions occur, the probability of one exposed occupant getting infected can go as high as {{ prob_inf | non_zero_percentage }}.
+ In this scenario, the probability the occupant(s) exposed to short-range interactions get infected can go as high as {{ prob_inf | non_zero_percentage }} and the expected number of new cases increases to {{ expected_new_cases | float_format }}.
{% endif %}
{% block probabilistic_exposure_probability %}
@@ -601,14 +610,16 @@
{% endif %}
{% if form.short_range_option == "short_range_yes" %}
-
- Short-range interactions: {{ form.short_range_interactions|length }}
-
+
Total number of occupants having short-range interactions: {{ form.short_range_occupants }}
{% for interaction in form.short_range_interactions %}
- - Expiratory activity {{ loop.index if form.short_range_interactions|length > 1 }}: {{ "Shouting/Singing" if interaction.expiration == "Shouting" else interaction.expiration }}
- - Start time {{ loop.index if form.short_range_interactions|length > 1 }}: {{ interaction.start_time }}
- - Duration {{ loop.index if form.short_range_interactions|length > 1 }}: {{ interaction.duration }} {{ "minutes" if interaction.duration|float > 1 else "minute" }}
+ - Interaction no. {{ loop.index }}:
+
+ - Expiratory activity: {{ "Shouting/Singing" if interaction.expiration == "Shouting" else interaction.expiration }}
+ - Start time: {{ interaction.start_time }}
+ - Duration: {{ interaction.duration }} {{ "minutes" if interaction.duration|float > 1 else "minute" }}
+
+
{% endfor %}
{% endif %}
diff --git a/caimira/apps/templates/cern/calculator.report.html.j2 b/caimira/apps/templates/cern/calculator.report.html.j2
index d482b1dc..701c2ab0 100644
--- a/caimira/apps/templates/cern/calculator.report.html.j2
+++ b/caimira/apps/templates/cern/calculator.report.html.j2
@@ -70,7 +70,7 @@
Acceptable:
{% endif %}
- Taking into account the uncertainties tied to the model variables, in this scenario and assuming all occupants are exposed equally (i.e. without short-range interactions), the probability of one exposed occupant getting infected is {{long_range_prob_inf | non_zero_percentage}} and the expected number of new cases is {{expected_new_cases | float_format}}*.
+ Taking into account the uncertainties tied to the model variables, in this scenario and assuming all occupants are exposed equally (i.e. without short-range interactions), the probability of one exposed occupant getting infected is {{long_range_prob_inf | non_zero_percentage}} and the expected number of new cases is {{ long_range_expected_cases | float_format }}*.
{% if form.short_range_option == "short_range_yes" %}
@@ -84,7 +84,7 @@
Acceptable:
{% endif %}
- In this scenario, assuming short-range interactions occur, the probability of one exposed occupant getting infected can go as high as {{prob_inf | non_zero_percentage}}.
+ In this scenario, the probability the occupant(s) exposed to short-range interactions get infected can go as high as {{ prob_inf | non_zero_percentage }} and the expected number of new cases increases to {{ expected_new_cases | float_format }}.
{% endif %}
diff --git a/caimira/models.py b/caimira/models.py
index 192a6afc..441b70ff 100644
--- a/caimira/models.py
+++ b/caimira/models.py
@@ -1579,6 +1579,9 @@ class ExposureModel:
#: Geographical data
geographical_data: Cases
+ #: Total people with short-range interactions
+ exposed_to_short_range: int = 0
+
#: The number of times the exposure event is repeated (default 1).
@property
def repeats(self) -> int:
@@ -1814,10 +1817,15 @@ def expected_new_cases(self) -> _VectorisedFloat:
"with dynamic occupancy")
"""
- The expect_new_cases should always take the long-range infection_probability and multiply by the occupants exposed to long-range.
+ The expected_new_cases may provide one or two different outputs:
+ 1) Long-range exposure: take the infection_probability and multiply by the occupants exposed to long-range.
+ 2) Short- and long-range exposure: take the infection_probability of long-range multiplied by the occupants exposed to long-range only,
+ plus the infection_probability of short- and long-range multiplied by the occupants exposed to short-range only.
"""
+
if self.short_range != ():
- return nested_replace(self, {'short_range': ()}).infection_probability() * self.exposed.number / 100
+ new_cases_long_range = nested_replace(self, {'short_range': (),}).infection_probability() * (self.exposed.number - self.exposed_to_short_range)
+ return (new_cases_long_range + (self.infection_probability() * self.exposed_to_short_range)) / 100
return self.infection_probability() * self.exposed.number / 100
diff --git a/caimira/tests/apps/calculator/conftest.py b/caimira/tests/apps/calculator/conftest.py
index 38c19e97..d774e333 100644
--- a/caimira/tests/apps/calculator/conftest.py
+++ b/caimira/tests/apps/calculator/conftest.py
@@ -11,3 +11,12 @@ def baseline_form_data():
@pytest.fixture
def baseline_form(baseline_form_data, data_registry):
return model_generator.VirusFormData.from_dict(baseline_form_data, data_registry)
+
+
+@pytest.fixture
+def baseline_form_with_sr(baseline_form_data, data_registry):
+ form_data_sr = baseline_form_data
+ form_data_sr['short_range_option'] = 'short_range_yes'
+ form_data_sr['short_range_interactions'] = '[{"expiration": "Shouting", "start_time": "10:30", "duration": "30"}]'
+ form_data_sr['short_range_occupants'] = 5
+ return model_generator.VirusFormData.from_dict(form_data_sr, data_registry)
\ No newline at end of file
diff --git a/caimira/tests/apps/calculator/test_report_generator.py b/caimira/tests/apps/calculator/test_report_generator.py
index 22355c5d..ba0295eb 100644
--- a/caimira/tests/apps/calculator/test_report_generator.py
+++ b/caimira/tests/apps/calculator/test_report_generator.py
@@ -7,7 +7,9 @@
import pytest
from caimira.apps.calculator import make_app
-from caimira.apps.calculator.report_generator import ReportGenerator, readable_minutes
+from caimira.apps.calculator.model_generator import VirusFormData
+from caimira.apps.calculator.report_generator import (ReportGenerator, readable_minutes, calculate_report_data,
+ manufacture_alternative_scenarios, interesting_times, comparison_report)
import caimira.apps.calculator.report_generator as rep_gen
@@ -90,3 +92,26 @@ def test_interesting_times_w_temp(exposure_model_w_outside_temp_changes):
5., 5.4, 5.8, 6.2, 6.6, 7., 7.4, 7.8, 8.
]
np.testing.assert_allclose(result, expected)
+
+
+def test_expected_new_cases(baseline_form_with_sr: VirusFormData):
+ model = baseline_form_with_sr.build_model()
+
+ executor_factory = partial(
+ concurrent.futures.ThreadPoolExecutor, 1,
+ )
+
+ # Short- and Long-range contributions
+ report_data = calculate_report_data(baseline_form_with_sr, model, executor_factory)
+ sr_lr_expected_new_cases = report_data['expected_new_cases']
+ sr_lr_prob_inf = report_data['prob_inf']/100
+
+ # Long-range contributions alone
+ scenario_sample_times = interesting_times(model)
+ alternative_scenarios = manufacture_alternative_scenarios(baseline_form_with_sr)
+ alternative_statistics = comparison_report(
+ baseline_form_with_sr, report_data, alternative_scenarios, scenario_sample_times, executor_factory=executor_factory,
+ )
+
+ lr_expected_new_cases = alternative_statistics['stats']['Base scenario without short-range interactions']['expected_new_cases']
+ np.testing.assert_almost_equal(sr_lr_expected_new_cases, lr_expected_new_cases + sr_lr_prob_inf * baseline_form_with_sr.short_range_occupants, 2)