handled expected number of new cases calculation (including tests)

caimira/src/caimira/calculator/models/models.py

@@ -1867,43 +1867,56 @@ class ExposureModel:
             return 0
 
     def expected_new_cases(self) -> _VectorisedFloat:
-        if (isinstance(self.concentration_model.infected.number, IntPiecewiseConstant) or
-            isinstance(self.exposed.number, IntPiecewiseConstant)):
-            raise NotImplementedError("Cannot compute expected new cases "
-                    "with dynamic occupancy")
-        
         """
         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.
+
+        In the case dynamic occupancy is defined, the maximum number of exposed occupants during the course of the simulation will be considered.
         """
+        exposed_occ: int = max(self.exposed.number.values) if isinstance(self.exposed.number, IntPiecewiseConstant) else self.exposed.number
 
         if self.short_range != ():
-            new_cases_long_range = nested_replace(self, {'short_range': (),}).infection_probability() * (self.exposed.number - self.exposed_to_short_range)
+            new_cases_long_range = nested_replace(self, {'short_range': [],}).infection_probability() * (exposed_occ - 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
+        return self.infection_probability() * exposed_occ / 100
 
     def reproduction_number(self) -> _VectorisedFloat:
         """
         The reproduction number can be thought of as the expected number of
         cases directly generated by one infected case in a population.
 
+        It handles the cases when dynamic occupancy for the infected population is defined. 
         """
-        if (isinstance(self.concentration_model.infected.number, IntPiecewiseConstant) or
-            isinstance(self.exposed.number, IntPiecewiseConstant)):
-            raise NotImplementedError("Cannot compute reproduction number "
-                    "with dynamic occupancy")
 
-        if self.concentration_model.infected.number == 1:
-            return self.expected_new_cases()
+        infected_number = self.concentration_model.infected.number
+        if isinstance(infected_number, IntPiecewiseConstant):
+            # Handle case when infected number is dynamic
+            max_occ = max(infected_number.values)
+            if max_occ == 1:
+                return self.expected_new_cases()
+            else:
+                # Adjust to treat dynamic occupancy, limiting infected to 1 when present
+                inf_occ_values = [1 if occ > 0 else occ for occ in infected_number.values]
+                single_exposure_model = nested_replace(
+                    self, {
+                        'concentration_model.infected.number.values': inf_occ_values
+                    }
+                )
+                return single_exposure_model.expected_new_cases()
+        
+        elif isinstance(infected_number, int):
+            # Handle case when infected number is a single integer
+            if infected_number == 1:
+                return self.expected_new_cases()
 
-        # Create an equivalent exposure model but with precisely
-        # one infected case.
-        single_exposure_model = nested_replace(
-            self, {
-                'concentration_model.infected.number': 1}
-        )
+            # Create an equivalent exposure model but with precisely
+            # one infected case.
+            single_exposure_model = nested_replace(
+                self, {
+                    'concentration_model.infected.number': 1}
+            )
 
-        return single_exposure_model.expected_new_cases()
+            return single_exposure_model.expected_new_cases()

caimira/src/caimira/calculator/report/virus_report_data.py

@@ -177,12 +177,6 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable
     if form.exposure_option == "p_probabilistic_exposure" and form.occupancy_format == "static":
         prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean()
     else: prob_probabilistic_exposure = -1
-    # Expected new cases
-    if (form.occupancy_format == "static"):
-        expected_new_cases = np.array(model.expected_new_cases()).mean()
-    else:
-        # With dynamic occupancy, the expected number of new cases feature is disabled.
-        expected_new_cases = -1
 
     exposed_presence_intervals = [list(interval) for interval in model.exposed.presence_interval().boundaries()]
 
@@ -213,7 +207,8 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable
         "prob_hist_count": list(prob_dist_count),
         "prob_hist_bins": list(prob_dist_bins),
         "prob_probabilistic_exposure": prob_probabilistic_exposure,
-        "expected_new_cases": expected_new_cases,
+        "expected_new_cases": np.array(model.expected_new_cases()).mean(),
+        "uncertainties_plot_src": uncertainties_plot_src,
         "CO2_concentrations": CO2_concentrations,
         "conditional_probability_data": conditional_probability_data,
         "uncertainties_plot_src": uncertainties_plot_src,
@@ -406,8 +401,14 @@ def manufacture_alternative_scenarios(form: VirusFormData) -> typing.Dict[str, m
             scenarios['Neither ventilation nor masks'] = without_mask_or_vent.build_mc_model()
 
     else:
-        no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[],
-                                                             total_people=form.total_people - form.short_range_occupants)
+        # When dynamic occupancy is defined, the replace of total people is useless - the expected number of new cases is not calculated.
+        if form.occupancy_format == 'static':
+            no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[], total_people=form.total_people - form.short_range_occupants)
+        elif form.occupancy_format == 'dynamic':
+            for occ in form.dynamic_exposed_occupancy: # Update the number of exposed people with long-range exposure
+                if occ['total_people'] > form.short_range_occupants: occ['total_people'] = max(0, occ['total_people'] - form.short_range_occupants)
+            no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[], dynamic_exposed_occupancy=form.dynamic_exposed_occupancy)
+        
         scenarios['Base scenario without short-range interactions'] = no_short_range_alternative.build_mc_model()
 
     return scenarios
@@ -417,7 +418,6 @@ def scenario_statistics(
     mc_model: mc.ExposureModel,
     sample_times: typing.List[float],
     compute_prob_exposure: bool,
-    compute_expected_new_cases: bool,
 ):
     model = mc_model.build_model(
         size=mc_model.data_registry.monte_carlo['sample_size'])
@@ -425,16 +425,11 @@ def scenario_statistics(
         # It means we have data to calculate the total_probability_rule
         prob_probabilistic_exposure = model.total_probability_rule()
     else:
-        prob_probabilistic_exposure = -1
-    
-    if (compute_expected_new_cases):
-        expected_new_cases = np.mean(model.expected_new_cases())
-    else:
-        expected_new_cases = -1
+        prob_probabilistic_exposure = -1 
 
     return {
         'probability_of_infection': np.mean(model.infection_probability()),
-        'expected_new_cases': expected_new_cases,
+        'expected_new_cases': np.mean(model.expected_new_cases()),
         'concentrations': [
             np.mean(model.concentration(time))
             for time in sample_times
@@ -464,8 +459,6 @@ def comparison_report(
         compute_prob_exposure = True
     else:
         compute_prob_exposure = False
-
-    compute_expected_new_cases = True if (form.occupancy_format == "static") else False
         
     with executor_factory() as executor:
         results = executor.map(
@@ -473,7 +466,6 @@ def comparison_report(
             scenarios.values(),
             [report_data['times']] * len(scenarios),
             [compute_prob_exposure] * len(scenarios),
-            [compute_expected_new_cases] * len(scenarios),
             timeout=60,
         )
 

caimira/tests/models/test_dynamic_population.py

@@ -230,32 +230,26 @@ def test_dynamic_total_probability_rule(
                                                             "(including incidence rate) with dynamic occupancy")):
         dynamic_population_exposure_model.total_probability_rule()
 
+
 def test_dynamic_expected_new_cases(
+        full_exposure_model: models.ExposureModel,
         dynamic_infected_single_exposure_model: models.ExposureModel,
         dynamic_exposed_single_exposure_model: models.ExposureModel,
         dynamic_population_exposure_model: models.ExposureModel):
 
-    with pytest.raises(NotImplementedError, match=re.escape("Cannot compute expected new cases "
-                                                            "with dynamic occupancy")):
-        dynamic_infected_single_exposure_model.expected_new_cases()
-    with pytest.raises(NotImplementedError, match=re.escape("Cannot compute expected new cases "
-                                                        "with dynamic occupancy")):
-        dynamic_exposed_single_exposure_model.expected_new_cases()
-    with pytest.raises(NotImplementedError, match=re.escape("Cannot compute expected new cases "
-                                                            "with dynamic occupancy")):
-        dynamic_population_exposure_model.expected_new_cases()
+    base_expected_new_cases = full_exposure_model.expected_new_cases()
+    npt.assert_almost_equal(base_expected_new_cases, dynamic_infected_single_exposure_model.expected_new_cases())
+    npt.assert_almost_equal(base_expected_new_cases, dynamic_exposed_single_exposure_model.expected_new_cases())
+    npt.assert_almost_equal(base_expected_new_cases, dynamic_population_exposure_model.expected_new_cases())
+
 
 def test_dynamic_reproduction_number(
+        full_exposure_model: models.ExposureModel,
         dynamic_infected_single_exposure_model: models.ExposureModel,
         dynamic_exposed_single_exposure_model: models.ExposureModel,
         dynamic_population_exposure_model: models.ExposureModel):
-
-    with pytest.raises(NotImplementedError, match=re.escape("Cannot compute reproduction number "
-                                                            "with dynamic occupancy")):
-        dynamic_infected_single_exposure_model.reproduction_number()
-    with pytest.raises(NotImplementedError, match=re.escape("Cannot compute reproduction number "
-                                                            "with dynamic occupancy")):
-        dynamic_exposed_single_exposure_model.reproduction_number()
-    with pytest.raises(NotImplementedError, match=re.escape("Cannot compute reproduction number "
-                                                            "with dynamic occupancy")):
-        dynamic_population_exposure_model.reproduction_number()
+    
+    base_reproduction_number = full_exposure_model.reproduction_number()
+    npt.assert_almost_equal(base_reproduction_number, dynamic_infected_single_exposure_model.reproduction_number())
+    npt.assert_almost_equal(base_reproduction_number, dynamic_exposed_single_exposure_model.reproduction_number())
+    npt.assert_almost_equal(base_reproduction_number, dynamic_population_exposure_model.reproduction_number())

cern_caimira/tests/test_report_generator.py

@@ -180,6 +180,6 @@ def test_static_vs_dynamic_occupancy_from_form(baseline_form_data, data_registry
             list(dynamic_occupancy_model.exposed.number.transition_times))
     
     np.testing.assert_almost_equal(static_occupancy_report_data['prob_inf'], dynamic_occupancy_report_data['prob_inf'], 1)
-    assert dynamic_occupancy_report_data['expected_new_cases'] == -1
+    np.testing.assert_almost_equal(static_occupancy_report_data['expected_new_cases'], dynamic_occupancy_report_data['expected_new_cases'], 1)
     assert dynamic_occupancy_report_data['prob_probabilistic_exposure'] == -1