Merge branch 'feature/p_one_infected' into 'master'

Probability that one individual is infected

See merge request cara/caimira!316

caimira/apps/calculator/__init__.py

@@ -33,7 +33,7 @@
 # calculator version. If the calculator needs to make breaking changes (e.g. change
 # form attributes) then it can also increase its MAJOR version without needing to
 # increase the overall CAiMIRA version (found at ``caimira.__version__``).
-__version__ = "4.3"
+__version__ = "4.4"
 
 
 class BaseRequestHandler(RequestHandler):

caimira/apps/calculator/model_generator.py

@@ -57,6 +57,10 @@ class FormData:
     location_name: str
     location_latitude: float
     location_longitude: float
+    geographic_population: int
+    geographic_cases: int
+    ascertainment_bias: str
+    exposure_option: str
     mask_type: str
     mask_wearing_option: str
     mechanical_ventilation_type: str
@@ -110,12 +114,16 @@ class FormData:
         'infected_lunch_finish': '13:30',
         'infected_lunch_option': True,
         'infected_lunch_start': '12:30',
-        'infected_people': _NO_DEFAULT,
+        'infected_people': 1,
         'infected_start': '08:30',
         'inside_temp': _NO_DEFAULT,
         'location_latitude': _NO_DEFAULT,
         'location_longitude': _NO_DEFAULT,
         'location_name': _NO_DEFAULT,
+        'geographic_population': 0,
+        'geographic_cases': 0,
+        'ascertainment_bias': 'confidence_low',
+        'exposure_option': 'p_deterministic_exposure',
         'mask_type': 'Type I',
         'mask_wearing_option': 'mask_off',
         'mechanical_ventilation_type': 'not-applicable',
@@ -261,7 +269,9 @@ def get_activity_mins(population):
                              ('volume_type', VOLUME_TYPES),
                              ('window_opening_regime', WINDOWS_OPENING_REGIMES),
                              ('window_type', WINDOWS_TYPES),
-                             ('event_month', MONTH_NAMES)]
+                             ('event_month', MONTH_NAMES),
+                             ('ascertainment_bias', CONFIDENCE_LEVEL_OPTIONS),]
+
         for attr_name, valid_set in validation_tuples:
             if getattr(self, attr_name) not in valid_set:
                 raise ValueError(f"{getattr(self, attr_name)} is not a valid value for {attr_name}")
@@ -329,6 +339,11 @@ def build_mc_model(self) -> mc.ExposureModel:
             ),
             short_range = tuple(short_range),
             exposed=self.exposed_population(),
+            geographical_data=mc.Cases(
+                geographic_population=self.geographic_population,
+                geographic_cases=self.geographic_cases,
+                ascertainment_bias=CONFIDENCE_LEVEL_OPTIONS[self.ascertainment_bias],
+            ), 
         )
 
     def build_model(self, sample_size=_DEFAULT_MC_SAMPLE_SIZE) -> models.ExposureModel:
@@ -477,6 +492,7 @@ def infected_population(self) -> mc.InfectedPopulation:
             'callcentre': ('Seated', 'Speaking'),
             'library': ('Seated', 'Breathing'),
             'training': ('Standing', 'Speaking'),
+            'training_attendee': ('Seated', 'Breathing'),
             'lab': (
                 'Light activity',
                 #Model 1/2 of time spent speaking in a lab.
@@ -515,6 +531,7 @@ def exposed_population(self) -> mc.Population:
             'callcentre': 'Seated',
             'library': 'Seated',
             'training': 'Seated',
+            'training_attendee': 'Seated',
             'workshop': 'Moderate activity',
             'lab':'Light activity',
             'gym':'Heavy exercise',
@@ -759,6 +776,9 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]:
         'location_latitude': 46.20833,
         'location_longitude': 6.14275,
         'location_name': 'Geneva',
+        'geographic_population': 0,
+        'geographic_cases': 0,
+        'ascertainment_bias': 'confidence_low',
         'mask_type': 'Type I',
         'mask_wearing_option': 'mask_off',
         'mechanical_ventilation_type': '',
@@ -785,7 +805,7 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]:
     }
 
 
-ACTIVITY_TYPES = {'office', 'smallmeeting', 'largemeeting', 'training', 'callcentre', 'controlroom-day', 'controlroom-night', 'library', 'workshop', 'lab', 'gym'}
+ACTIVITY_TYPES = {'office', 'smallmeeting', 'largemeeting', 'training', 'training_attendee', 'callcentre', 'controlroom-day', 'controlroom-night', 'library', 'workshop', 'lab', 'gym'}
 MECHANICAL_VENTILATION_TYPES = {'mech_type_air_changes', 'mech_type_air_supply', 'not-applicable'}
 MASK_TYPES = {'Type I', 'FFP2'}
 MASK_WEARING_OPTIONS = {'mask_on', 'mask_off'}
@@ -794,9 +814,8 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]:
 VOLUME_TYPES = {'room_volume_explicit', 'room_volume_from_dimensions'}
 WINDOWS_OPENING_REGIMES = {'windows_open_permanently', 'windows_open_periodically', 'not-applicable'}
 WINDOWS_TYPES = {'window_sliding', 'window_hinged', 'not-applicable'}
-
 COFFEE_OPTIONS_INT = {'coffee_break_0': 0, 'coffee_break_1': 1, 'coffee_break_2': 2, 'coffee_break_4': 4}
-
+CONFIDENCE_LEVEL_OPTIONS = {'confidence_low': 10, 'confidence_medium': 5, 'confidence_high': 2}
 MONTH_NAMES = [
     'January', 'February', 'March', 'April', 'May', 'June', 'July',
     'August', 'September', 'October', 'November', 'December',

caimira/apps/calculator/report_generator.py

@@ -131,6 +131,7 @@ def calculate_report_data(form: FormData, model: models.ExposureModel) -> typing
     ])
 
     prob = np.array(model.infection_probability()).mean()
+    prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean()
     er = np.array(model.concentration_model.infected.emission_rate_when_present()).mean()
     exposed_occupants = model.exposed.number
     expected_new_cases = np.array(model.expected_new_cases()).mean()
@@ -147,6 +148,7 @@ def calculate_report_data(form: FormData, model: models.ExposureModel) -> typing
         "cumulative_doses": list(cumulative_doses),
         "long_range_cumulative_doses": list(long_range_cumulative_doses),
         "prob_inf": prob,
+        "prob_probabilistic_exposure": prob_probabilistic_exposure,
         "emission_rate": er,
         "exposed_occupants": exposed_occupants,
         "expected_new_cases": expected_new_cases,
@@ -272,8 +274,13 @@ def manufacture_alternative_scenarios(form: FormData) -> typing.Dict[str, mc.Exp
     return scenarios
 
 
-def scenario_statistics(mc_model: mc.ExposureModel, sample_times: typing.List[float]):
+def scenario_statistics(mc_model: mc.ExposureModel, sample_times: typing.List[float], compute_prob_exposure: bool):
     model = mc_model.build_model(size=_DEFAULT_MC_SAMPLE_SIZE)
+    if (compute_prob_exposure):
+        # It means we have data to calculate the total_probability_rule
+        prob_probabilistic_exposure = model.total_probability_rule()
+    else:
+        prob_probabilistic_exposure = 0.
 
     return {
         'probability_of_infection': np.mean(model.infection_probability()),
@@ -282,6 +289,7 @@ def scenario_statistics(mc_model: mc.ExposureModel, sample_times: typing.List[fl
             np.mean(model.concentration(time))
             for time in sample_times
         ],
+        'prob_probabilistic_exposure': prob_probabilistic_exposure,
     }
 
 
@@ -303,11 +311,17 @@ def comparison_report(
     else:
         statistics = {}
 
+    if (form.short_range_option == "short_range_yes" and form.exposure_option == "p_probabilistic_exposure"):
+        compute_prob_exposure = True
+    else:
+        compute_prob_exposure = False
+
     with executor_factory() as executor:
         results = executor.map(
             scenario_statistics,
             scenarios.values(),
             [sample_times] * len(scenarios),
+            [compute_prob_exposure] * len(scenarios),
             timeout=60,
         )
 

caimira/apps/calculator/static/css/form.css

@@ -113,4 +113,4 @@
   transition-delay: 0.5s; /* Starting after the grow effect */
   transition-duration: 0.2s;
   transform: translateX(-50%) scaleY(1);
-}
+}

caimira/apps/calculator/static/js/form.js

@@ -61,6 +61,14 @@ function require_fields(obj) {
     case "hepa_no":
       require_hepa(false);
       break;
+    case "p_probabilistic_exposure":
+      require_population(true);
+      require_infected(false);
+      break;
+    case "p_deterministic_exposure":
+      require_population(false);
+      require_infected(true);
+      break;
     case "mask_on":
       require_mask(true);
       break;
@@ -172,6 +180,16 @@ function require_lunch(id, option) {
   }
 }
 
+function require_population(option) {
+  require_input_field("#geographic_population", option);
+  require_input_field("#geographic_cases", option);
+  require_input_field("#ascertainment_bias", option);
+}
+
+function require_infected(option) {
+  require_input_field("#infected_people", option);
+}
+
 function require_mask(option) {
   $("#mask_type_1").prop('required', option);
   $("#mask_type_ffp2").prop('required', option);
@@ -269,6 +287,23 @@ function on_hepa_option_change() {
   })
 }
 
+function on_exposure_change() {
+  p_recurrent = $('input[type=radio][name=exposure_option]')
+  p_recurrent.each(function (index) {
+    if (this.checked) {
+      getChildElement($(this)).show();
+      require_fields(this);
+    }
+    else {
+      getChildElement($(this)).hide();
+      unrequire_fields(this);
+
+      //Clear invalid inputs for this newly hidden child element
+      removeInvalid("#"+getChildElement($(this)).find('input').not('input[type=radio]').attr('id'));
+    }
+  })
+}
+
 function on_wearing_mask_change() {
   wearing_mask = $('input[type=radio][name=mask_wearing_option]')
   wearing_mask.each(function (index) {
@@ -538,6 +573,20 @@ function validate_form(form) {
     }
   }
 
+  // Validate cases < population
+  if ($("#p_probabilistic_exposure").prop('checked')) {
+    // Set number of infected people as 1
+    $("#infected_people").val(1);
+    var geographicPopulationObj = document.getElementById("geographic_population");
+    var geographicCasesObj = document.getElementById("geographic_cases");
+    removeErrorFor(geographicCasesObj);
+
+    if (parseInt(geographicPopulationObj.value) < parseInt(geographicCasesObj.value)) {
+      insertErrorFor(geographicCasesObj, "Cases > Population");
+      submit = false;
+    }
+  }
+
   // Generate the short-range interactions list
   var short_range_interactions = [];
   $(".form_field_outer_row").each(function (index, element){
@@ -870,6 +919,12 @@ $(document).ready(function () {
   // Call the function now to handle forward/back button presses in the browser.
   on_hepa_option_change();
 
+  // When the exposure_option changes we want to make its respective
+  // children show/hide.
+  $("input[type=radio][name=exposure_option]").change(on_exposure_change);
+  // Call the function now to handle forward/back button presses in the browser.
+  on_exposure_change();
+
   // When the mask_wearing_option changes we want to make its respective
   // children show/hide.
   $("input[type=radio][name=mask_wearing_option]").change(on_wearing_mask_change);

caimira/apps/expert.py

@@ -847,6 +847,7 @@ def present(self):
         mask=models.Mask.types['No mask'],
         host_immunity=0.,
     ),
+    geographical_data=models.Cases(),
 )
 
 

caimira/apps/static/css/style.css

@@ -276,6 +276,10 @@ footer img {
     display: inline!important;
   }
 
+  #event_data_tooltip:before{
+    max-width: 350px!important;
+  }
+
 }
 
 @media (max-width: 40em) {

caimira/apps/templates/base/calculator.form.html.j2

@@ -303,7 +303,9 @@
 
     <!-- Event Options -->
     <b>Event data:</b>
-    <div data-tooltip="The total no. of occupants in the room and how many of them you assume are infected.">
+    <div id="event_data_tooltip" data-tooltip="The total no. of occupants in the room. 
+    Deterministic exposure: add no. occupants that are infected.
+    Probabilistic exposure: event at a given time & location (e.g. meeting or conference), considering the incidence rate in that area.">
         <span class="tooltip_text">?</span>
     </div><br>
 
@@ -312,11 +314,44 @@
       <div class="col-sm-6 align-self-center"><input type="number" id="total_people" class="form-control" name="total_people" placeholder="Number" min=1 required></div>
     </div>
 
-    <div class="form-group row">
-      <div class="col-sm-4" style="top: -2px"><label>Number of infected people: </label></div>
-      <div class="col-sm-6"><input type="number" id="infected_people" class="form-control" name="infected_people" min=1 value=1 required></div>
+    <div class="form-group mb-1">
+    <input type="radio" id="p_deterministic_exposure" name="exposure_option" value="p_deterministic_exposure" checked="checked" data-enables="#DIVp_deterministic_exposure">
+      <label for="p_deterministic_exposure">Deterministic exposure</label>
+    </div>
+    <div class="form-group">
+    <input type="radio" id="p_probabilistic_exposure"  name="exposure_option" value="p_probabilistic_exposure" data-enables="#DIVp_probabilistic_exposure">
+      <label for="p_probabilistic_exposure">Probabilistic exposure (incidence rate)</label>
+    </div>
+
+    <div id="DIVp_deterministic_exposure" class="tabbed" style="display: none">
+      <div class="form-group row">
+        <div class="col-sm-4"><label class="col-form-label">Number of infected people: </label></div>
+        <div class="col-sm-6 pl-0 align-self-center"><input type="number" id="infected_people" class="form-control" name="infected_people" min=1 value=1></div>
+      </div>
+    </div>
+
+    <div id="DIVp_probabilistic_exposure" class="tabbed" style="display: none">
+      <div class="form-group row">
+        <div class="col-sm-4"><label class="col-form-label">Population:</label></div>
+        <div class="col-sm-6 pl-0 align-self-center"><input type="number" step="any" id="geographic_population" class="non_zero form-control" name="geographic_population" placeholder="Inhabitants (#)" min="0"></div>
+      </div>
+      <div class="form-group row">
+        <div class="col-sm-4"><label class="col-form-label">New confirmed cases (weekly):</label></div>
+        <div class="col-sm-6 pl-0 align-self-center"><input type="number" step="any" id="geographic_cases" class="non_zero form-control" name="geographic_cases" placeholder="Cases (#7-day rolling avg)" min="0"></div>
+      </div>
+      <div class="form-group row">
+      <div class="col-sm-4"><label class="col-form-label">Confidence level:</label></div>
+      <div class="col-sm-6 pl-0 align-self-center">
+        <select id="ascertainment_bias" name="ascertainment_bias" class="form-control">
+          <option value="confidence_low">Low - surveillance only for sympotmatic patients</option>
+          <option value="confidence_medium">Medium - recommended population wide surveillance</option>
+          <option value="confidence_high">High - mandatory population wide surveillance</option>
+        </select>
+      </div>
+      </div>
     </div>
 
+    <span id="training_limit_error" class="red_text" hidden>Conference/Training activities limited to 1 infected<br></span>
     <hr width="80%">
 
     <div class="form-group row">
@@ -332,7 +367,8 @@
         <option value="library">Library</option>
         <option value="lab">Laboratory</option>
         <option value="workshop">Workshop</option>
-        <option value="training">Conference/Training</option>
+        <option value="training">Conference/Training (speaker infected)</option>
+        <option value="training_attendee">Conference/Training (attendee infected)</option>
         <option value="gym">Gym</option>
       </select>
     </div>
@@ -615,8 +651,9 @@
     <li>Library = all seated, no talking, just breathing,</li>
     <li>Laboratory = light physical activity, talking 50% of the time,</li>
     <li>Workshop = moderate physical activity, talking 50% of the time,</li>
-    <li>Conference/Training = speaker/trainer standing and talking, rest seated and talking quietly.
+    <li>Conference/Training (speaker infected) = speaker/trainer standing and talking, rest seated and talking quietly.
     Speaker/Trainer assumed infected (worst case scenario),</li>
+    <li>Conference/Training (attendee infected) = someone in the audience is infected, all are seated and breathing.</li>
     <li>Gym = heavy exercise, no talking, just breathing.</li>
   </ul>
   <b>Activity breaks:</b><br>