introduce the probability of checking and correct diagnosis for a stu…

…nted person to calibrate the use of U5Malnutr appointment (#831)

src/tlo/methods/stunting.py

@@ -120,6 +120,11 @@ class Stunting(Module):
         'effectiveness_of_food_supplementation_in_stunting_reduction': Parameter(
             Types.REAL,
             'Probability of stunting being reduced by one standard deviation (category) by supplementary feeding.'),
+
+        # The probability of a (severe) stunting person being checked and correctly diagnosed
+        'prob_stunting_diagnosed_at_generic_appt': Parameter(
+            Types.REAL,
+            'Probability of a stunted or severely stunted person being checked and correctly diagnosed'),
     }
 
     PROPERTIES = {
@@ -274,15 +279,17 @@ def do_routine_assessment_for_chronic_undernutrition(self, person_id):
         df = self.sim.population.props
         person = df.loc[person_id]
         is_stunted = person.un_HAZ_category in ('HAZ<-3', '-3<=HAZ<-2')
+        p_stunting_diagnosed = self.parameters['prob_stunting_diagnosed_at_generic_appt']
 
         if not is_stunted:
             return
 
-        # Schedule the HSI for provision of treatment
-        self.sim.modules['HealthSystem'].schedule_hsi_event(
-            hsi_event=HSI_Stunting_ComplementaryFeeding(module=self, person_id=person_id),
-            priority=2,  # <-- lower priority that for wasting and most other HSI
-            topen=self.sim.date)
+        # Schedule the HSI for provision of treatment based on the probability of stunting diagnosis
+        if p_stunting_diagnosed > self.rng.random_sample():
+            self.sim.modules['HealthSystem'].schedule_hsi_event(
+                hsi_event=HSI_Stunting_ComplementaryFeeding(module=self, person_id=person_id),
+                priority=2,  # <-- lower priority that for wasting and most other HSI
+                topen=self.sim.date)
 
     def do_treatment(self, person_id, prob_success):
         """Represent the treatment with supplementary feeding. If treatment is successful, effect the recovery

tests/test_stunting.py

@@ -221,9 +221,9 @@ def test_polling_event_progression(seed):
     assert (df.loc[df.is_alive & (df.age_years >= 5), 'un_HAZ_category'] == 'HAZ>=-2').all()
 
 
-def test_routine_assessment_for_chronic_undernutrition_if_stunted(seed):
+def test_routine_assessment_for_chronic_undernutrition_if_stunted_and_correctly_diagnosed(seed):
     """Check that a call to `do_routine_assessment_for_chronic_undernutrition` can lead to immediate recovery for a
-    stunted child (via an HSI)."""
+    stunted child (via an HSI), if there is checking and correct diagnosis."""
     popsize = 100
     sim = get_sim(seed)
     sim.make_initial_population(n=popsize)
@@ -237,6 +237,9 @@ def test_routine_assessment_for_chronic_undernutrition_if_stunted(seed):
     df.loc[person_id, 'age_exact_year'] = 2.0
     df.loc[person_id, 'un_HAZ_category'] = '-3<=HAZ<-2'
 
+    # Make the probability of stunting checking/diagnosis as 1.0
+    sim.modules['Stunting'].parameters['prob_stunting_diagnosed_at_generic_appt'] = 1.0
+
     # Subject the person to `do_routine_assessment_for_chronic_undernutrition`
     sim.modules['Stunting'].do_routine_assessment_for_chronic_undernutrition(person_id=person_id)
 
@@ -281,6 +284,41 @@ def test_routine_assessment_for_chronic_undernutrition_if_stunted(seed):
     ]
 
 
+def test_routine_assessment_for_chronic_undernutrition_if_stunted_but_no_checking(seed):
+    """Check that a call to `do_routine_assessment_for_chronic_undernutrition` does not lead to an HSI for a stunted
+    child, if there is no checking/diagnosis."""
+    popsize = 100
+    sim = get_sim(seed)
+    sim.make_initial_population(n=popsize)
+    sim.simulate(end_date=sim.start_date)
+    sim.modules['HealthSystem'].reset_queue()
+
+    # Make one person have severe stunting
+    df = sim.population.props
+    person_id = 0
+    df.loc[person_id, 'age_years'] = 2
+    df.loc[person_id, 'age_exact_year'] = 2.0
+    df.loc[person_id, 'un_HAZ_category'] = 'HAZ<-3'
+
+    # Make the probability of stunting checking/diagnosis as 0.0
+    sim.modules['Stunting'].parameters['prob_stunting_diagnosed_at_generic_appt'] = 0.0
+
+    # Subject the person to `do_routine_assessment_for_chronic_undernutrition`
+    sim.modules['Stunting'].do_routine_assessment_for_chronic_undernutrition(person_id=person_id)
+
+    # Check that there is no HSI scheduled for this person
+    hsi_event_scheduled = [ev[1] for ev in sim.modules['HealthSystem'].find_events_for_person(person_id) if
+                           isinstance(ev[1], HSI_Stunting_ComplementaryFeeding)]
+    assert 0 == len(hsi_event_scheduled)
+
+    # Then make the probability of stunting checking/diagnosis as 1.0 and check the HSI is scheduled for this person
+    sim.modules['Stunting'].parameters['prob_stunting_diagnosed_at_generic_appt'] = 1.0
+    sim.modules['Stunting'].do_routine_assessment_for_chronic_undernutrition(person_id=person_id)
+    hsi_event_scheduled = [ev[1] for ev in sim.modules['HealthSystem'].find_events_for_person(person_id) if
+                           isinstance(ev[1], HSI_Stunting_ComplementaryFeeding)]
+    assert 1 == len(hsi_event_scheduled)
+
+
 def test_routine_assessment_for_chronic_undernutrition_if_not_stunted(seed):
     """Check that a call to `do_routine_assessment_for_chronic_undernutrition` does not lead to an HSI if there is no
     stunting."""
@@ -300,7 +338,7 @@ def test_routine_assessment_for_chronic_undernutrition_if_not_stunted(seed):
     # Subject the person to `do_routine_assessment_for_chronic_undernutrition`
     sim.modules['Stunting'].do_routine_assessment_for_chronic_undernutrition(person_id=person_id)
 
-    # Check that there is an HSI scheduled for this person
+    # Check that there is no HSI scheduled for this person
     hsi_event_scheduled = [ev[1] for ev in sim.modules['HealthSystem'].find_events_for_person(person_id) if
                            isinstance(ev[1], HSI_Stunting_ComplementaryFeeding)]
     assert 0 == len(hsi_event_scheduled)