New analysis functionality for the maternal and newborn health modules (intervention analysis) (#1531)

Co-authored-by: Tim Hallett <[email protected]>

Author: joehcollins

resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking/main.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:5ed51ce9c98bd7c9203894d14c40d6311d4f1ed27259651e597d45731b2170ac
-size 10804
+oid sha256:254e87bdc9b5839dee01df0477d468f7373c2208f5bee8b07f15cd6991a2559e
+size 10776

resources/ResourceFile_LabourSkilledBirthAttendance/parameter_values.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:be621298177fff272051d8b519dd890f812c427603f24e70a66386e528157047
-size 11243
+oid sha256:572e3e4f91cdbf0aa74360233e0a8478dfb70aa545aa477c112ee1175ca1597d
+size 10058

resources/ResourceFile_PregnancySupervisor/parameter_values.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:702d26f19582a9fc603265da9f0b61f89fede8aa3582ab8cee551cf4109a49b1
-size 12966
+oid sha256:b4d6e0147ff710cc5eedd4882ec5db84ecdca4f76938617cace8e44a12d4f9d5
+size 13738

src/tlo/methods/care_of_women_during_pregnancy.py

@@ -900,8 +900,11 @@ def kangaroo_mother_care(self, hsi_event):
         if (df.at[person_id, 'nb_low_birth_weight_status'] != 'normal_birth_weight') or \
            (df.at[person_id, 'nb_low_birth_weight_status'] != 'macrosomia'):
 
+            kmc_delivered = pregnancy_helper_functions.check_int_deliverable(
+            self, int_name='kmc', hsi_event=hsi_event, q_param=[params['prob_kmc_available']])
+
             # Check KMC can be delivered
-            if self.rng.random_sample() < params['prob_kmc_available']:
+            if kmc_delivered:
                 # Store treatment as a property of the newborn used to apply treatment effect
                 df.at[person_id, 'nb_kangaroo_mother_care'] = True
 
@@ -952,42 +955,38 @@ def assessment_and_treatment_newborn_sepsis(self, hsi_event, facility_type):
         """
         df = self.sim.population.props
         person_id = int(hsi_event.target)
+        l_params = self.sim.modules['Labour'].current_parameters
+        pnc_location = 'hc' if facility_type == '1a' else 'hp'
 
         # We assume that only hospitals are able to deliver full supportive care for neonatal sepsis, full supportive
         # care evokes a stronger treatment effect than injectable antibiotics alone
 
         if df.at[person_id, 'nb_early_onset_neonatal_sepsis'] or df.at[person_id, 'pn_sepsis_late_neonatal'] or\
            df.at[person_id, 'pn_sepsis_early_neonatal']:
 
-            # Run HCW check
-            sf_check = pregnancy_helper_functions.check_emonc_signal_function_will_run(self.sim.modules['Labour'],
-                                                                                       sf='iv_abx',
-                                                                                       hsi_event=hsi_event)
             if facility_type != '1a':
 
-                # check consumables
-                avail = pregnancy_helper_functions.return_cons_avail(
-                    self, hsi_event,
+                neo_sepsis_treatment_delivered = pregnancy_helper_functions.check_int_deliverable(
+                    self, int_name='neo_sepsis_treatment_supp_care', hsi_event=hsi_event,
+                    q_param=[l_params['prob_hcw_avail_iv_abx'], l_params[f'mean_hcw_competence_{pnc_location}']],
                     cons=self.item_codes_nb_consumables['sepsis_supportive_care_core'],
-                    opt_cons=self.item_codes_nb_consumables['sepsis_supportive_care_optional'])
+                    opt_cons=self.item_codes_nb_consumables['sepsis_supportive_care_optional'],
+                    equipment={'Drip stand', 'Infusion pump'})
 
-                # Then, if the consumables are available, treatment for sepsis is delivered
-                if avail and sf_check:
+                if neo_sepsis_treatment_delivered:
                     df.at[person_id, 'nb_supp_care_neonatal_sepsis'] = True
-                    pregnancy_helper_functions.log_met_need(self, 'neo_sep_supportive_care', hsi_event)
-                    hsi_event.add_equipment({'Drip stand', 'Infusion pump'})
 
             # The same pattern is then followed for health centre care
             else:
-                avail = pregnancy_helper_functions.return_cons_avail(
-                    self, hsi_event,
+                neo_sepsis_treatment_delivered = pregnancy_helper_functions.check_int_deliverable(
+                    self, int_name='neo_sepsis_treatment_abx', hsi_event=hsi_event,
+                    q_param=[l_params['prob_hcw_avail_iv_abx'], l_params[f'mean_hcw_competence_{pnc_location}']],
                     cons=self.item_codes_nb_consumables['sepsis_abx'],
-                    opt_cons=self.item_codes_nb_consumables['iv_drug_equipment'])
+                    opt_cons=self.item_codes_nb_consumables['iv_drug_equipment'],
+                    equipment={'Drip stand', 'Infusion pump'})
 
-                if avail and sf_check:
+                if neo_sepsis_treatment_delivered:
                     df.at[person_id, 'nb_inj_abx_neonatal_sepsis'] = True
-                    pregnancy_helper_functions.log_met_need(self, 'neo_sep_abx', hsi_event)
-                    hsi_event.add_equipment({'Drip stand', 'Infusion pump', 'Oxygen cylinder, with regulator'})
 
     def link_twins(self, child_one, child_two, mother_id):
         """

src/tlo/methods/labour.py

@@ -656,7 +656,7 @@ def log_new_progressed_cases(disease):
             del self.sim.modules['PregnancySupervisor'].mother_and_newborn_info[person]
 
         # ----------------------------------------- CARE SEEKING ------------------------------------------------------
-        # We now use the the pn_emergency_event_mother property that has just been set for women who are experiencing
+        # We now use the pn_emergency_event_mother property that has just been set for women who are experiencing
         # severe complications to select a subset of women who may choose to seek care
         can_seek_care = df.loc[df['is_alive'] & df['la_is_postpartum'] & (df['pn_postnatal_period_in_weeks'] == week) &
                                df['pn_emergency_event_mother'] & ~df['hs_is_inpatient']]