More tests and consumables for CMD (#1625)

thewati · upile-n · Precious29-web · web-flow · commit 3aafb7384bd6 · 2025-12-08T13:19:23.000Z
* Initial Changes

* Initial Changes

* fix errors

* Addressing comments

* Fix condition error

* fix errors

* fix errors

* creating_HSI

* Haemodialysis_Refill priority

* Haemodialysis_Refill HSI

* capitalise

* Dialysis_Refill HSI fix errors

* Dialysis_Refill HSI fix errors

* resolving conflicts

* resolving conflicts 2.0

* fix errors

* Fix files from Schisto merge and nc_hypertension error

* Add equipment for dialysis refill HSI

* Added HSI Dialysis Refill Logic

* Rollback diabetes logic

* Add counter for total dialysis sessions in lifetime

* Edit Priority Ranking

* change ckd_total_dialysis_sessions to INT

* Addressing comments

* reduce line length

* Dialysis Upgrade

* Dialysis Update

* remove comment

* remove num_sessions counter since never used

* roll baxk change to equipmnet

* isolate change to consumables to single added line

* reorder so that CDM HSI are all together

* update priority codes to match other for CDM

* roll back irrelevant changes to isolate importnat change, and update 'cat' to match extant file

* roll back change to test file that seems unneccessary

* remove comment and roll back incidental changes

* roll back incidental changes

* properties need to be filled in at birht too.

* reschedule self rather than creating new events

* remove weekly counter and simplify logic (the weekly counter would not be reliable if an HSI event did not run). I couldn't see the point of it!??

* if the HSI is not run, let the chain of attempted HSI continue.

* addressing comments

* addressing comments

* reformat comments

* reformat comments

* drop whitespace

---------

Co-authored-by: upile-n &lt;upilen10@gmail.com&gt;
Co-authored-by: Precious29-web &lt;pchibwe@kuhes.ac.mw&gt;
Co-authored-by: Tim Hallett &lt;39991060+tbhallett@users.noreply.github.com&gt;
diff --git a/resources/cmd/ResourceFile_cmd_condition_hsi/chronic_kidney_disease.csv b/resources/cmd/ResourceFile_cmd_condition_hsi/chronic_kidney_disease.csv
@@ -1,3 +1,3 @@
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diff --git a/resources/cmd/ResourceFile_cmd_condition_hsi/diabetes.csv b/resources/cmd/ResourceFile_cmd_condition_hsi/diabetes.csv
@@ -1,3 +1,3 @@
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diff --git a/resources/cmd/ResourceFile_cmd_parameters.csv b/resources/cmd/ResourceFile_cmd_parameters.csv
@@ -1,3 +1,3 @@
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diff --git a/resources/healthsystem/consumables/ResourceFile_Consumables_Items_and_Packages.csv b/resources/healthsystem/consumables/ResourceFile_Consumables_Items_and_Packages.csv
@@ -1,3 +1,3 @@
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diff --git a/resources/healthsystem/human_resources/clinics/ResourceFile_ClinicConfigurations/Default.csv b/resources/healthsystem/human_resources/clinics/ResourceFile_ClinicConfigurations/Default.csv
@@ -1 +1,3 @@
-Facility_ID,Officer_Type_Code,GenericClinic
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/CVD.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/CVD.csv
@@ -1,3 +1,3 @@
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/ClinicallyVulnerable.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/ClinicallyVulnerable.csv
@@ -1,3 +1,3 @@
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Default.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Default.csv
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/EHP_III.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/EHP_III.csv
@@ -1,3 +1,3 @@
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/LCOA_EHP.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/LCOA_EHP.csv
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Naive.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Naive.csv
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/RMNCH.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/RMNCH.csv
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test Mode 1.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test Mode 1.csv
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test.csv
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diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/VerticalProgrammes.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/VerticalProgrammes.csv
@@ -1,3 +1,3 @@
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diff --git a/src/scripts/data_file_processing/healthsystem/consumables/processing_data_from_one_health/generate_consumables_item_codes_and_packages.py b/src/scripts/data_file_processing/healthsystem/consumables/processing_data_from_one_health/generate_consumables_item_codes_and_packages.py
@@ -376,6 +376,16 @@ def add_record(df: pd.DataFrame, record: Dict):
     'Unit_Cost': np.nan},
 )
 
+cons = add_record(
+    cons, {
+        'Intervention_Cat': "Added by UN",
+        'Intervention_Pkg': "Misc",
+        'Intervention_Pkg_Code': -99,
+        'Items': "Haemodialysis dialysate flow of 500 ml/min",
+        'Item_Code': 282,
+        'Expected_Units_Per_Case': 1.0,
+        'Unit_Cost': 200},
+)
 
 # --------------
 # --------------
diff --git a/src/tlo/methods/cardio_metabolic_disorders.py b/src/tlo/methods/cardio_metabolic_disorders.py
@@ -149,7 +149,9 @@ class CardioMetabolicDisorders(Module, GenericFirstAppointmentsMixin):
         **hsi_events_param_dicts, **initial_prev_param_dicts, **other_params_dict,
         'prob_care_provided_given_seek_emergency_care': Parameter(
             Types.REAL, "The probability that correct care is fully provided to persons that have sought emergency care"
-                        " for a Cardio-metabolic disorder.")
+                        " for a Cardio-metabolic disorder."),
+        'prob_ckd_patient_gets_dialysis': Parameter(
+            Types.REAL, "The probability that patient with ckd has disease progression ultimately needing dialysis")
     }
 
     # Convert conditions and events to dicts and merge together into PROPERTIES
@@ -210,7 +212,9 @@ class CardioMetabolicDisorders(Module, GenericFirstAppointmentsMixin):
                                                             'treatment'),
                   'nc_weight_loss_worked': Property(Types.BOOL,
                                                     'whether or not weight loss treatment worked'),
-                  'nc_risk_score': Property(Types.INT, 'score to represent number of risk conditions the person has')
+                  'nc_risk_score': Property(Types.INT, 'score to represent number of risk conditions the person has'),
+                  'nc_ckd_total_dialysis_sessions': Property(Types.INT,
+                                                          'total number of dialysis sessions the person has ever had'),
                   }
 
     def __init__(self, name=None, do_log_df: bool = False, do_condition_combos: bool = False):
@@ -426,7 +430,6 @@ def sample_eligible_treatment_success(_filter, _p, _condition):
             sample_eligible_treatment_success(on_med, p_treatment_works, condition)
 
             # ----- Impose the symptom on random sample of those with each condition to have:
-            # TODO: @britta make linear model data-specific and add in needed complexity
             for symptom in self.prob_symptoms[condition].keys():
                 lm_init_symptoms = LinearModel(
                     LinearModelType.MULTIPLICATIVE,
@@ -462,6 +465,7 @@ def sample_eligible_treatment_success(_filter, _p, _condition):
         # ----- Set all other parameters to False / NaT
         df.loc[df.is_alive, 'nc_ever_weight_loss_treatment'] = False
         df.loc[df.is_alive, 'nc_weight_loss_worked'] = False
+        df.loc[df.is_alive, 'nc_ckd_total_dialysis_sessions'] = 0
 
     def initialise_simulation(self, sim):
         """Schedule:
@@ -749,6 +753,7 @@ def on_birth(self, mother_id, child_id):
             df.at[child_id, f'nc_{event}_scheduled_date_death'] = pd.NaT
             df.at[child_id, f'nc_{event}_medication_prevents_death'] = False
         df.at[child_id, 'nc_risk_score'] = 0
+        df.at[child_id, 'nc_ckd_total_dialysis_sessions'] = 0
 
     def update_risk_score(self):
         """
@@ -1362,7 +1367,8 @@ def proportion_of_something_in_a_groupby_ready_for_logging(_df, something, group
                     {'count': x['nc_n_conditions'].count()}))
                 n_comorbidities_all.loc[:, num] = col['count']
 
-            prop_comorbidities_all = n_comorbidities_all.div(n_comorbidities_all.sum(axis=1), axis=0)
+            row_sums = n_comorbidities_all.sum(axis=1)
+            prop_comorbidities_all = n_comorbidities_all.div(row_sums.where(row_sums != 0), axis=0).fillna(0)
 
             logger.info(key='mm_prevalence_by_age_all',
                         description='annual summary of multi-morbidities by age for all',
@@ -1588,9 +1594,8 @@ def __init__(self, module, person_id, condition):
 
         self.TREATMENT_ID = 'CardioMetabolicDisorders_Prevention_WeightLoss'
         self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({'Over5OPD': 1})
-        self.ACCEPTED_FACILITY_LEVEL = '1b'
-
         self.condition = condition
+        self.ACCEPTED_FACILITY_LEVEL = '3' if condition == 'chronic_kidney_disease' else '1b'
 
     def apply(self, person_id, squeeze_factor):
 
@@ -1617,9 +1622,10 @@ def apply(self, person_id, squeeze_factor):
         # Monthly doses of medications as follows. Diabetes - 1000mg metformin daily (1000*30.5),
         # hypertension - 25mg hydrochlorothiazide daily (25*30.5), CKD 1 dialysis bag (estimate),
         # lower back pain - 2400mg aspirin daily  (2400*30.5), CIHD - 75mg aspirin daily (75*30.5)
+        #todo adjust the dosages for diabetes second and third dosage
         dose = {'diabetes': 30_500,
                 'hypertension': 610,
-                'chronic_kidney_disease': 1,
+                'chronic_kidney_disease': 12,  # 8 in a month: dialysis two times a week
                 'chronic_lower_back_pain': 73_200,
                 'chronic_ischemic_hd': 2288,
                 'ever_stroke': 2288,
@@ -1643,6 +1649,19 @@ def apply(self, person_id, squeeze_factor):
                 topen=self.sim.date + DateOffset(months=1),
                 tclose=self.sim.date + DateOffset(months=1) + DateOffset(days=7)
             )
+            # Schedule dialysis refill for those with chronic_kidney_disease and start
+            # scheduling immediately, if possible
+            if self.condition == "chronic_kidney_disease":
+                if self.module.rng.random_sample() < self.module.parameters["prob_ckd_patient_gets_dialysis"]:
+                    self.sim.modules["HealthSystem"].schedule_hsi_event(
+                        hsi_event=HSI_CardioMetabolicDisorders_Dialysis_Refill(
+                            module=self.module,
+                            person_id=person_id
+                        ),
+                        priority=1,
+                        topen=self.sim.date,
+                        tclose=self.sim.date + pd.DateOffset(days=1)
+                    )
         else:
             # If person 'decides to' seek another appointment, schedule a new HSI appointment for tomorrow.
             # NB. With a probability of 1.0, this will keep occurring, and the person will never give up coming back to
@@ -1671,9 +1690,8 @@ def __init__(self, module, person_id, condition):
 
         self.TREATMENT_ID = 'CardioMetabolicDisorders_Treatment'
         self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({'Over5OPD': 1})
-        self.ACCEPTED_FACILITY_LEVEL = '1b'
-
         self.condition = condition
+        self.ACCEPTED_FACILITY_LEVEL = '3' if condition == 'chronic_kidney_disease' else '1b'
 
     def apply(self, person_id, squeeze_factor):
         df = self.sim.population.props
@@ -1696,16 +1714,19 @@ def apply(self, person_id, squeeze_factor):
             return self.sim.modules['HealthSystem'].get_blank_appt_footprint()
 
         # Monthly doses of medications as follows. Diabetes - 1000mg metformin daily (1000*30.5),
-        # hypertension - 25mg hydrochlorothiazide daily (25*30.5), CKD 1 dialysis bag (estimate),
-        # lower back pain - 2400mg aspirin daily  (2400*30.5), CIHD - 75mg aspirin daily (75*30.5)
+        # hypertension - 25mg hydrochlorothiazide daily (25*30.5), CKD 2 dialysis sessions per week
+        # (8 sessions in a month),lower back pain - 2400mg aspirin daily  (2400*30.5),
+        # CIHD - 75mg aspirin daily (75*30.5)
         dose = {'diabetes': 30_500,
                 'hypertension': 610,
-                'chronic_kidney_disease': 1,
+                'chronic_kidney_disease': 8,  # 8 in a month: dialysis two times a week
                 'chronic_lower_back_pain': 73_200,
                 'chronic_ischemic_hd': 2288,
                 'ever_stroke': 2288,
                 'ever_heart_attack': 2288}
 
+
+
         # Check availability of medication for condition
         if self.get_consumables(
             item_codes={self.module.parameters[f'{self.condition}_hsi'].get('medication_item_code').astype(int)
@@ -1738,6 +1759,48 @@ def did_not_run(self):
         self.sim.population.props.at[person_id, f'nc_{self.condition}_on_medication'] = False
 
 
+class HSI_CardioMetabolicDisorders_Dialysis_Refill(HSI_Event, IndividualScopeEventMixin):
+    """This is a Health System Interaction Event in which a person receives a dialysis session 2 times a week
+    adding up to 8 times a month."""
+
+    def __init__(self, module, person_id):
+        super().__init__(module, person_id=person_id)
+
+        self.TREATMENT_ID = 'CardioMetabolicDisorders_Treatment_Haemodialysis'
+        self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({'Over5OPD': 1})
+        self.ACCEPTED_FACILITY_LEVEL = '3'
+
+    def apply(self, person_id, squeeze_factor):
+
+        df = self.sim.population.props
+
+        if not df.at[person_id, 'is_alive'] or not df.at[person_id, 'nc_chronic_kidney_disease']:
+            return self.sim.modules['HealthSystem'].get_blank_appt_footprint()
+
+        # Increment total number of dialysis sessions the person has ever had in their lifetime
+        df.at[person_id, 'nc_ckd_total_dialysis_sessions'] += 1
+
+
+        self.add_equipment({'Chair', 'Dialysis Machine', 'Dialyser (Artificial Kidney)',
+                            'Bloodlines', 'Dialysate solution', 'Dialysis water treatment system'})
+
+        next_session_date = self.sim.date + pd.DateOffset(days=3)
+        self.sim.modules['HealthSystem'].schedule_hsi_event(self,
+            topen=next_session_date,
+            tclose=next_session_date + pd.DateOffset(days=1),
+            priority=1
+        )
+
+    def never_ran(self) -> None:
+        """What to do if the event is never run by the HealthSystem"""
+        # Reschedule this HSI to happen again 3 days time.
+        next_session_date = self.sim.date + pd.DateOffset(days=3)
+        self.sim.modules['HealthSystem'].schedule_hsi_event(self,
+            topen=next_session_date,
+            tclose=next_session_date + pd.DateOffset(days=1),
+            priority=1
+        )
+
 class HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment(HSI_Event, IndividualScopeEventMixin):
     """
     This is a Health System Interaction Event.
