Param Revamp - Other Adult Cancer (#1669)

* param revamp

* add polling params and update param labeling

* add params

* fix linting

* change init prob to local

* add comment documenting discrepancy in values and parameters

* change age70 back to agege70, update comments, update param labeling

* update comments

* make post treatment check months 12 to preserve orginal intention, since updated in master

* small changes by TH

* remove old and non-relevant comment

* clean up old comments

---------

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

Author: mmsuarezcosta

resources/ResourceFile_Other_Adult_Cancers/parameter_values.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a1e58d645af62de859bc52792354881df4f0556787cdb6e3b1498de62966407d
-size 1265
+oid sha256:33ff1e674b139c469f85a9f50a96ec484fa658e21a2e145b5536574ef68a9e2b
+size 2819

src/tlo/methods/breast_cancer.py

@@ -444,32 +444,6 @@ def initialise_simulation(self, sim):
             )
         )
 
-        # todo: possibly un-comment out below when can discuss with Tim
-        """
-        self.sim.modules['HealthSystem'].dx_manager.register_dx_test(
-            biopsy_for_breast_cancer_stage2=DxTest(
-                property='brc_status',
-                sensitivity=self.parameters['sensitivity_of_biopsy_for_stage2_breast_cancer'],
-                target_categories=["stage1", "stage2", "stage3", "stage4"]
-            )
-        )
-
-        self.sim.modules['HealthSystem'].dx_manager.register_dx_test(
-            biopsy_for_breast_cancer_stage3=DxTest(
-                property='brc_status',
-                sensitivity=self.parameters['sensitivity_of_biopsy_for_stage3_breast_cancer'],
-                target_categories=["stage1", "stage2", "stage3", "stage4"]
-            )
-        )
-
-        self.sim.modules['HealthSystem'].dx_manager.register_dx_test(
-            biopsy_for_breast_cancer_stage4=DxTest(
-                property='brc_status',
-                sensitivity=self.parameters['sensitivity_of_biopsy_for_stage4_breast_cancer'],
-                target_categories=["stage1", "stage2", "stage3", "stage4"]
-            )
-        )
-        """
         # ----- DISABILITY-WEIGHT -----
         if "HealthBurden" in self.sim.modules:
             # For those with cancer (any stage prior to stage 4) and never treated
@@ -627,9 +601,8 @@ def apply(self, population):
             df.loc[idx_gets_new_stage, 'brc_status'] = stage
             df.loc[idx_gets_new_stage, 'brc_new_stage_this_month'] = True
 
-        # todo: people can move through more than one stage per month (this event runs every month)
-        # todo: I am guessing this is somehow a consequence of this way of looping through the stages
-        # todo: I imagine this issue is the same for bladder cancer and oesophageal cancer
+        # NB: people can move through more than one stage per month in rare cases
+        # (this is due to the looping through the stages)
 
         # -------------------- UPDATING OF SYMPTOM OF breast_lump_discernible OVER TIME --------------------------------
         # Each time this event is called (event 3 months) individuals may develop the symptom of breast_lump_
@@ -764,11 +737,6 @@ def apply(self, person_id, squeeze_factor):
                     )
 
 
-#   todo: we would like to note that the symptom has been investigated in a diagnostic test and the diagnosis was
-#   todo: was missed, so the same test will not likely be repeated, at least not in the short term, so we even
-#   todo: though the symptom remains we don't want to keep repeating the HSI which triggers the diagnostic test
-
-
 class HSI_BreastCancer_StartTreatment(HSI_Event, IndividualScopeEventMixin):
     """
     This event is scheduled by HSI_BreastCancer_Investigation_Following_breast_lump_discernible following a diagnosis of

src/tlo/methods/other_adult_cancers.py

@@ -175,7 +175,40 @@ def __init__(self, name=None):
         "sensitivity_of_diagnostic_device_for_other_adult_cancer_with_other_adult_ca_metastatic": Parameter(
             Types.REAL, "sensitivity of diagnostic_device_for diagnosis of other_adult cancer for those with "
                         "other_adult_ca metastatic"
-        )
+        ),
+        "odds_ratio_health_seeking_in_adults_early_other_adult_ca_symptom": Parameter(
+            Types.REAL, "odds ratio for health seeking in adults with early other adult cancer symptom"
+        ),
+        "post_treatment_check_months": Parameter(
+            Types.REAL, "months to first post-treatment check appointment"
+        ),
+        "follow_up_appt_months": Parameter(
+            Types.REAL, "months between follow-up appointments after treatment"
+        ),
+        "palliative_care_interval_months": Parameter(
+            Types.REAL, "months between palliative care appointments"
+        ),
+        "treatment_bed_days": Parameter(
+            Types.REAL, "number of bed days required for cancer treatment"
+        ),
+        "palliative_care_bed_days": Parameter(
+            Types.REAL, "number of bed days required for palliative care"
+        ),
+        "min_age_adult_cancer": Parameter(
+            Types.REAL, "minimum age for adult cancer"
+        ),
+        "initial_polling_start_months": Parameter(
+            Types.INT, "initial polling months delay"
+        ),
+        "initial_polling_start_months_palliative_care": Parameter(
+            Types.REAL, "initial polling months delay for pal care"
+        ),
+        "initial_polling_start_delay_weeks_palliative_care": Parameter(
+            Types.REAL, "week delay after initial_polling_start_months_palliative_care for initial pal care"
+        ),
+        "main_polling_event_frequency_months": Parameter(
+            Types.REAL, "frequency of main polling event"
+        ),
     }
 
     PROPERTIES = {
@@ -223,7 +256,7 @@ def read_parameters(self, resourcefilepath: Optional[Path] = None):
         # Register Symptom that this module will use
         self.sim.modules['SymptomManager'].register_symptom(
             Symptom(name='early_other_adult_ca_symptom',
-                    odds_ratio_health_seeking_in_adults=4.00,
+                    odds_ratio_health_seeking_in_adults=self.parameters['odds_ratio_health_seeking_in_adults_early_other_adult_ca_symptom'],
                     no_healthcareseeking_in_children=True)
         )
 
@@ -374,6 +407,7 @@ def initialise_simulation(self, sim):
         * Define the Disability-weights
         * Schedule the palliative care appointments for those that are on palliative care at initiation
         """
+        p = self.parameters
         # We call the following function to store the required consumables for the simulation run within the appropriate
         # dictionary
         self.item_codes_other_can = get_consumable_item_codes_cancers(self)
@@ -384,7 +418,8 @@ def initialise_simulation(self, sim):
 
         # ----- SCHEDULE MAIN POLLING EVENTS -----
         # Schedule main polling event to happen immediately
-        sim.schedule_event(OtherAdultCancerMainPollingEvent(self), sim.date + DateOffset(months=1))
+        sim.schedule_event(OtherAdultCancerMainPollingEvent(self), sim.date +
+                           DateOffset(months=p['initial_polling_start_months']))
 
         # ----- LINEAR MODELS -----
         # Define LinearModels for the progression of cancer, in each 3 month period
@@ -512,8 +547,9 @@ def initialise_simulation(self, sim):
             self.sim.modules['HealthSystem'].schedule_hsi_event(
                 hsi_event=HSI_OtherAdultCancer_PalliativeCare(module=self, person_id=person_id),
                 priority=0,
-                topen=self.sim.date + DateOffset(months=1),
-                tclose=self.sim.date + DateOffset(months=1) + DateOffset(weeks=1)
+                topen=self.sim.date + DateOffset(months=p['initial_polling_start_months_palliative_care']),
+                tclose=self.sim.date + DateOffset(months=p['initial_polling_start_months_palliative_care']) +
+                       DateOffset(weeks=p['initial_polling_start_delay_weeks_palliative_care'])
             )
 
     def on_birth(self, mother_id, child_id):
@@ -582,7 +618,10 @@ def do_at_generic_first_appt(
         schedule_hsi_event: HSIEventScheduler,
         **kwargs
     ) -> None:
-        if individual_properties["age_years"] > 5 and "early_other_adult_ca_symptom" in symptoms:
+        p = self.parameters
+
+        if (individual_properties["age_years"] > p["min_age_adult_cancer"] and
+            "early_other_adult_ca_symptom" in symptoms):
             event = HSI_OtherAdultCancer_Investigation_Following_early_other_adult_ca_symptom(
                 person_id=person_id,
                 module=self,
@@ -603,7 +642,8 @@ class OtherAdultCancerMainPollingEvent(RegularEvent, PopulationScopeEventMixin):
     """
 
     def __init__(self, module):
-        super().__init__(module, frequency=DateOffset(months=1))
+        p = module.parameters
+        super().__init__(module, frequency=DateOffset(months=p['main_polling_event_frequency_months']))
         # scheduled to run every 1 month : do not change as this is hard-wired into the values of all the parameters.
 
     def apply(self, population):
@@ -763,11 +803,13 @@ def __init__(self, module, person_id):
         self.TREATMENT_ID = "OtherAdultCancer_Treatment"
         self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({"MajorSurg": 1})
         self.ACCEPTED_FACILITY_LEVEL = '3'
-        self.BEDDAYS_FOOTPRINT = self.make_beddays_footprint({"general_bed": 5})
+        self.BEDDAYS_FOOTPRINT = (
+            self.make_beddays_footprint({"general_bed": int(self.module.parameters['treatment_bed_days'])}))
 
     def apply(self, person_id, squeeze_factor):
         df = self.sim.population.props
         hs = self.sim.modules["HealthSystem"]
+        p = self.module.parameters
 
         if not df.at[person_id, 'is_alive']:
             return hs.get_blank_appt_footprint()
@@ -823,7 +865,7 @@ def apply(self, person_id, squeeze_factor):
                     module=self.module,
                     person_id=person_id,
                 ),
-                topen=self.sim.date + DateOffset(months=12),
+                topen=self.sim.date + DateOffset(months=p['post_treatment_check_months']),
                 tclose=None,
                 priority=0
             )
@@ -890,7 +932,7 @@ def apply(self, person_id, squeeze_factor):
                     module=self.module,
                     person_id=person_id
                 ),
-                topen=self.sim.date + DateOffset(months=3),
+                topen=self.sim.date + DateOffset(months=self.module.parameters['follow_up_appt_months']),
                 tclose=None,
                 priority=0
             )
@@ -917,11 +959,13 @@ def __init__(self, module, person_id):
         self.TREATMENT_ID = "OtherAdultCancer_PalliativeCare"
         self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({})
         self.ACCEPTED_FACILITY_LEVEL = '2'
-        self.BEDDAYS_FOOTPRINT = self.make_beddays_footprint({'general_bed': 15})
+        self.BEDDAYS_FOOTPRINT = (
+            self.make_beddays_footprint({'general_bed': int(self.module.parameters['palliative_care_bed_days'])}))
 
     def apply(self, person_id, squeeze_factor):
         df = self.sim.population.props
         hs = self.sim.modules["HealthSystem"]
+        p = self.module.parameters
 
         if not df.at[person_id, 'is_alive']:
             return hs.get_blank_appt_footprint()
@@ -950,13 +994,13 @@ def apply(self, person_id, squeeze_factor):
             if pd.isnull(df.at[person_id, "oac_date_palliative_care"]):
                 df.at[person_id, "oac_date_palliative_care"] = self.sim.date
 
-            # Schedule another instance of the event for one month
+            # Schedule another instance of the event
             hs.schedule_hsi_event(
                 hsi_event=HSI_OtherAdultCancer_PalliativeCare(
                     module=self.module,
                     person_id=person_id
                 ),
-                topen=self.sim.date + DateOffset(months=1),
+                topen=self.sim.date + DateOffset(months=p['palliative_care_interval_months']),
                 tclose=None,
                 priority=0
             )