Secular Time-trend in Availability of Consumables

src/tlo/analysis/utils.py

@@ -1127,9 +1127,10 @@ def get_parameters_for_status_quo() -> Dict:
             "cons_availability": "default",
             "beds_availability": "default",
             "equip_availability": "all",  # <--- NB. Existing calibration is assuming all equipment is available
+            # "consumables_availability_time_trend": True, # <-- not included yet, but future update should include.
         },
     }
-    
+
 def get_parameters_for_standard_mode2_runs() -> Dict:
     """
     Returns a dictionary of parameters and their updated values to indicate

src/tlo/methods/consumables.py

@@ -34,7 +34,9 @@ def __init__(self,
                  availability_data: pd.DataFrame = None,
                  item_code_designations: pd.DataFrame = None,
                  rng: np.random = None,
-                 availability: str = 'default'
+                 availability: str = 'default',
+                 use_time_trend: bool = False,
+                 time_trend_data: dict = None,
                  ) -> None:
 
         self._options_for_availability = {
@@ -56,8 +58,10 @@ def __init__(self,
         self._is_unknown_item_available = None  # Whether an unknown item is available, by facility_id
         self._not_recognised_item_codes = set()  # The item codes requested but which are not recognised.
 
-        # Save designations
+        # Save designations and time-trend info
         self._item_code_designations = item_code_designations
+        self._time_trend_data = time_trend_data
+        self._use_time_trend = use_time_trend
 
         # Save all item_codes that are defined and pd.Series with probs of availability from ResourceFile
         self.item_codes,  self._processed_consumables_data = \
@@ -266,7 +270,7 @@ def _lookup_availability_of_consumables(self,
 
     def on_simulation_end(self):
         """Do tasks at the end of the simulation.
-         
+
         Raise warnings and enter to log about item_codes not recognised.
         """
         if self._not_recognised_item_codes:
@@ -289,6 +293,26 @@ def on_simulation_end(self):
     def on_end_of_year(self):
         self._summary_counter.write_to_log_and_reset_counters()
 
+        # Update consumables availability (for next year) to reflect secular trend
+        self._update_availability()
+
+    def _update_availability(self):
+        """Update availability of consumables"""
+        if not self._use_time_trend:
+            return  # Do nothing if there should not be a time-trend in the availability
+
+        # Data on the changes in availability
+        data = self._time_trend_data
+
+        # Annual multiplier on availability for each category....
+
+        # Items in each category.... (look up from the categories provided in the sheet)
+
+        # For each group, multiply availabilities in `self._prob_item_codes_available`, and clip to 1.0
+
+
+
+
 
 def get_item_codes_from_package_name(lookup_df: pd.DataFrame, package: str) -> dict:
     """Helper function to provide the item codes and quantities in a dict of the form {<item_code>:<quantity>} for

src/tlo/methods/healthsystem.py

@@ -189,6 +189,12 @@ class HealthSystem(Module):
             " When using 'all' or 'none', requests for consumables are not logged. NB. This parameter is over-ridden"
             "if an argument is provided to the module initialiser."
             "Note that other options are also available: see the `Consumables` class."),
+        'consumables_availability_time_trend': Parameter(
+            Types.BOOL, "Whether to incorporate the observed time-trend in availability of consumables."
+        ),
+        'availability_estimates_time_trend': Parameter(
+            Types.DICT, "Dict of dataframes describing the trend over time in the availability of consumables."
+        ),
 
         # Infrastructure and Equipment
         'BedCapacity': Parameter(
@@ -564,6 +570,11 @@ def read_parameters(self, data_folder):
         ).set_index('Item_Code')
         self.parameters['availability_estimates'] = pd.read_csv(
             path_to_resourcefiles_for_healthsystem / 'consumables' / 'ResourceFile_Consumables_availability_small.csv')
+        self.parameters['availability_estimates_time_trend'] = pd.read_excel(
+            path_to_resourcefiles_for_healthsystem / 'consumables' /
+            'ResourceFile_Consumables_availability_estimates_time_trend.xlsx',
+            sheet_name=None
+        )
 
         # Data on the number of beds available of each type by facility_id
         self.parameters['BedCapacity'] = pd.read_csv(
@@ -663,7 +674,9 @@ def pre_initialise_population(self):
                 self.parameters['availability_estimates']),
             item_code_designations=self.parameters['consumables_item_designations'],
             rng=rng_for_consumables,
-            availability=self.get_cons_availability()
+            availability=self.get_cons_availability(),
+            use_time_trend=self.parameters['consumables_availability_time_trend'],
+            time_trend_data=self.parameters['availability_estimates_time_trend']
         )
 
         # Determine equip_availability