Merge pull request #154 from The-Strategy-Unit/add-cost-values-to-outputs

Add cost values to outputs

Author: yiwen-h

renal_capacity_model/config.py

@@ -88,4 +88,5 @@ def __init__(
         self.time_to_event_curves = load_time_to_event_curves(
             path_to_time_to_event_curves
         )
+        self.daily_costs = config_dict["daily_costs"]
         logger.info("🔧 Config loaded successfully")

renal_capacity_model/config_values.py

@@ -246,6 +246,12 @@
     "pre_emptive_transplant_cadaver_donor_dist": {
         y: {"early": 0.22, "late": 0.05} for y in range(1, 14)
     },
+    "daily_costs": {
+        "ichd": 62842 / 365,
+        "hhd": 51122 / 365,
+        "pd": 39391 / 365,
+        "transplant": 9005 / 365,
+    },
 }
 
 # Time to death: conservative care

renal_capacity_model/load_scenario.py

@@ -901,7 +901,7 @@ def load_scenario_from_excel(
         "ichd": input_scenario.iat[36, 1],
         "hhd": input_scenario.iat[37, 1],
         "pd": input_scenario.iat[38, 1],
-        "living_with_transplant": input_scenario.iat[39, 1],
+        "transplant": input_scenario.iat[39, 1],
     }
 
     return config_from_excel

renal_capacity_model/main.py

@@ -60,9 +60,7 @@ def main(
         )
         for excel_file in [path_to_inputs_file, path_to_outputs_file]:
             filepaths.append(copy_excel_files(excel_file, run_start_time))
-        write_results_to_excel(
-            filepaths[1], combined_results, trial.yearly_activity_duration
-        )
+        write_results_to_excel(filepaths[1], combined_results, trial.costs_dfs)
 
 
 if __name__ == "__main__":

renal_capacity_model/process_outputs.py

@@ -194,14 +194,14 @@ def copy_excel_files(path_to_file: str, run_start_time: str) -> str:
 def write_results_to_excel(
     path_to_results_excel_file: str,
     combined_df: pd.DataFrame,
-    yearly_activity_duration: pd.DataFrame,
+    costs_dfs: dict[str, pd.DataFrame],
 ):
     """Write combined model results from all model runs to Excel file
 
     Args:
         path_to_excel_file (str): Path to Excel file
         combined_df (pd.DataFrame): Dataframe of all model results combined and processed
-        yearly_activity_duration (pd.DataFrame): Dataframe of counts of activity for each year of
+        costs_dfs (pd.DataFrame): Dataframe of costs of activity for each year of
         model simulation, for each model run
     """
     with pd.ExcelWriter(
@@ -214,10 +214,33 @@ def write_results_to_excel(
             combined_df.loc[outcome].to_excel(
                 writer, sheet_name=outcome.replace("waiting_for_transplant", "wft")
             )
-        for activity in ["ichd", "hhd", "pd", "transplant"]:
-            yearly_activity_duration.pivot(
-                index="model_run", columns="year", values=activity
-            ).sort_index(axis=1).to_excel(writer, sheet_name=f"{activity}_yearly")
+        for activity, df in costs_dfs.items():
+            df.to_excel(writer, sheet_name=f"{activity}_yearly")
     logger.info(
         f"✅ 💾 Excel format model results written to: \n{path_to_results_excel_file}"
     )
+
+
+def convert_activity_to_costs(
+    yearly_activity_duration: pd.DataFrame, daily_costs: dict[str, float]
+) -> dict[str, pd.DataFrame]:
+    """Converts yearly activity duration dataframe into costs for each type of activity
+
+    Args:
+        yearly_activity_duration (pd.DataFrame): Dataframe with yearly activity durations
+        for each of the activity types
+        daily_costs (dict[str, float]): Daily costs dictionary, set in config
+
+    Returns:
+        dict[str, pd.DataFrame]: Dictionary where keys are treatment modality and
+        values are a DataFrame with the yearly costs for each across each of the model runs
+    """
+    costs_dfs = {}
+    for activity in ["ichd", "hhd", "pd", "transplant"]:
+        costs_dfs[activity] = (
+            yearly_activity_duration.pivot(
+                index="model_run", columns="year", values=activity
+            ).sort_index(axis=1)
+            * daily_costs[activity]
+        )
+    return costs_dfs

renal_capacity_model/trial.py

@@ -10,6 +10,7 @@
     create_results_folder,
     save_result_files,
     calculate_activity_duration_per_year,
+    convert_activity_to_costs,
 )
 import numpy as np
 from tqdm import tqdm
@@ -96,6 +97,9 @@ def run_trial(self):
         self.yearly_activity_duration = calculate_activity_duration_per_year(
             self.event_log_dfs
         )
+        self.costs_dfs = convert_activity_to_costs(
+            self.yearly_activity_duration, self.config.daily_costs
+        )
         logger.info("💾 Saving full trial results")
         self.save_trial_results(
             self.process_eventlog_dfs(self.activity_change_dfs), "activity_change"