fix supplemented data

analysis/report_tables.py

@@ -324,10 +324,7 @@ def report_state_change(
 definitions_sus_5_ctv3 = ["ethnicity_5", "any"]
 definitions_sus_16 = ["ethnicity_new_16", "any"]
 definitions_sus_16_ctv3 = ["ethnicity_16", "any"]
-definitions_supplemented_ctv3_5 = ["ethnicity_5", "supplemented"]
-definitions_supplemented_5 = ["ethnicity_new_5", "supplemented"]
-definitions_supplemented_16 = ["ethnicity_new_16", "supplemented"]
-definitions_supplemented_ctv3_16 = ["ethnicity_16", "supplemented"]
+
 covariates = [
     "_age_band",
     "_sex",
@@ -547,7 +544,7 @@ def main():
         missing=False,
     )
     report_patient_counts(
-        definitions_supplemented_ctv3_5,
+        definitions_sus_5_ctv3,
         group_5,
         "ctv3_sus",
         input_path_sus,
@@ -593,7 +590,7 @@ def main():
         missing=False,
     )
     report_patient_counts(
-        definitions_supplemented_ctv3_16,
+        definitions_sus_16_ctv3,
         group_16,
         "ctv3_sus",
         input_path_sus,
@@ -605,7 +602,7 @@ def main():
     )
 
     report_patient_counts(
-        definitions_supplemented_16,
+        definitions_sus_16,
         group_16,
         "new_sus",
         input_path_sus,

notebooks_jupyter/local_runs.ipynb

@@ -29,7 +29,8 @@
     "        ).set_index([\"group\", \"subgroup\"])\n",
     "        for col in df_append.columns[df_append.columns.str.endswith('supplemented')]:\n",
     "            df_append=df_append.rename(columns={col: f\"{col}_filled\"})\n",
-    "        \n",
+    "        for col in df_append.columns[df_append.columns.str.endswith(\"any\")]:\n",
+    "            df_append = df_append.rename(columns={col: f\"{col}_filled\"})\n",
     "        # df_append.drop(\"population\", inplace=True, axis=1)\n",
     "        for definition in definitions:\n",
     "            \n",