Add ctv3 sus analysis

opensafely · Dec 6, 2023 · 1bbb62a · 1bbb62a
1 parent ebb8a44
commit 1bbb62a
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Showing 2 changed files with 4 additions and 51 deletions.
diff --git a/analysis/sus/simple_validation_script_ctv3_sus.py b/analysis/sus/simple_validation_script_ctv3_sus.py
@@ -21,7 +21,7 @@
         4: "4",
         5: "5 Least deprived",
     },
-    "ethnicity_new_5": {1: "White", 2: "Mixed", 3: "Asian", 4: "Black", 5: "Other"},
+    "ethnicity_5": {1: "White", 2: "Mixed", 3: "Asian", 4: "Black", 5: "Other"},
     "ethnicity_sus_5": {1: "White", 2: "Mixed", 3: "Asian", 4: "Black", 5: "Other"},
 }
 
@@ -79,55 +79,8 @@ def main():
         registered=registered,
         dates_check=False,
     )
-    # Count patients with records
-    simple_patient_counts(
-        df_clean,
-        definitions,
-        reg,
-        demographic_covariates,
-        clinical_covariates,
-        output_path,
-        grouping,
-    )
-
-    # Count patients by categories
-    simple_patient_counts(
-        df_clean,
-        definitions,
-        reg,
-        demographic_covariates,
-        clinical_covariates,
-        output_path,
-        grouping,
-        categories=True,
-    )
 
-    simple_sus_crosstab(df_clean, output_path, grouping, reg)
-
-    # Latest v most common
-    simple_latest_common_comparison(
-        df_clean,
-        definitions,
-        reg,
-        other_vars_combined,
-        output_path,
-        grouping,
-        code_dict,
-    )
-
-    # State change
-    simple_state_change(
-        df_clean,
-        definitions,
-        reg,
-        other_vars_combined,
-        output_path,
-        grouping,
-    )
-    # # records over time
-    # records_over_time_perc(
-    #     df_clean, definitions, demographic_covariates, clinical_covariates, output_path, "",grouping,reg
-    #     )
+    simple_ctv3_sus_crosstab(df_clean, output_path, grouping, reg)
 
 
 ########################## DO NOT EDIT – RUNS SCRIPT ##############################

diff --git a/project.yaml b/project.yaml
@@ -91,11 +91,11 @@ actions:
 #        figures: output/sus/simplified_output/5_group/figures/*.png
 
   execute_simple_validation_analyses_ctv3_sus:
-    run: python:latest python analysis/sus/simple_validation_script_sus.py
+    run: python:latest python analysis/sus/simple_validation_script_ctv3_sus.py
     needs: [generate_study_population_5]
     outputs:
       moderately_sensitive: 
-        tables: output/sus/simplified_output/5_group/tables/*.csv
+        tables: output/sus/simplified_output/5_group/tables/*ctv3*.csv
 #        figures: output/sus/simplified_output/5_group/figures/*.png
 
   execute_simple_validation_analyses_16_sus: