Make codelist names consistent, and remove repeated codelists.

Author: viv3ckj

analysis/codelists.py

@@ -21,62 +21,59 @@
     category_column="term",
 )
 
-acute_otitis_media_tx_cod = codelist_from_csv(
+acute_otitis_media_tx_codelist = codelist_from_csv(
     "codelists/opensafely-pharmacy-first-acute-otitis-media-treatment-dmd.csv",
     column="code",
 )
 
-impetigo_treatment_tx_cod = codelist_from_csv(
+impetigo_treatment_tx_codelist = codelist_from_csv(
     "codelists/opensafely-pharmacy-first-impetigo-treatment-dmd.csv",
     column="code",
 )
 
-infected_insect_bites_tx_cod = codelist_from_csv(
+infected_insect_bites_tx_codelist = codelist_from_csv(
     "codelists/opensafely-pharmacy-first-infected-insect-bites-treatment-dmd.csv",
     column="code",
 )
 
-shingles_treatment_tx_cod = codelist_from_csv(
+shingles_treatment_tx_codelist = codelist_from_csv(
     "codelists/opensafely-pharmacy-first-shingles-treatment-dmd.csv",
     column="code",
 )
 
-sinusitis_tx_cod = codelist_from_csv(
+sinusitis_tx_codelist = codelist_from_csv(
     "codelists/opensafely-pharmacy-first-sinusitis-treatment-dmd.csv",
     column="code",
 )
 
-sore_throat_tx_cod = codelist_from_csv(
+sore_throat_tx_codelist = codelist_from_csv(
     "codelists/opensafely-pharmacy-first-sore-throat-treatment-dmd.csv",
     column="code",
 )
 
-urinary_tract_infection_tx_cod = codelist_from_csv(
+urinary_tract_infection_tx_codelist = codelist_from_csv(
     "codelists/opensafely-pharmacy-first-urinary-tract-infection-treatment-dmd.csv",
     column="code",
 )
 
 pharmacy_first_med_codelist = (
-    acute_otitis_media_tx_cod
-    + impetigo_treatment_tx_cod
-    + infected_insect_bites_tx_cod
-    + shingles_treatment_tx_cod
-    + sinusitis_tx_cod
-    + sore_throat_tx_cod
-    + urinary_tract_infection_tx_cod
+    acute_otitis_media_tx_codelist
+    + impetigo_treatment_tx_codelist
+    + infected_insect_bites_tx_codelist
+    + shingles_treatment_tx_codelist
+    + sinusitis_tx_codelist
+    + sore_throat_tx_codelist
+    + urinary_tract_infection_tx_codelist
 )
 # Community Pharmacist Consultation Service for minor illness - 1577041000000109
 # Pharmacy First service - 983341000000102
 # Community Pharmacy First Service - 2129921000000100
-pharmacy_first_consultation_codelist = ["1577041000000109", "983341000000102", "2129921000000100"]
-
-# PF codes separated for individual analysis
-pharmacy_first_event_codes = {
+pharmacy_first_event_codelist = {
     # Community Pharmacist (CP) Consultation Service for minor illness (procedure)
-    "consultation_service": ["1577041000000109"],
+    "pf_consultation_cp_minorillness": ["1577041000000109"],
     # Pharmacy First service (qualifier value)
-    "pharmacy_first_service": ["983341000000102"],
+    "pf_consultation_service": ["983341000000102"],
     # Community Pharmacy Pharmacy First Service
-    "community_pharmacy_first_service": ["2129921000000100"],
-    "combined_pf_service": ["1577041000000109", "983341000000102", "2129921000000100"],
+    "pf_consultation_cp_service": ["2129921000000100"],
+    "pf_consultation_services_combined": ["1577041000000109", "983341000000102", "2129921000000100"],
 }

analysis/measures_definition_pf_breakdown.py

@@ -12,7 +12,7 @@
 )
 
 from pf_dataset import get_latest_ethnicity
-from codelists import pharmacy_first_event_codes, pharmacy_first_consultation_codelist
+from codelists import pharmacy_first_event_codelist
 from config import start_date_measure_pf_breakdown, monthly_intervals_measure_pf_breakdown
 from pf_variables_library import select_events
 
@@ -59,7 +59,7 @@
     otherwise="Missing",
 )
 
-pharmacy_first_ids = select_events(clinical_events, codelist=pharmacy_first_consultation_codelist).consultation_id
+pharmacy_first_ids = select_events(clinical_events, codelist=pharmacy_first_event_codelist["pf_consultation_services_combined"]).consultation_id
 
 # # Select clinical events in interval date range
 selected_events = select_events(clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date).where(
@@ -79,7 +79,7 @@
 denominator = registration.exists_for_patient() & patients.sex.is_in(["male", "female"])
 
 # Create measures for pharmacy first services
-for pharmacy_first_event, codelist in pharmacy_first_event_codes.items():
+for pharmacy_first_event, codelist in pharmacy_first_event_codelist.items():
     condition_events = selected_events.where(
         selected_events.snomedct_code.is_in(codelist)
     )

analysis/measures_definition_pf_condition_provider.py

@@ -8,7 +8,7 @@
     pharmacy_first_conditions_codes,
     imd_quintile,
 )
-from codelists import pharmacy_first_consultation_codelist
+from codelists import pharmacy_first_event_codelist
 from config import start_date_measure_condition_provider, monthly_intervals_measure_condition_provider
 from pf_variables_library import select_events
 
@@ -23,7 +23,7 @@
 selected_events = select_events(clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date)
 
 # Create variable which contains boolean values of whether pharmacy first event exists for patient
-has_pharmacy_first = select_events(selected_events, codelist=pharmacy_first_consultation_codelist).exists_for_patient()
+has_pharmacy_first = select_events(selected_events, codelist=pharmacy_first_event_codelist["pf_consultation_services_combined"]).exists_for_patient()
 
 for condition_name, condition_code in pharmacy_first_conditions_codes.items():
     condition_events = selected_events.where(

analysis/measures_definition_pf_consultation_med_counts.py

@@ -8,7 +8,7 @@
 
 from config import start_date_measure_med_counts, monthly_intervals_measure_med_counts
 from codelists import (
-    pharmacy_first_consultation_codelist,
+    pharmacy_first_event_codelist,
     pharmacy_first_med_codelist,
 )
 from pf_variables_library import select_events
@@ -29,7 +29,7 @@
     start_date=INTERVAL.start_date, 
     end_date=INTERVAL.end_date).where(
         clinical_events.snomedct_code.is_in(
-            pharmacy_first_consultation_codelist
+            pharmacy_first_event_codelist["pf_consultation_services_combined"]
         )
     )
 

analysis/measures_definition_pf_descriptive_stats.py

@@ -5,7 +5,7 @@
 from pf_variables_library import select_events
 from codelists import (
     pharmacy_first_med_codelist,
-    pharmacy_first_consultation_codelist,
+    pharmacy_first_event_codelist,
     pharmacy_first_conditions_codelist,
 )
 from config import (
@@ -39,7 +39,7 @@
 # Select all Pharmacy First consultation events
 pf_consultation_events = select_events(
     selected_events,
-    codelist=pharmacy_first_consultation_codelist,
+    codelist=pharmacy_first_event_codelist["pf_consultation_services_combined"],
 )
 
 # Extract Pharmacy First consultation IDs and dates

analysis/measures_definition_pf_medications.py

@@ -5,7 +5,7 @@
     practice_registrations,
 )
 from ehrql.tables.raw.tpp import medications
-from codelists import pharmacy_first_consultation_codelist, pharmacy_first_med_codelist
+from codelists import pharmacy_first_event_codelist, pharmacy_first_med_codelist
 from config import start_date_measure_medications, monthly_intervals_measure_medications
 from pf_variables_library import select_events
 
@@ -21,7 +21,7 @@
 
 # Select Pharmacy First consultations during interval date range
 pharmacy_first_events = select_events(clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date).where(
-    clinical_events.snomedct_code.is_in(pharmacy_first_consultation_codelist)
+    clinical_events.snomedct_code.is_in(pharmacy_first_event_codelist["pf_consultation_services_combined"])
 )
 
 pharmacy_first_ids = pharmacy_first_events.consultation_id

lib/functions/tidy_measures.R

@@ -1,9 +1,9 @@
 # Define dictionaries with tidy names and mappings for measures
 pf_measures_name_dict <- list(
-  consultation_service = "Consultation Service",
-  pharmacy_first_service = "Pharmacy First Consultation",
-  community_pharmacy_first_service = "Community Pharmacy First Service",
-  combined_pf_service = "Pharmacy First Consultations (Combined)",
+  pf_consultation_cp_minorillness = "Consultation Service",
+  pf_consultation_service = "Pharmacy First Consultation",
+  pf_consultation_cp_service = "Community Pharmacy First Service",
+  pf_consultation_services_combined = "Pharmacy First Consultations (Combined)",
   acute_otitis_media = "Acute Otitis Media",
   herpes_zoster = "Herpes Zoster",
   acute_sinusitis = "Acute Sinusitis",
@@ -14,10 +14,10 @@ pf_measures_name_dict <- list(
 )
 
 pf_measures_name_mapping <- list(
-  consultation_service = "clinical_service",
-  pharmacy_first_service = "clinical_service",
-  community_pharmacy_first_service = "clinical_service",
-  combined_pf_service = "pharmacy_first_services",
+  pf_consultation_cp_minorillness = "clinical_service",
+  pf_consultation_service = "clinical_service",
+  pf_consultation_cp_service = "clinical_service",
+  pf_consultation_services_combined = "pharmacy_first_services",
   acute_otitis_media = "clinical_condition",
   herpes_zoster = "clinical_condition",
   acute_sinusitis = "clinical_condition",