Merge pull request #96 from opensafely/viv3ckj/refactor-codelists

Make codelist names consistent, and remove repeated codelists.

analysis/codelists.py

@@ -1,7 +1,7 @@
 from ehrql import codelist_from_csv
 
 # Import pharmacy first conditions codelist
-pharmacy_first_conditions_codelist = codelist_from_csv(
+pf_conditions_codelist = codelist_from_csv(
     "codelists/user-chriswood-pharmacy-first-clinical-pathway-conditions.csv",
     column="code",
     category_column="term",
@@ -21,62 +21,64 @@
     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
+pf_med_codelist = (
+    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
+pf_consultation_cp_minorillness = ["1577041000000109"]
 # Pharmacy First service - 983341000000102
+pf_consultation_service = ["983341000000102"]
 # Community Pharmacy First Service - 2129921000000100
-pharmacy_first_consultation_codelist = ["1577041000000109", "983341000000102", "2129921000000100"]
+pf_consultation_cp_service = ["2129921000000100"]
 
-# PF codes separated for individual analysis
-pharmacy_first_event_codes = {
+pf_consultation_events_dict = {
     # Community Pharmacist (CP) Consultation Service for minor illness (procedure)
-    "consultation_service": ["1577041000000109"],
+    "pf_consultation_cp_minorillness": pf_consultation_cp_minorillness,
     # Pharmacy First service (qualifier value)
-    "pharmacy_first_service": ["983341000000102"],
+    "pf_consultation_service": pf_consultation_service,
     # Community Pharmacy Pharmacy First Service
-    "community_pharmacy_first_service": ["2129921000000100"],
-    "combined_pf_service": ["1577041000000109", "983341000000102", "2129921000000100"],
+    "pf_consultation_cp_service": pf_consultation_cp_service,
+    "pf_consultation_services_combined": pf_consultation_cp_minorillness
+    + pf_consultation_service + pf_consultation_cp_service,
 }

analysis/measures_definition_pf_breakdown.py

@@ -7,12 +7,12 @@
     ethnicity_from_sus,
 )
 from codelists import (
-    pharmacy_first_conditions_codelist,
+    pf_conditions_codelist,
     ethnicity_codelist,
 )
 
 from pf_dataset import get_latest_ethnicity
-from codelists import pharmacy_first_event_codes, pharmacy_first_consultation_codelist
+from codelists import pf_consultation_events_dict
 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=pf_consultation_events_dict["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 pf_consultation_events_dict.items():
     condition_events = selected_events.where(
         selected_events.snomedct_code.is_in(codelist)
     )
@@ -118,7 +118,7 @@
 
 # Create measures for pharmacy first conditions
 pharmacy_first_conditions_codes = {}
-for codes, term in pharmacy_first_conditions_codelist.items():
+for codes, term in pf_conditions_codelist.items():
     normalised_term = term.lower().replace(" ", "_")
     codes = [codes]
     pharmacy_first_conditions_codes[normalised_term] = codes

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 pf_consultation_events_dict
 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=pf_consultation_events_dict["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

@@ -8,8 +8,8 @@
 
 from config import start_date_measure_med_counts, monthly_intervals_measure_med_counts
 from codelists import (
-    pharmacy_first_consultation_codelist,
-    pharmacy_first_med_codelist,
+    pf_consultation_events_dict,
+    pf_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
+            pf_consultation_events_dict["pf_consultation_services_combined"]
         )
     )
 
@@ -47,7 +47,7 @@
     selected_medications.sort_by(selected_medications.date).first_for_patient().dmd_code
 )
 # Boolean variable that selected medication is part of pharmacy first med codelists
-has_pharmacy_first_medication = first_selected_medication.is_in(pharmacy_first_med_codelist)
+has_pharmacy_first_medication = first_selected_medication.is_in(pf_med_codelist)
 
 # Numerator, patients with a PF medication
 # This allows me to count all (first) medications linked to a PF consultation

analysis/measures_definition_pf_descriptive_stats.py

@@ -4,9 +4,9 @@
 
 from pf_variables_library import select_events
 from codelists import (
-    pharmacy_first_med_codelist,
-    pharmacy_first_consultation_codelist,
-    pharmacy_first_conditions_codelist,
+    pf_med_codelist,
+    pf_consultation_events_dict,
+    pf_conditions_codelist,
 )
 from config import (
     start_date_measure_descriptive_stats,
@@ -39,7 +39,7 @@
 # Select all Pharmacy First consultation events
 pf_consultation_events = select_events(
     selected_events,
-    codelist=pharmacy_first_consultation_codelist,
+    codelist=pf_consultation_events_dict["pf_consultation_services_combined"],
 )
 
 # Extract Pharmacy First consultation IDs and dates
@@ -51,12 +51,12 @@
 # Select Pharmacy First conditions by ID and date
 selected_pf_id_conditions = selected_events.where(
     selected_events.consultation_id.is_in(pf_ids)
-).where(selected_events.snomedct_code.is_in(pharmacy_first_conditions_codelist))
+).where(selected_events.snomedct_code.is_in(pf_conditions_codelist))
 
 selected_pf_date_conditions = (
     selected_events.where(selected_events.consultation_id.is_not_in(pf_ids))
     .where(selected_events.date.is_in(pf_dates))
-    .where(selected_events.snomedct_code.is_in(pharmacy_first_conditions_codelist))
+    .where(selected_events.snomedct_code.is_in(pf_conditions_codelist))
 )
 
 has_pf_id_condition = selected_pf_id_conditions.exists_for_patient()
@@ -65,12 +65,12 @@
 # Select Pharmacy First Medications by ID and date
 selected_pf_id_medications = selected_medications.where(
     selected_medications.consultation_id.is_in(pf_ids)
-).where(selected_medications.dmd_code.is_in(pharmacy_first_med_codelist))
+).where(selected_medications.dmd_code.is_in(pf_med_codelist))
 
 selected_pf_date_medications = (
     selected_medications.where(selected_medications.consultation_id.is_not_in(pf_ids))
     .where(selected_medications.date.is_in(pf_dates))
-    .where(selected_medications.dmd_code.is_in(pharmacy_first_med_codelist))
+    .where(selected_medications.dmd_code.is_in(pf_med_codelist))
 )
 
 has_pf_id_medication = selected_pf_id_medications.exists_for_patient()

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 pf_consultation_events_dict, pf_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(pf_consultation_events_dict["pf_consultation_services_combined"])
 )
 
 pharmacy_first_ids = pharmacy_first_events.consultation_id
@@ -39,7 +39,7 @@
 
 # Check if a medication is from our PF codelists 
 has_pharmacy_first_medication = first_selected_medication.is_in(
-    pharmacy_first_med_codelist
+    pf_med_codelist
 )
 
 # Numerator, patients with a PF medication

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",