Merge pull request #36 from opensafely/viv3ckj/consultations

Add pharmacy first id filter to selected_events

Author: viv3ckj

analysis/measures_definition_pf_codes_conditions.py

@@ -11,7 +11,7 @@
     ethnicity_codelist,
 )
 
-from pf_dataset import pharmacy_first_event_codes
+from pf_dataset import pharmacy_first_event_codes, pharmacy_first_codes
 
 measures = create_measures()
 measures.configure_dummy_data(population_size=1000)
@@ -93,12 +93,17 @@
     otherwise="Missing",
 )
 
+pharmacy_first_ids = clinical_events.where(
+    clinical_events.snomedct_code.is_in(pharmacy_first_codes)
+).consultation_id
 
 # Select clinical events in interval date range
-selected_events = clinical_events.where(
-    clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date)
+selected_events = (clinical_events.where(
+    clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date))
+.where(clinical_events.consultation_id.is_in(pharmacy_first_ids))
 )
 
+
 # Breakdown metrics to be produced as graphs
 breakdown_metrics = {
     "age_band": age_band,

analysis/pf_dataset.py

@@ -13,6 +13,13 @@
     "combined_service": ["1577041000000109", "983341000000102"],
 }
 
+# Pharmacy first clinical codes
+pharmacy_first_codes = [
+    "1659111000000107",
+    "1659121000000101",
+    "1577041000000109",
+    "983341000000102",
+]
 
 # Create denominator variables for each clinical condition
 # These are based on NHS England rules using sex, age, pregnancy status and repeated diagnoses