Viv3ckj/update development report

analysis/dataset_definition_med_status_data_development.py

@@ -16,6 +16,7 @@
 
 # Time interval for selecting medications pre and post Pharmacy First launch date
 time_interval = months(6)
+pf_period = months(25)
 
 pharmacy_first_ids = clinical_events.where(
     clinical_events.snomedct_code.is_in(pharmacy_first_event_codes)
@@ -96,7 +97,7 @@
 selected_medications_pfmed_post = (
     medications.where(
         medications.date.is_on_or_between(
-            pharmacy_first_launch_date, pharmacy_first_launch_date + time_interval
+            pharmacy_first_launch_date, pharmacy_first_launch_date + pf_period
         )
     )
     .where(medications.dmd_code.is_in(pharmacy_first_med_codes))
@@ -108,7 +109,7 @@
 selected_medications_pfmed_pfid_post = (
     medications.where(
         medications.date.is_on_or_between(
-            pharmacy_first_launch_date, pharmacy_first_launch_date + time_interval
+            pharmacy_first_launch_date, pharmacy_first_launch_date + pf_period
         )
     )
     .where(medications.dmd_code.is_in(pharmacy_first_med_codes))
@@ -120,7 +121,7 @@
 selected_medications_anymed_pfid_post = (
     medications.where(
         medications.date.is_on_or_between(
-            pharmacy_first_launch_date, pharmacy_first_launch_date + time_interval
+            pharmacy_first_launch_date, pharmacy_first_launch_date + pf_period
         )
     )
     .where(medications.consultation_id.is_in(pharmacy_first_ids))
@@ -131,7 +132,7 @@
 selected_medications_pfdate_pfid_post = (
     medications.where(
         medications.date.is_on_or_between(
-            pharmacy_first_launch_date, pharmacy_first_launch_date + time_interval
+            pharmacy_first_launch_date, pharmacy_first_launch_date + pf_period
         )
     )
     .where(medications.consultation_id.is_in(pharmacy_first_ids))
@@ -156,7 +157,7 @@
 selected_medications_pfmed_pfdate_post = (
     medications.where(
         medications.date.is_on_or_between(
-            pharmacy_first_launch_date, pharmacy_first_launch_date + time_interval
+            pharmacy_first_launch_date, pharmacy_first_launch_date + pf_period
         )
     )
     .where(medications.dmd_code.is_in(pharmacy_first_med_codes))
@@ -180,7 +181,7 @@
 selected_medications_anymed_pfdate_post = (
     medications.where(
         medications.date.is_on_or_between(
-            pharmacy_first_launch_date, pharmacy_first_launch_date + time_interval
+            pharmacy_first_launch_date, pharmacy_first_launch_date + pf_period
         )
     )
     .where(medications.date.is_in(pharmacy_first_dates))

analysis/measures_definition_clinical_codes.py

@@ -6,6 +6,10 @@
 
 # Dictionary of pharmacy first codes
 pharmacy_first_event_codes = {
+    # Blood Pressure Check Service (1659111000000107)
+    "blood_pressure_service": ["1659111000000107"],
+    # Contraception service (1659121000000101)
+    "contraception_service": ["1659121000000101"],
     # Community Pharmacist (CP) Consultation Service for minor illness (procedure)
     "consultation_service": ["1577041000000109"],
     # Pharmacy First service (qualifier value)
@@ -29,7 +33,7 @@
     pharmacy_first_code_counts[f"count_{code_desc}"] = count_codes_query
 
 # Define intervals and measures
-intervals = months(18).starting_on("2023-02-01")
+intervals = months(37).starting_on("2023-02-01")
 
 for measures_name, code_counts in pharmacy_first_code_counts.items():
     measures.define_measure(

analysis/measures_med_status_counts.py

@@ -0,0 +1,21 @@
+from ehrql import create_dataset, months, days, INTERVAL, create_measures
+from ehrql.tables.tpp import patients, clinical_events
+from ehrql.tables.raw.tpp import medications
+
+from codelists import pharmacy_first_event_codes
+measures = create_measures()
+start_date = "2023-08-01"
+monthly_intervals = 32
+
+pharmacy_first_ids = clinical_events.where(clinical_events.snomedct_code.is_in(pharmacy_first_event_codes)).consultation_id
+
+pf_medications = medications.where(medications.consultation_id.is_in(pharmacy_first_ids)).where(medications.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date)).sort_by(medications.date).first_for_patient()
+medication_status = pf_medications.medication_status
+
+measures.define_measure(
+    name="pf_medications_by_med_status",
+    numerator=pf_medications.count_for_patient(),
+    denominator=pf_medications.count_for_patient(),
+    group_by={"medication_status": medication_status},
+    intervals=months(monthly_intervals).starting_on(start_date),
+)

analysis/test_dataset_definition_pf_data_development.py

@@ -122,9 +122,9 @@
             "post_all_count_pf_events": 2,
             "post_pfid_count_pf_events": 2,
             "post_pfdate_count_pf_events": 2,
-            "post_all_count_pf_pathways": 2,
+            "post_all_count_pf_pathways": 3,
             "post_pfid_count_pf_pathways": 1,
-            "post_pfdate_count_pf_pathways": 3,
+            "post_pfdate_count_pf_pathways": 2,
         },
     },
 }

project.yaml

@@ -86,4 +86,12 @@ actions:
       --output output/measures/consultation_med_counts_measures.csv
     outputs:
       moderately_sensitive:
-        measure: output/measures/consultation_med_counts_measures.csv
+        measure: output/measures/consultation_med_counts_measures.csv
+
+  generate_med_status_counts_measures:
+    run: >
+      ehrql:v1 generate-measures analysis/measures_med_status_counts.py
+      --output output/measures/measures_med_status_counts.csv
+    outputs:
+      moderately_sensitive:
+        measure: output/measures/measures_med_status_counts.csv