Address run errors

Author: viv3ckj

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_event_codes,
-    pharmacy_first_med_codes,
+    pharmacy_first_consultation_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_event_codes
+            pharmacy_first_consultation_codelist
         )
     )
 
@@ -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_codes)
+has_pharmacy_first_medication = first_selected_medication.is_in(pharmacy_first_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

@@ -34,6 +34,10 @@
     medications.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date)
 )
 
+selected_clinical_pathways = select_events(
+    clinical_events, codelist=pharmacy_first_conditions_codelist
+).where(clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date))
+
 # Create variable which contains boolean values of whether pharmacy first event exists for patient
 has_pf_consultation = select_events(
     selected_clinical_events, codelist=pharmacy_first_consultation_codelist).exists_for_patient()
@@ -43,15 +47,15 @@
     selected_clinical_events, codelist=pharmacy_first_conditions_codelist).exists_for_patient()
 
 # Dates of pharmacy first consultations
-pharmacy_first_dates = select_events(clinical_events, codelist=pharmacy_first_ids).date
+pharmacy_first_dates = select_events(clinical_events, codelist=pharmacy_first_consultation_codelist).date
 
 # Specify whether a patient has been prescribed a PF medication on the same day as a PF consultation code
-has_pfmed_on_pfdate = selected_med_events.where(medications.date.is_in(pharmacy_first_dates))
+has_pfmed_on_pfdate = selected_med_events.where(medications.date.is_in(pharmacy_first_dates)).exists_for_patient()
 
 # Specify whether a patient has a PF condition
-has_pfpathway_on_pfdate = has_pf_condition.where(
-    has_pf_condition.date.is_in(pharmacy_first_dates)
-)
+has_pfpathway_on_pfdate = selected_clinical_pathways.where(
+    selected_clinical_pathways.date.is_in(pharmacy_first_dates)
+).exists_for_patient()
 
 # PF consultations with prescribed PF medication
 has_pf_medication = selected_med_events.where(