Viv3ckj/clean repo

analysis/dep_reg_dataset.py

@@ -1,62 +1,76 @@
-from ehrql import create_dataset
-from ehrql.codes import codelist_from_csv
+# 1) Import the required ehrql functions
+from ehrql import create_dataset, codelist_from_csv
 
+# 2) Import relevant tables from the TPP backend (OpenSAFELY-TPP)
 from ehrql.tables.tpp import (
     clinical_events,
     patients,
     practice_registrations,
 )
 
-dataset = create_dataset()
-# Quality Service Start Date
-qs_start_date = '2024-04-01' 
-# Fixed date used in DEPR1_REG and DEPCC01 logic.
-# Depression register: Patients aged at least 18 years old whose latest
-# unresolved episode of depression is since 1 st April 2006.
-min_date = '2006-04-01'
+# 3) Load SNOMED-CT codelists from CSV files
 
-# import codelists
+# Depression codes
 dep_codelist = codelist_from_csv(
     'codelists/nhsd-primary-care-domain-refsets-depr_cod.csv',
     column='code')
+# Resolved depression codes
 depres_codelist = codelist_from_csv(
     'codelists/nhsd-primary-care-domain-refsets-depres_cod.csv',
     column='code')
 
-# inclusion criteria
-has_registration = (practice_registrations
-                    .for_patient_on(qs_start_date)
-                    .exists_for_patient())
-
-# Create disease variables
-# - DEPR_DAT = Latest date of depression diagnosis
-# - DEPRES_DAT = Latest depression resolved date
-# - PAT_AGE = Age at quality service start date
-
-dataset.depr_dat = ((clinical_events.
-                    where(clinical_events
-                          .snomedct_code
-                          .is_in(dep_codelist))
-                          ).sort_by(clinical_events.date)
-                          .last_for_patient()
-                          .date)
-dataset.depres_dat = (clinical_events
-                      .where(clinical_events
-                             .snomedct_code
-                             .is_in(depres_codelist))
-                             .sort_by(clinical_events.date)
-                             .last_for_patient()
-                             .date)
+# 4) Define variables and the study population
+
+# Utility function: return the most recent event (if any) for a patient matching a given codelist
+def last_matching_event(events, codelist, where=True):
+    return (
+        events.where(where)
+        .where(events.snomedct_code.is_in(codelist))
+        .sort_by(events.date)
+        .last_for_patient()
+    )
+
+# Quality Service Start Date (Index date)
+qs_start_date = '2024-04-01' 
+
+# Fixed date used in DEPR1_REG and DEPCC01 logic.
+# Depression register: Patients aged at least 18 years old whose latest unresolved episode of depression is since 1st April 2006.
+min_date = '2006-04-01'
+# Create a dataset object
+dataset = create_dataset()
+
+# Identify patients who were registered on the index date
+has_registration = practice_registrations.for_patient_on(
+        qs_start_date
+).exists_for_patient()
+
+# Filter clinical events to only those on or before the index date
+prior_events = clinical_events.where(clinical_events.date.is_on_or_before(qs_start_date))
+
+# Field number: 4
+# PAT_AGE: The age of the patient in full years at the index date.
 dataset.pat_age = (patients
                    .age_on(qs_start_date))
 
-# --- Creating rules ---
-# Have their latest first or new episode of depression on or after 1 st April 2006.
-# Latest episode of depression is not followed by a depression resolved code.
-# Must be aged 18 or over on the achievement date
+# Field number 5: 
+# DEPR_DAT: Date of the latest depression episode at the index date
+dataset.depr_dat = last_matching_event(prior_events, dep_codelist).date
 
+# Field number 6:
+# DEPRES_DAT: Date of the most recent depression resolved code at the index date
+dataset.depres_dat = last_matching_event(prior_events, depres_codelist).date
+
+# DEP_REG rule 1: 
+# Include patients that have their latest episode of unresolved depression on or after 1st April 2006.
 dep1_reg_r1 = ((dataset.depr_dat.is_on_or_after(min_date))
                & (dataset.depres_dat.is_null()))
-dep2_reg_r2 = dataset.pat_age >= 18
 
-dataset.define_population(has_registration & dep1_reg_r1 & dep2_reg_r2)
+# DEP_REG rule 2:
+# Include patients under the age of 18 on the index date
+dep2_reg_r2 = dataset.pat_age < 18
+
+# Define the final population:
+# - Registered on index date
+# - Meet rule 1 (active depression diagnosis)
+# - Do not meet rule 2 (i.e. are 18 or older)
+dataset.define_population(has_registration & dep1_reg_r1 & ~dep2_reg_r2)