added breakdown by IMD

analysis/measures_definition_pf_codes_conditions.py

@@ -1,5 +1,5 @@
 from ehrql import INTERVAL, create_measures, months, codelist_from_csv, case, when
-from ehrql.tables.tpp import clinical_events, practice_registrations, patients
+from ehrql.tables.tpp import clinical_events, practice_registrations, patients, addresses
 
 measures = create_measures()
 measures.configure_dummy_data(population_size=1000)
@@ -28,6 +28,7 @@
 
 registration = practice_registrations.for_patient_on(INTERVAL.end_date)
 
+# Age bands for age breakdown
 age = patients.age_on(INTERVAL.start_date)
 age_band = case(
     when((age >= 0) & (age < 20)).then("0-19"),
@@ -38,6 +39,17 @@
     when(age.is_null()).then("Missing"),
 )
 
+# IMD groupings for IMD breakdown
+imd = addresses.for_patient_on(INTERVAL.start_date).imd_rounded
+imd_quintile = case(
+    when((imd >=0) & (imd < int(32844 * 1 / 5))).then("1 (most deprived)"),
+    when(imd < int(32844 * 2 / 5)).then("2"),
+    when(imd < int(32844 * 3 / 5)).then("3"),
+    when(imd < int(32844 * 4 / 5)).then("4"),
+    when(imd < int(32844 * 5 / 5)).then("5 (least deprived)"),
+    otherwise="unknown"
+)
+
 # 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)
@@ -83,6 +95,17 @@
         intervals=months(monthly_intervals).starting_on(start_date),
     )
 
+    # Measures for IMD breakdown of clinical services
+    measures.define_measure(
+        name=f"count_{pharmacy_first_event}_by_imd",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "imd": imd_quintile,
+        },
+        intervals=months(monthly_intervals).starting_on(start_date),
+    )
+
 # Create measures for pharmacy first conditions
 pharmacy_first_conditions_codes = {}
 for codes, term in pharmacy_first_conditions_codelist.items():
@@ -128,3 +151,14 @@
         },
         intervals=months(monthly_intervals).starting_on(start_date),
     )
+
+    # Measures for imd breakdown of clinical conditions
+    measures.define_measure(
+        name=f"count_{condition_name}_by_imd",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "imd": imd_quintile,
+        },
+        intervals=months(monthly_intervals).starting_on(start_date),
+    )

reports/pharmacy_first_report.Rmd

@@ -57,6 +57,17 @@ pf_clinical_condition_dict_by_sex <- c(
   "count_uncomplicated_urinary_tract_infection_by_sex" = "UTI"
 )
 
+# Define the custom labels for clinical conditions by IMD
+pf_clinical_condition_dict_by_imd <- c(
+  "count_acute_otitis_media_by_imd" = "Acute Otitis Media",
+  "count_herpes_zoster_by_imd" = "Herpes Zoster",
+  "count_acute_sinusitis_by_imd" = "Acute Sinusitis",
+  "count_impetigo_by_imd" = "Impetigo",
+  "count_infected_insect_bite_by_imd" = "Infected Insect Bite",
+  "count_acute_pharyngitis_by_imd" = "Acute Pharyngitis",
+  "count_uncomplicated_urinary_tract_infection_by_imd" = "UTI"
+)
+
 # Define the custom labels for clinical services
 pf_clinical_service_dict <- c(
   "count_blood_pressure_service" = "Blood Pressure Service",
@@ -80,6 +91,14 @@ pf_clinical_service_dict_by_sex <- c(
   "count_consultation_service_by_sex" = "Consultation Service",
   "count_pharmacy_first_service_by_sex" = "Pharmacy First Service"
 )
+
+# Define the custom labels for clinical services by IMD
+pf_clinical_service_dict_by_imd <- c(
+  "count_blood_pressure_service_by_imd" = "Blood Pressure Service",
+  "count_contraception_service_by_imd" = "Contraception Service",
+  "count_consultation_service_by_imd" = "Consultation Service",
+  "count_pharmacy_first_service_by_imd" = "Pharmacy First Service"
+)
 ```
 
 # Background
@@ -140,6 +159,20 @@ plot_measures(df_measures,
   rotate_x_labels = TRUE
 )
 ```
+
+### Clinical Services by IMD
+
+```{r, message=FALSE, warning=FALSE}
+
+plot_measures(df_measures,
+  title = "Number of consultations for each clinical service by IMD per month",
+  measure_names = names(pf_clinical_service_dict_by_imd),
+  custom_labels = pf_clinical_service_dict_by_imd,
+  y_label = "Number of codes for consultations",
+  facet_var = "imd",
+  rotate_x_labels = TRUE
+)
+```
 ## Clinical Pathways
 
 This section focuses on the Clinical Pathways element of that Pharmacy First service.  
@@ -184,4 +217,18 @@ plot_measures(df_measures,
   facet_var = "sex",
   rotate_x_labels = TRUE
 )
+```
+
+### Clinical Conditions by IMD
+
+```{r, message=FALSE, warning=FALSE}
+
+plot_measures(df_measures,
+  title = "Number of consultations for each clinical condition by IMD per month",
+  measure_names = names(pf_clinical_condition_dict_by_imd),
+  custom_labels = pf_clinical_condition_dict_by_imd,
+  y_label = "Number of codes for consultations",
+  facet_var = "imd",
+  rotate_x_labels = TRUE
+)
 ```