added breakdown graphs and facet function

analysis/measures_definition_pf_codes_conditions.py

@@ -1,5 +1,5 @@
-from ehrql import INTERVAL, create_measures, months, codelist_from_csv
-from ehrql.tables.tpp import clinical_events, practice_registrations
+from ehrql import INTERVAL, create_measures, months, codelist_from_csv, case, when
+from ehrql.tables.tpp import clinical_events, practice_registrations, patients, addresses, ethnicity_from_sus
 
 measures = create_measures()
 measures.configure_dummy_data(population_size=1000)
@@ -28,6 +28,29 @@
 
 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"),
+    when((age >= 20) & (age < 40)).then("20-39"),
+    when((age >= 40) & (age < 60)).then("40-59"),
+    when((age >= 60) & (age < 80)).then("60-79"),
+    when(age >= 80).then("80+"),
+    when(age.is_null()).then("Missing"),
+)
+
+# IMD groupings for IMD breakdown
+imd = addresses.for_patient_on(INTERVAL.start_date).imd_rounded
+max_imd = 32844
+imd_quintile = case(
+    when((imd >=0) & (imd < int(max_imd * 1 / 5))).then("1"),
+    when(imd < int(max_imd * 2 / 5)).then("2"),
+    when(imd < int(max_imd * 3 / 5)).then("3"),
+    when(imd < int(max_imd * 4 / 5)).then("4"),
+    when(imd <= max_imd).then("5"),
+    otherwise="Missing"
+)
+
 # 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)
@@ -43,7 +66,7 @@
     numerator = condition_events.count_for_patient()
 
     # Define the denominator as the number of patients registered
-    denominator = registration.exists_for_patient()
+    denominator = registration.exists_for_patient() & patients.sex.is_in(["male", "female", "intersex"])
 
     measures.define_measure(
         name=f"count_{pharmacy_first_event}",
@@ -52,6 +75,61 @@
         intervals=months(monthly_intervals).starting_on(start_date),
     )
 
+    # Measures for age breakdown of clinical services
+    measures.define_measure(
+        name=f"count_{pharmacy_first_event}_by_age",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "age_band": age_band,
+        },
+        intervals=months(monthly_intervals).starting_on(start_date),
+    )
+
+    # Measures for sex breakdown of clinical services
+    measures.define_measure(
+        name=f"count_{pharmacy_first_event}_by_sex",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "sex": patients.sex,
+        },
+        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),
+    )
+
+    # Measures for region breakdown of clinical services
+    measures.define_measure(
+        name=f"count_{pharmacy_first_event}_by_region",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "region": registration.practice_nuts1_region_name,
+        },
+        intervals=months(monthly_intervals).starting_on(start_date),
+    )
+
+    # Measures for ethnicity code breakdown of clinical services
+    measures.define_measure(
+        name=f"count_{pharmacy_first_event}_by_ethnicity",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "ethnicity": ethnicity_from_sus.code,
+        },
+        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():
@@ -76,3 +154,57 @@
         denominator=denominator,
         intervals=months(monthly_intervals).starting_on(start_date),
     )
+    # Measures for age breakdown of clinical conditions
+    measures.define_measure(
+        name=f"count_{condition_name}_by_age",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "age_band": age_band,
+        },
+        intervals=months(monthly_intervals).starting_on(start_date),
+    )
+
+    # Measures for age breakdown of clinical conditions
+    measures.define_measure(
+        name=f"count_{condition_name}_by_sex",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "sex": patients.sex,
+        },
+        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),
+    )
+
+    # Measures for region breakdown of clinical conditions
+    measures.define_measure(
+        name=f"count_{condition_name}_by_region",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "region": registration.practice_nuts1_region_name,
+        },
+        intervals=months(monthly_intervals).starting_on(start_date),
+    )
+
+    # Measures for region breakdown of clinical conditions
+    measures.define_measure(
+        name=f"count_{condition_name}_by_ethnicity",
+        numerator=numerator,
+        denominator=denominator,
+        group_by={
+            "ethnicity": ethnicity_from_sus.code,
+        },
+        intervals=months(monthly_intervals).starting_on(start_date),
+    )

lib/functions/function_plot_measures.R

@@ -24,7 +24,9 @@ plot_measures <- function(
     title = NULL,
     x_label = NULL,
     y_label = NULL,
+    facet_var = NULL,
     color_label = NULL,
+    rotate_x_labels = FALSE,
     axis_x_text_size = 7) {
   # Check if the necessary columns exist in the data
   if (date_col %in% names(data) == FALSE) {
@@ -99,5 +101,16 @@ plot_measures <- function(
       date_labels = "%b %Y"
     )
 
+    if (!is.null(facet_var)) {
+    facet_sym <- sym(facet_var)
+    plot1 <- plot1 + facet_wrap(vars(!!facet_sym), scales = "free_x")
+
+  }
+
+# Conditionally apply x-axis label rotation if rotate_x_labels is TRUE
+  if (rotate_x_labels) {
+    plot1 <- plot1 + theme(axis.text.x = element_text(angle = 45, hjust = 1))
+  }
+
   plot1
 }