From 9431d0b562d251081a1b444c7845abd943bff474 Mon Sep 17 00:00:00 2001
From: viv3ckj <viveck.kingsley@gmail.com>
Date: Tue, 14 Jan 2025 12:06:56 +0000
Subject: [PATCH] Create new msoa measures, and add action

---
 analysis/measures_definition_pf_breakdown.py  |  2 -
 .../measures_definition_pf_deciles_table.py   | 39 +++++++++++++++++++
 lib/functions/plot_measures.R                 | 11 ------
 project.yaml                                  | 20 +++++++++-
 4 files changed, 58 insertions(+), 14 deletions(-)
 create mode 100644 analysis/measures_definition_pf_deciles_table.py

diff --git a/analysis/measures_definition_pf_breakdown.py b/analysis/measures_definition_pf_breakdown.py
index 33159d4..54e4596 100644
--- a/analysis/measures_definition_pf_breakdown.py
+++ b/analysis/measures_definition_pf_breakdown.py
@@ -59,7 +59,6 @@
     otherwise="Missing",
 )
 
-msoa_code = addresses.for_patient_on(INTERVAL.start_date).msoa_code
 pharmacy_first_ids = select_events(clinical_events, codelist=pf_consultation_events_dict["pf_consultation_services_combined"]).consultation_id
 
 # # Select clinical events in interval date range
@@ -74,7 +73,6 @@
     "imd": imd_quintile,
     "region": latest_region,
     "ethnicity": ethnicity_combined,
-    "msoa_code": msoa_code
 }
 
 # Define the denominator as the number of patients registered
diff --git a/analysis/measures_definition_pf_deciles_table.py b/analysis/measures_definition_pf_deciles_table.py
new file mode 100644
index 0000000..05db4a9
--- /dev/null
+++ b/analysis/measures_definition_pf_deciles_table.py
@@ -0,0 +1,39 @@
+from ehrql import INTERVAL, create_measures, months
+from ehrql.tables.tpp import (
+    clinical_events,
+    practice_registrations,
+    patients,
+    addresses,
+)
+
+from codelists import pf_consultation_events_dict
+from config import start_date_measure_pf_breakdown, monthly_intervals_measure_pf_breakdown
+from pf_variables_library import select_events
+
+measures = create_measures()
+measures.configure_dummy_data(population_size=1000)
+
+start_date = start_date_measure_pf_breakdown
+monthly_intervals = monthly_intervals_measure_pf_breakdown
+
+registration = practice_registrations.for_patient_on(INTERVAL.end_date)
+msoa_code = addresses.for_patient_on(INTERVAL.start_date).msoa_code
+pharmacy_first_ids = select_events(clinical_events, codelist=pf_consultation_events_dict["pf_consultation_services_combined"]).consultation_id
+# # Select clinical events in interval date range
+selected_events = select_events(clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date).where(
+    clinical_events.consultation_id.is_in(pharmacy_first_ids)
+)
+
+# Define the denominator as the number of patients registered
+denominator = registration.exists_for_patient() & patients.sex.is_in(["male", "female"])
+
+condition_events = select_events(select_events, codelist=pf_consultation_events_dict["pf_consultation_services_combined"])
+numerator = condition_events.count_for_patient()
+
+measures.define_measure(
+    name="count_pf_consultation_services_by_msoa",
+    numerator=numerator,
+    denominator=denominator,
+    group_by=msoa_code,
+    intervals=months(monthly_intervals).starting_on(start_date),
+)
diff --git a/lib/functions/plot_measures.R b/lib/functions/plot_measures.R
index f2eb725..b39d0d5 100644
--- a/lib/functions/plot_measures.R
+++ b/lib/functions/plot_measures.R
@@ -161,17 +161,6 @@ save_figure <- function(figure, width = 10, height = 6) {
   )
 }
 
-compute_deciles <- function(data, column, measure_column, date_column) {
-  decile_probs <- seq(10, 90, 10)
-  data %>%
-      reframe(
-        measure = first(measure_column),
-        date = first(date_column),
-        decile_values = quantile(column, decile_probs),
-        decile_labels = decile_probs
-      )
-}
-
 # Colour palettes
 gradient_palette <- c("#001F4D", "#0056B3", "#007BFF", "#66B3E2", "#A4D8E1", "grey")
 region_palette <- c("red", "navy", "#018701", "#ffa600ca", "purple", "brown", "#f4a5b2", "cyan", "green", "grey")
diff --git a/project.yaml b/project.yaml
index e02eb17..f7f14b4 100644
--- a/project.yaml
+++ b/project.yaml
@@ -56,4 +56,22 @@ actions:
       --output output/measures/consultation_med_counts_measures.csv
     outputs:
       moderately_sensitive:
-        measure: output/measures/consultation_med_counts_measures.csv
\ No newline at end of file
+        measure: output/measures/consultation_med_counts_measures.csv
+
+  generate_measures_deciles_table:
+    run: >
+      ehrql:v1 generate-measures analysis/measures_definition_pf_deciles_table.py
+      --dummy-tables dummy_tables
+      --output output/measures/deciles_measures.csv
+    outputs:
+      highly_sensitive:
+        cohort: output/measures/deciles_measures.csv
+
+  generate_deciles:
+  run: >
+    ehrql:v1 generate-measures analysis/measures_definition_pf_consultation_med_counts.py
+    --dummy-tables dummy_tables
+    --output output/measures/consultation_med_counts_measures.csv
+  outputs:
+    moderately_sensitive:
+      measure: output/measures/consultation_med_counts_measures.csv
\ No newline at end of file