Merge pull request #30 from opensafely/viv3ckj/denominators

Modify denominators to be specific for each clinical condition

Author: viv3ckj

analysis/codelists.py

@@ -13,3 +13,10 @@
     column="snomedcode",
     category_column="Grouping_6",
 )
+
+# Import pregnancy codelist
+pregnancy_codelist = codelist_from_csv(
+    "codelists/nhsd-primary-care-domain-refsets-preg_cod.csv",
+    column="code",
+    category_column="term",
+)

analysis/measures_definition_pf_codes_conditions.py

@@ -6,26 +6,19 @@
     addresses,
     ethnicity_from_sus,
 )
-from codelists import pharmacy_first_conditions_codelist, ethnicity_codelist
+from codelists import (
+    pharmacy_first_conditions_codelist,
+    ethnicity_codelist,
+)
+
+from pf_dataset import pharmacy_first_event_codes
 
 measures = create_measures()
 measures.configure_dummy_data(population_size=1000)
 
 start_date = "2023-11-01"
 monthly_intervals = 9
 
-# Create dictionary of pharmacy first codes
-pharmacy_first_event_codes = {
-    # Community Pharmacy (CP) Blood Pressure (BP) Check Service (procedure)
-    "blood_pressure_service": ["1659111000000107"],
-    # Community Pharmacy (CP) Contraception Service (procedure)
-    "contraception_service": ["1659121000000101"],
-    # Community Pharmacist (CP) Consultation Service for minor illness (procedure)
-    "consultation_service": ["1577041000000109"],
-    # Pharmacy First service (qualifier value)
-    "pharmacy_first_service": ["983341000000102"],
-}
-
 registration = practice_registrations.for_patient_on(INTERVAL.end_date)
 
 latest_ethnicity_from_codes_category_num = (
@@ -70,7 +63,6 @@
     otherwise="Missing",
 )
 
-
 # Age bands for age breakdown
 age = patients.age_on(INTERVAL.start_date)
 age_band = case(
@@ -95,12 +87,13 @@
 )
 
 latest_region = case(
-    when(
-        registration.practice_nuts1_region_name.is_not_null()
-    ).then(registration.practice_nuts1_region_name),
+    when(registration.practice_nuts1_region_name.is_not_null()).then(
+        registration.practice_nuts1_region_name
+    ),
     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)
@@ -145,6 +138,17 @@
             intervals=months(monthly_intervals).starting_on(start_date),
         )
 
+# Create dictionary for clinical condition denominators
+pf_condition_denominators = {
+    "uncomplicated_urinary_tract_infection": denominator,
+    "herpes_zoster": denominator,
+    "impetigo": denominator,
+    "infected_insect_bite": denominator,
+    "acute_pharyngitis": denominator,
+    "acute_sinusitis": denominator,
+    "acute_otitis_media": denominator,
+}
+
 # Create measures for pharmacy first conditions
 pharmacy_first_conditions_codes = {}
 for codes, term in pharmacy_first_conditions_codelist.items():
@@ -164,7 +168,7 @@
     measures.define_measure(
         name=f"count_{condition_name}",
         numerator=numerator,
-        denominator=denominator,
+        denominator=pf_condition_denominators[condition_name],
         intervals=months(monthly_intervals).starting_on(start_date),
     )
 
@@ -173,7 +177,7 @@
         measures.define_measure(
             name=f"count_{condition_name}_by_{breakdown}",
             numerator=numerator,
-            denominator=denominator,
+            denominator=pf_condition_denominators[condition_name],
             group_by={breakdown: variable},
             intervals=months(monthly_intervals).starting_on(start_date),
         )

analysis/pf_dataset.py

@@ -0,0 +1,117 @@
+from pf_variables_library import check_pregnancy_status, count_past_events
+
+# Create dictionary of pharmacy first codes
+pharmacy_first_event_codes = {
+    # # Community Pharmacy (CP) Blood Pressure (BP) Check Service (procedure)
+    # "blood_pressure_service": ["1659111000000107"],
+    # # Community Pharmacy (CP) Contraception Service (procedure)
+    # "contraception_service": ["1659121000000101"],
+    # Community Pharmacist (CP) Consultation Service for minor illness (procedure)
+    "consultation_service": ["1577041000000109"],
+    # Pharmacy First service (qualifier value)
+    "pharmacy_first_service": ["983341000000102"],
+    "combined_service": ["1577041000000109", "983341000000102"],
+}
+
+
+# Create denominator variables for each clinical condition
+# These are based on NHS England rules using sex, age, pregnancy status and repeated diagnoses
+# NOTE: The following exclusions have not been added:
+# - urinary catheter for URT,
+# - bullous impetigo,
+# - chronic sinusitis and immunosuppressed individuals for acute sinusitis
+def get_uncomplicated_uti_denominator(index_date, selected_events, pregnancy_codelist):
+    urt_code = ["1090711000000102"]
+    count_urt_6m = count_past_events(index_date, selected_events, urt_code, 6)
+    count_urt_12m = count_past_events(index_date, selected_events, urt_code, 12)
+
+    age = patients.age_on(index_date)
+    pregnancy_status = check_pregnancy_status(
+        index_date, selected_events, pregnancy_codelist
+    )
+
+    return (
+        (age >= 16)
+        & (age <= 64)
+        & (patients.sex.is_in(["female"]) & pregnancy_status.is_null())
+        | (count_urt_6m < 2)
+        | (count_urt_12m < 3)
+    )
+
+
+def get_shingles_denominator(index_date, selected_events, pregnancy_codelist):
+    age = patients.age_on(index_date)
+    pregnancy_status = check_pregnancy_status(
+        index_date, selected_events, pregnancy_codelist
+    )
+
+    return (age >= 18) & pregnancy_status.is_null()
+
+
+def get_impetigo_denominator(index_date, selected_events, pregnancy_codelist):
+    impetigo_code = ["48277006"]
+    count_impetigo_12m = count_past_events(
+        index_date, selected_events, impetigo_code, 12
+    )
+
+    age = patients.age_on(index_date)
+    pregnancy_status = check_pregnancy_status(
+        index_date, selected_events, pregnancy_codelist
+    )
+
+    return (
+        (age >= 1)
+        | (pregnancy_status.is_not_null() & (age >= 16))
+        | (count_impetigo_12m < 2)
+    )
+
+
+def get_infected_insect_bites_denominator(
+    index_date, selected_events, pregnancy_codelist
+):
+    age = patients.age_on(index_date)
+    pregnancy_status = check_pregnancy_status(
+        index_date, selected_events, pregnancy_codelist
+    )
+
+    return (age >= 1) | (pregnancy_status.is_not_null() & (age >= 16))
+
+
+def get_acute_sore_throat_denominator(index_date, selected_events, pregnancy_codelist):
+    age = patients.age_on(index_date)
+    pregnancy_status = check_pregnancy_status(
+        index_date, selected_events, pregnancy_codelist
+    )
+
+    return (age >= 5) | (pregnancy_status.is_not_null() & (age >= 16))
+
+
+def get_acute_sinusitis_denominator(index_date, selected_events, pregnancy_codelist):
+    age = patients.age_on(index_date)
+    pregnancy_status = check_pregnancy_status(
+        index_date, selected_events, pregnancy_codelist
+    )
+
+    return (age >= 12) | (pregnancy_status.is_not_null() & (age >= 16))
+
+
+def get_acute_otitis_media_denominator(index_date, selected_events, pregnancy_codelist):
+    acute_otitis_code = ["3110003"]
+    count_acute_otitis_6m = count_past_events(
+        index_date, selected_events, acute_otitis_code, 6
+    )
+    count_acute_otitis_12m = count_past_events(
+        index_date, selected_events, acute_otitis_code, 12
+    )
+
+    age = patients.age_on(index_date)
+    pregnancy_status = check_pregnancy_status(
+        index_date, selected_events, pregnancy_codelist
+    )
+
+    return (
+        (age >= 1) & (age <= 17)
+        | (pregnancy_status.is_not_null() & (age >= 16))
+        | (count_acute_otitis_6m < 3)
+        | (count_acute_otitis_12m < 4)
+    )

analysis/pf_variables_library.py

@@ -0,0 +1,22 @@
+# Function to check status of a condition within a specified time window
+def check_pregnancy_status(index_date, selected_events, codelist):
+    return (
+        selected_events.where(selected_events.snomedct_code.is_in(codelist))
+        .where(
+            selected_events.date.is_on_or_between(index_date - months(1), index_date)
+        )
+        .exists_for_patient()
+    )
+
+
+# Function to count number of coded events within a specified time window
+def count_past_events(index_date, selected_events, codelist, num_months):
+    return (
+        selected_events.where(selected_events.snomedct_code.is_in(codelist))
+        .where(
+            selected_events.date.is_on_or_between(
+                index_date - months(num_months), index_date
+            )
+        )
+        .count_for_patient()
+    )

codelists/codelists.json

@@ -11,6 +11,12 @@
       "url": "https://www.opencodelists.org/codelist/opensafely/ethnicity-snomed-0removed/2e641f61/",
       "downloaded_at": "2024-10-03 11:34:59.878387Z",
       "sha": "8b849b5b785d80306e488d0109640c8c1d2da01b"
+    },
+    "nhsd-primary-care-domain-refsets-preg_cod.csv": {
+      "id": "nhsd-primary-care-domain-refsets/preg_cod/20200812",
+      "url": "https://www.opencodelists.org/codelist/nhsd-primary-care-domain-refsets/preg_cod/20200812/",
+      "downloaded_at": "2024-10-10 13:27:57.825804Z",
+      "sha": "4a1cbc5c12ce8589030b376905ac47f5a68b2503"
     }
   }
 }

codelists/codelists.txt

@@ -1,2 +1,3 @@
 user/chriswood/pharmacy-first-clinical-pathway-conditions/7ec97762
-opensafely/ethnicity-snomed-0removed/2e641f61
+opensafely/ethnicity-snomed-0removed/2e641f61
+nhsd-primary-care-domain-refsets/preg_cod/20200812

codelists/nhsd-primary-care-domain-refsets-preg_cod.csv

@@ -0,0 +1,41 @@
+code,term
+10231000132102,In-vitro fertilization pregnancy
+1109951000000101,Pregnancy insufficiently advanced for reliable antenatal screening
+1109971000000105,Pregnancy too advanced for reliable antenatal screening
+1148801000000108,Monochorionic monoamniotic triplet pregnancy
+1148811000000105,Trichorionic triamniotic triplet pregnancy
+1148821000000104,Dichorionic triamniotic triplet pregnancy
+1148841000000106,Dichorionic diamniotic triplet pregnancy
+1149411000000103,Monochorionic diamniotic triplet pregnancy
+1149421000000109,Monochorionic triamniotic triplet pregnancy
+134781000119106,High risk pregnancy due to recurrent miscarriage
+16356006,Multiple pregnancy
+169488004,Contraceptive intrauterine device failure - pregnant
+169501005,"Pregnant, diaphragm failure"
+169508004,"Pregnant, sheath failure"
+169560008,Pregnant - urine test confirms
+169561007,Pregnant - blood test confirms
+169562000,Pregnant - vaginal examination confirms
+169563005,Pregnant - on history
+169564004,Pregnant - on abdominal palpation
+169565003,Pregnant - planned
+169566002,Pregnancy unplanned but wanted
+237238006,Pregnancy with uncertain dates
+237239003,Low risk pregnancy
+276367008,Wanted pregnancy
+314204000,Early stage of pregnancy
+439311009,Intends to continue pregnancy
+444661007,High risk pregnancy due to history of preterm labor
+459166009,Dichorionic diamniotic twin pregnancy
+459167000,Monochorionic twin pregnancy
+459168005,Monochorionic diamniotic twin pregnancy
+459171002,Monochorionic monoamniotic twin pregnancy
+47200007,High risk pregnancy
+60810003,Quadruplet pregnancy
+64254006,Triplet pregnancy
+65147003,Twin pregnancy
+713575004,Dizygotic twin pregnancy
+713576003,Monozygotic twin pregnancy
+72957006,Diamniotic-monochorionic twins
+77386006,Pregnant
+80997009,Quintuplet pregnancy

reports/pharmacy_first_report.Rmd

@@ -26,10 +26,11 @@ df_measures <- readr::read_csv(
 
 # Define dictionaries with tidy names and mappings for measures
 pf_measures_name_dict <- list(
-  blood_pressure_service = "Blood Pressure Service",
-  contraception_service = "Contraception Service",
+  # blood_pressure_service = "Blood Pressure Service",
+  # contraception_service = "Contraception Service",
   consultation_service = "Consultation Service",
   pharmacy_first_service = "Pharmacy First Service",
+  combined_service = "Pharmacy First Services",
   acute_otitis_media = "Acute Otitis Media",
   herpes_zoster = "Herpes Zoster",
   acute_sinusitis = "Acute Sinusitis",
@@ -40,10 +41,11 @@ pf_measures_name_dict <- list(
 )
 
 pf_measures_name_mapping <- list(
-  blood_pressure_service = "clinical_service",
-  contraception_service = "clinical_service",
+  # blood_pressure_service = "clinical_service",
+  # contraception_service = "clinical_service",
   consultation_service = "clinical_service",
   pharmacy_first_service = "clinical_service",
+  combined_service = "pharmacy_first_services",
   acute_otitis_media = "clinical_condition",
   herpes_zoster = "clinical_condition",
   acute_sinusitis = "clinical_condition",
@@ -146,7 +148,7 @@ plot_measures(
 ```{r, message=FALSE, warning=FALSE, fig.height=8, fig.width=8}
 # Select measures and breakdown
 df_measures_selected <- df_measures %>%
-  filter(measure_desc == "clinical_service") %>%
+  filter(measure_desc == "pharmacy_first_services") %>%
   filter(group_by == "Age band")
 
 # Create visualisation
@@ -168,7 +170,7 @@ plot_measures(
 ```{r, message=FALSE, warning=FALSE, fig.height=8, fig.width=8}
 # Select measures and breakdown
 df_measures_selected <- df_measures %>%
-  filter(measure_desc == "clinical_service") %>%
+  filter(measure_desc == "pharmacy_first_services") %>%
   filter(group_by == "Sex")
 
 # Create visualisation
@@ -190,7 +192,7 @@ plot_measures(
 ```{r, message=FALSE, warning=FALSE, fig.height=8, fig.width=8}
 # Select measures and breakdown
 df_measures_selected <- df_measures %>%
-  filter(measure_desc == "clinical_service") %>%
+  filter(measure_desc == "pharmacy_first_services") %>%
   filter(group_by == "IMD")
 
 # Create visualisation
@@ -212,7 +214,7 @@ plot_measures(
 ```{r, message=FALSE, warning=FALSE, fig.height=8, fig.width=8}
 # Select measures and breakdown
 df_measures_selected <- df_measures %>%
-  filter(measure_desc == "clinical_service") %>%
+  filter(measure_desc == "pharmacy_first_services") %>%
   filter(group_by == "Region")
 
 # Create visualisation
@@ -236,7 +238,7 @@ plot_measures(
 
 # Select measures and breakdown
 df_measures_selected <- df_measures %>%
-  filter(measure_desc == "clinical_service") %>%
+  filter(measure_desc == "pharmacy_first_services") %>%
   filter(group_by == "Ethnicity")
 
 # Create visualisation