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Author: viv3ckj

analysis/codelists.py

@@ -19,4 +19,4 @@
     "codelists/nhsd-primary-care-domain-refsets-preg_cod.csv",
     column="code",
     category_column="term",
-)
+)

analysis/measures_definition_pf_codes_conditions.py

@@ -6,7 +6,11 @@
     addresses,
     ethnicity_from_sus,
 )
-from codelists import pharmacy_first_conditions_codelist, ethnicity_codelist, pregnancy_codelist
+from codelists import (
+    pharmacy_first_conditions_codelist,
+    ethnicity_codelist,
+    pregnancy_codelist,
+)
 
 measures = create_measures()
 measures.configure_dummy_data(population_size=1000)
@@ -24,7 +28,7 @@
     "consultation_service": ["1577041000000109"],
     # Pharmacy First service (qualifier value)
     "pharmacy_first_service": ["983341000000102"],
-    "combined_service": ["1577041000000109", "983341000000102"]
+    "combined_service": ["1577041000000109", "983341000000102"],
 }
 
 registration = practice_registrations.for_patient_on(INTERVAL.end_date)
@@ -96,29 +100,37 @@
 )
 
 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",
 )
 
 # Create variable which when not null, indicates patient is pregnant
 pregnancy_status = (
     clinical_events.where(clinical_events.snomedct_code.is_in(pregnancy_codelist))
-    .where(clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date))
+    .where(
+        clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date)
+    )
     .sort_by(clinical_events.date)
     .last_for_patient()
     .date
 )
 
+
 # Create function to count number of diagnosis of a condition, and the length of time window
 def condition_history(condition_code, month):
     return (
         clinical_events.where(clinical_events.snomedct_code.is_in(condition_code))
-        .where(clinical_events.date.is_on_or_between(INTERVAL.start_date - months(month), INTERVAL.start_date))
+        .where(
+            clinical_events.date.is_on_or_between(
+                INTERVAL.start_date - months(month), INTERVAL.start_date
+            )
+        )
         .count_for_patient()
     )
 
+
 # Call function to create variables which contain the number of repeated diagnoses
 urt_code = ["1090711000000102"]
 impetigo_code = ["48277006"]
@@ -175,24 +187,43 @@ def condition_history(condition_code, month):
         )
 
 # Create denominator variables for each clinical condition based on NHS England rules using sex, age, pregnancy status and repeated diagnoses
-# The following exclusions have not been added: urinary catheter for URT, bullous impetigo, chronic sinusitis and immunosuppressed individuals for acute sinusitis 
-denominator_uncomplicated_uti = (age>=16) & (age<=64) & (patients.sex.is_in(["female"]) & pregnancy_status.is_null()) | (urt_6m<2) | (urt_12m<3)
-denominator_shingles = (age>=18) & pregnancy_status.is_null()
-denominator_impetigo = (age>=1) | (pregnancy_status.is_not_null() & (age>=16)) | (impetigo_12m<2)
-denominator_infected_insect_bites = (age>=1) | (pregnancy_status.is_not_null() & (age>=16))
-denominator_acute_sore_throat = (age>=5) | (pregnancy_status.is_not_null() & (age>=16))
-denominator_acute_sinusitis = (age>=12) | (pregnancy_status.is_not_null() & (age>=16))
-denominator_acute_otitis_media = (age>=1) & (age<=17) | (pregnancy_status.is_not_null() & (age>=16)) |(acute_otitis_6m<3) | (acute_otitis_12m<4)
+# The following exclusions have not been added: urinary catheter for URT, bullous impetigo, chronic sinusitis and immunosuppressed individuals for acute sinusitis
+denominator_uncomplicated_uti = (
+    (age >= 16)
+    & (age <= 64)
+    & (patients.sex.is_in(["female"]) & pregnancy_status.is_null())
+    | (urt_6m < 2)
+    | (urt_12m < 3)
+)
+denominator_shingles = (age >= 18) & pregnancy_status.is_null()
+denominator_impetigo = (
+    (age >= 1) | (pregnancy_status.is_not_null() & (age >= 16)) | (impetigo_12m < 2)
+)
+denominator_infected_insect_bites = (age >= 1) | (
+    pregnancy_status.is_not_null() & (age >= 16)
+)
+denominator_acute_sore_throat = (age >= 5) | (
+    pregnancy_status.is_not_null() & (age >= 16)
+)
+denominator_acute_sinusitis = (age >= 12) | (
+    pregnancy_status.is_not_null() & (age >= 16)
+)
+denominator_acute_otitis_media = (
+    (age >= 1) & (age <= 17)
+    | (pregnancy_status.is_not_null() & (age >= 16))
+    | (acute_otitis_6m < 3)
+    | (acute_otitis_12m < 4)
+)
 
 # Create dictionary for clinical condition denominators
 pf_condition_denominators = {
-    "uncomplicated_urinary_tract_infection" : denominator_uncomplicated_uti,
-    "herpes_zoster" : denominator_shingles,
-    "impetigo" : denominator_impetigo,
+    "uncomplicated_urinary_tract_infection": denominator_uncomplicated_uti,
+    "herpes_zoster": denominator_shingles,
+    "impetigo": denominator_impetigo,
     "infected_insect_bite": denominator_infected_insect_bites,
-    "acute_pharyngitis" : denominator_acute_sore_throat,
-    "acute_sinusitis" : denominator_acute_sinusitis,
-    "acute_otitis_media" : denominator_acute_otitis_media,
+    "acute_pharyngitis": denominator_acute_sore_throat,
+    "acute_sinusitis": denominator_acute_sinusitis,
+    "acute_otitis_media": denominator_acute_otitis_media,
 }
 
 # Create measures for pharmacy first conditions