update outcomes and portability

analysis/additional_comorbidities.py

@@ -0,0 +1,328 @@
+import json, sys
+from pathlib import Path 
+
+from datetime import date, datetime
+from ehrql import Dataset, case, when, maximum_of, minimum_of, years, days
+from ehrql.tables.tpp import ( 
+  patients, 
+  medications,
+  ons_deaths,
+  addresses, 
+  clinical_events,
+  practice_registrations,
+  household_memberships_2020,
+  vaccinations,
+  apcs,
+  emergency_care_attendances
+)
+
+from variable_lib import (
+  has_a_continuous_practice_registration_spanning,
+  most_recent_bmi,
+  practice_registration_as_of,
+  emergency_care_diagnosis_matches,
+  hospitalisation_diagnosis_matches
+)
+
+import codelists
+
+dataset = Dataset()
+
+#######################################################################################
+# Import study dates defined in "./analysis/design/study-dates.R" script and then exported
+# to JSON
+#######################################################################################
+study_dates = json.loads(
+  Path("analysis/design/study-dates.json").read_text(),
+)
+
+args = sys.argv
+
+#define dataset definition settings from command line arguments
+cohort = args[1]
+codelist_type = args[4]
+investigation_type = args[5]
+
+# Change these in ./analysis/design/study-dates.R if necessary
+study_start_date = study_dates[args[2]]
+study_end_date = study_dates[args[3]]
+index_date = study_start_date
+registration_date = index_date - years(1)
+
+#define patients age
+age_at_start = patients.age_on(study_start_date)
+age_at_end = patients.age_on(study_end_date)
+age_months = (index_date - patients.date_of_birth).months
+age_at_start_months = (study_start_date - patients.date_of_birth).months
+
+#events occurring before index date
+prior_events = clinical_events.where(clinical_events.date.is_on_or_before(index_date))
+
+#query prior_events for existence of event-in-codelist
+def has_prior_event(codelist, where = True):
+    return (
+        prior_events.where(where)
+        .where(prior_events.snomedct_code.is_in(codelist))
+        .exists_for_patient()
+    )
+
+#query prior_events for date of most recent event-in-codelist
+def last_prior_event(codelist, where = True):
+    return (
+        prior_events.where(where)
+        .where(prior_events.snomedct_code.is_in(codelist))
+        .sort_by(clinical_events.date)
+        .last_for_patient()
+    )
+
+#query prior_events for date of earliest event-in-codelist
+def first_prior_event(codelist, where = True):
+    return (
+        prior_events.where(where)
+        .where(prior_events.snomedct_code.is_in(codelist))
+        .sort_by(clinical_events.date)
+        .first_for_patient()
+    )
+
+#meds occurring before booster date
+prior_meds = medications.where(medications.date.is_on_or_before(index_date))
+
+#query prior_meds for existence of event-in-codelist
+def has_prior_meds(codelist, where = True):
+    return (
+        prior_meds.where(where)
+        .where(prior_meds.dmd_code.is_in(codelist))
+        .exists_for_patient()
+    )
+
+#query prior meds for date of most recent med-in-codelist
+def last_prior_meds(codelist, where = True):
+    return (
+        prior_meds.where(where)
+        .where(prior_meds.dmd_code.is_in(codelist))
+        .sort_by(medications.date)
+        .last_for_patient()
+    )
+
+#query prior_events for date of earliest event-in-codelist
+def first_prior_meds(codelist, where = True):
+    return (
+        prior_meds.where(where)
+        .where(prior_meds.dmd_code.is_in(codelist))
+        .sort_by(medications.date)
+        .first_for_patient()
+    )
+
+##comorbidities for secondary investigation
+
+def filter_codes_by_category(codelist, include):
+    return {k:v for k,v in codelist.items() if v in include}
+
+#lifestyle
+
+
+#smoking 
+
+###############################################################################
+# from https://github.com/opensafely/early-inflammatory-arthritis/blob/069e61712fcc9a0c2ec2804ff36a9b773073291c/analysis/dataset_definition.py#L136
+###############################################################################
+
+most_recent_smoking_code = (
+  (clinical_events.where(clinical_events.ctv3_code
+  .is_in(codelists.clear_smoking_codes))
+  .sort_by(clinical_events.date).last_for_patient()
+  .ctv3_code.to_category(codelists.clear_smoking_codes))
+)
+ever_smoked = (
+  clinical_events.where(clinical_events.ctv3_code
+  .is_in(filter_codes_by_category(codelists
+  .clear_smoking_codes, include = ["S", "E"])))
+  .exists_for_patient()
+)
+smoking_status = (case(
+  when(most_recent_smoking_code == "S").then("S"),
+  when((most_recent_smoking_code == "E") 
+  | ((most_recent_smoking_code == "N") 
+  & (ever_smoked == True))).then("E"),
+  when((most_recent_smoking_code == "N") 
+  & (ever_smoked == False)).then("N"),
+  otherwise = "M")
+)
+
+#drinking 
+hazardous_drinking = has_prior_event(codelists.drinking_codelist)
+
+#drug usage 
+drug_usage = (
+  (has_prior_event(codelists.drug_usage_codelist + 
+  codelists.drug_intervention_codelist +
+  codelists.drug_assessment_declination_codelist))
+)
+
+#medication date
+medication_date = index_date - years(1)
+
+#reactive airway disease diagnosis 
+has_reactive_airway = has_prior_event(codelists.reactive_airway_disease_code)
+
+#has asthma if there is an asthma diagnosis and a recent medication prescribed 
+has_asthma = (
+  (has_prior_event(codelists.asthma_codelist))
+  & (has_prior_meds(codelists.asthma_oral_medications,
+  where = medications.date.is_on_or_between(medication_date, index_date))
+  |(has_prior_meds(codelists.asthma_inhaled_medications)))
+)
+
+#copd diagnosis
+has_copd = (
+  (has_prior_event(codelists.copd_codelist))
+  & (has_prior_meds(codelists.copd_medications))
+  & (last_prior_event(codelists.copd_codelist).date
+  .is_on_or_after(last_prior_event(codelists
+  .copd_resolved_codelist).date))
+)
+
+#pulmonary fibrosis diagnosis
+has_pulmonary_fibrosis = (
+  has_prior_event(codelists
+  .pulmonary_fibrosis_codelist)
+)
+
+#cystic fibrosis diagnosis
+has_cystic_fibrosis = (
+  clinical_events.where(clinical_events.ctv3_code.
+  is_in(codelists.cystic_fibrosis_codelist))
+  .exists_for_patient()
+)
+
+#diabetes diagnosis
+diab_date = last_prior_event(codelists.diabetes_codelist).date
+dmres_date = last_prior_event(codelists.diabetes_resolved_codelist).date
+has_diabetes = (case(
+  when(dmres_date < diab_date).then(True),
+  when(diab_date.is_not_null() & dmres_date.is_null())
+  .then(True), otherwise = False)
+)
+
+#addison's disease diagnosis
+has_addisons = (
+  clinical_events.where(clinical_events.snomedct_code
+  .is_in(codelists.addisons_codelist))
+  .where(clinical_events.date.is_on_or_before(index_date))
+  .exists_for_patient()
+)
+
+#Calculate BMI
+
+###############################################################################
+# from https://github.com/opensafely/comparative-booster-spring2023/blob/main/analysis/dataset_definition.py
+###############################################################################
+
+# BMI
+bmi_measurement = most_recent_bmi(
+  where = clinical_events.date.is_after(index_date - years(5)),
+  minimum_age_at_measurement = 16,
+)
+bmi_value = bmi_measurement.numeric_value
+bmi = case(
+  when(bmi_value < 30).then("Not obese"), # include this here to ensure this value is the 1st level in the factor
+  when((bmi_value >= 30.0) & (bmi_value < 35.0)).then("Obese I (30-34.9)"),
+  when((bmi_value >= 35.0) & (bmi_value < 40.0)).then("Obese II (35-39.9)"),
+  # Set maximum to avoid any impossibly extreme values being classified as obese
+  when((bmi_value >= 40.0) & (bmi_value < 100.0)).then("Obese III (40+)"),
+  otherwise = "Not obese", # assume missing is non-obese
+)
+
+# Severe Obesity
+bmi_stage_event = last_prior_event(codelists.bmi_stage_codelist)
+sev_obesity_event = last_prior_event(
+  codelists.severe_obesity_codelist,
+  where = ((clinical_events.date >= bmi_stage_event.date) 
+  & (clinical_events.numeric_value != 0.0)),
+)
+bmi_event = last_prior_event(codelists.bmi_codelist, 
+  where = (clinical_events.numeric_value != 0.0))
+severe_obesity = case(
+  when(sev_obesity_event.date > bmi_event.date).then(True),
+  when(bmi_event.numeric_value >= 40.0).then(True),
+  otherwise = False
+)
+
+#Chronic Heart Disease
+has_chd = has_prior_event(codelists.chd_codelist)
+
+#Chronic Kidney Disease
+
+###############################################################################
+# from https://github.com/opensafely/comparative-booster-spring2023/blob/main/analysis/dataset_definition.py
+###############################################################################  
+
+#chronic kidney disease diagnostic codes 
+ckd = has_prior_event(codelists.ckd_codelist)
+#chronic kidney disease codes - all stages
+ckd15_date = last_prior_event(codelists.ckd15_codelist).date
+#chronic kidney disease codes-stages 3 - 5
+ckd35_date = last_prior_event(codelists.ckd35_codelist).date
+has_ckd = case(
+  when(ckd).then(True),
+  when((ckd35_date >= ckd15_date)).then(True),
+  otherwise = False
+)
+
+#Chronic Liver Disease
+has_cld = has_prior_event(codelists.cld_codelist)
+
+#Chronic Neurological Disease including Significant Learning Disorder
+has_cnd = has_prior_event(codelists.cnd_codelist)
+
+#Chronic Respiratory Disease
+has_crd = has_prior_event(codelists.crd_codelist)
+
+#Cancer within 3 years 
+has_cancer = (
+  has_prior_event(codelists.cancer_codelist +
+  codelists.haemotalogical_cancer_codelist +
+  codelists.lung_cancer_codelist, 
+  where = clinical_events.date.is_after(index_date - years(3)))
+)
+
+#Immunosuppression
+
+###############################################################################
+# from https://github.com/opensafely/comparative-booster-spring2023/blob/main/analysis/dataset_definition.py
+###############################################################################    
+
+#Immunosuppression diagnosis 
+immdx = has_prior_event(codelists.immunosuppression_diagnosis_codelist)
+
+#Immunosuppression medication 
+immrx = has_prior_meds(
+  codelists.immunosuppression_medications_codelist,
+  where = (medications.date.is_on_or_after(index_date - years(3)))
+)
+
+#Immunosuppression admin date
+immadm = has_prior_event(
+  codelists.immunosuppression_admin_codelist,
+  where = (clinical_events.date
+  .is_on_or_after(index_date - years(3)))
+)
+
+#Chemotherapy medication date
+dxt_chemo = has_prior_event(
+  codelists.chemo_codelist,
+  where = (clinical_events.date
+  .is_on_or_after(index_date - years(3)))
+)
+
+#Immunosuppression group
+immunosuppressed = immdx | immrx | immadm | dxt_chemo
+
+#Sickle Cell Disease
+has_sickle_cell = has_prior_event(codelists.sickle_cell_codelist)
+
+#Heart Failure
+has_heart_failure = has_prior_event(codelists.heart_failure_codelist)
+
+#Prior MI 
+has_prior_mi = has_prior_event(codelists.prior_mi_codelist)