Merge pull request #1704 from opensafely-core/bot/update-external-stu…

…dies

Update `external_studies` test code

tests/acceptance/external_studies/openprompt-long-covid-economics/analysis/dataset_definition_hx_matched_comp.py

@@ -68,6 +68,10 @@ class matched_hx_comparator(PatientFrame):
 dataset.end_deregist = matched_hx_comparator.end_deregist
 dataset.end_lc_cure = matched_hx_comparator.end_lc_cure
 dataset.end_date = minimum_of(dataset.end_death, dataset.end_deregist, dataset.end_lc_cure, study_end_date)
+dataset.total_hx_drug_visit = total_hx_drug_visit # historical prescription visits
+
+# Add current prescription visits 
+total_drug_visit(dataset, dataset.index_date, end_date=dataset.end_date)
 
 # Outcome visit
 # Historical GP visits: 2019-3-1 to 2020-3-1

tests/acceptance/external_studies/openprompt-long-covid-economics/analysis/dataset_definition_hx_matched_exp_lc.py

@@ -66,6 +66,11 @@ class matched_hx_cases(PatientFrame):
 dataset.end_deregist = matched_hx_cases.end_deregist
 dataset.end_lc_cure = matched_hx_cases.end_lc_cure
 dataset.end_date = minimum_of(dataset.end_death, dataset.end_deregist, dataset.end_lc_cure, study_end_date)
+dataset.total_hx_drug_visit = total_hx_drug_visit # historical prescription visits
+
+# Add current prescription visits 
+total_drug_visit(dataset, dataset.index_date, end_date=dataset.end_date)
+
 
 # Outcome visit
 # Historical GP visits: 2019-3-1 to 2020-3-1

tests/acceptance/external_studies/openprompt-long-covid-economics/analysis/dataset_definition_matched_cases_drug_costs.py

@@ -48,19 +48,7 @@ class matched_cases(PatientFrame):
 dataset.exposure = matched_cases.exposure
 
 # Add visits for any prescriptions:
-total_drug_visit(dataset, dataset.index_date, num_months=1, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=2, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=3, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=4, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=5, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=6, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=7, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=8, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=9, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=10, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=11, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=12, end_date=dataset.end_date)
-
+total_drug_visit(dataset, dataset.index_date, end_date=dataset.end_date)
 
 # Add drug prescription frequencies by BNF chapters 
 # drugs: bnf ch1 : gi drugs

tests/acceptance/external_studies/openprompt-long-covid-economics/analysis/dataset_definition_matched_cases_updated.py

@@ -173,21 +173,6 @@ class matched_cases(PatientFrame):
 outpatient_visit(dataset, from_date=dataset.index_date, num_months=11, end_date=dataset.end_date)
 outpatient_visit(dataset, from_date=dataset.index_date, num_months=12, end_date=dataset.end_date)
 
-# Outpatient visit for long COVID
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=1, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=2, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=3, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=4, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=5, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=6, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=7, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=8, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=9, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=10, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=11, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=12, end_date=dataset.end_date)
-
-
 # Hospital admission costs
 cost_apc_fn(dataset, from_date=dataset.index_date, num_months=1, end_date=dataset.end_date)
 cost_apc_fn(dataset, from_date=dataset.index_date, num_months=2, end_date=dataset.end_date)

tests/acceptance/external_studies/openprompt-long-covid-economics/analysis/dataset_definition_matched_control_drug_costs.py

@@ -44,19 +44,7 @@ class matched_matches(PatientFrame):
 dataset.exposure = matched_matches.exposure
 
 # Add visits for any prescriptions:
-total_drug_visit(dataset, dataset.index_date, num_months=1, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=2, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=3, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=4, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=5, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=6, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=7, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=8, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=9, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=10, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=11, end_date=dataset.end_date)
-total_drug_visit(dataset, dataset.index_date, num_months=12, end_date=dataset.end_date)
-
+total_drug_visit(dataset, dataset.index_date, end_date=dataset.end_date)
 
 # Add drug prescription frequencies by BNF chapters 
 # drugs: bnf ch1 : gi drugs

tests/acceptance/external_studies/openprompt-long-covid-economics/analysis/dataset_definition_matched_control_updated.py

@@ -168,21 +168,6 @@ class matched_matches(PatientFrame):
 outpatient_visit(dataset, from_date=dataset.index_date, num_months=11, end_date=dataset.end_date)
 outpatient_visit(dataset, from_date=dataset.index_date, num_months=12, end_date=dataset.end_date)
 
-# Outpatient visit for long COVID
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=1, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=2, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=3, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=4, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=5, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=6, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=7, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=8, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=9, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=10, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=11, end_date=dataset.end_date)
-outpatient_lc_dx_visit(dataset, from_date=dataset.index_date, num_months=12, end_date=dataset.end_date)
-
-
 # Hospital admission costs
 cost_apc_fn(dataset, from_date=dataset.index_date, num_months=1, end_date=dataset.end_date)
 cost_apc_fn(dataset, from_date=dataset.index_date, num_months=2, end_date=dataset.end_date)

tests/acceptance/external_studies/openprompt-long-covid-economics/analysis/hx_covariates.py

@@ -6,7 +6,7 @@
 from datetime import date
 from databuilder.ehrql import Dataset, days, years,  case, when
 from databuilder.tables.beta.tpp import (
-    patients, addresses, appointments,
+    patients, addresses, appointments, medications,
     practice_registrations, clinical_events,
     sgss_covid_all_tests, ons_deaths, hospital_admissions,
 )
@@ -16,6 +16,7 @@
 from variables import hospitalisation_diagnosis_matches
 
 hx_study_start_date = date(2019, 3, 1)
+hx_study_end_date = date(2020, 3, 1)
 
 # Function for extracting clinical factors
 def clinical_ctv3_matches(gpevent, codelist):
@@ -107,6 +108,12 @@ def clinical_ctv3_matches(gpevent, codelist):
 # # temporary immunosuppression
 temporary_immune_suppress = clinical_ctv3_matches(clinical_events, codelists.temporary_immune_suppress_code)
 
+# Add historical prescription visit counts:
+total_hx_drug_visit = medications \
+    .where((medications.date >= hx_study_start_date) &              
+           (medications.date  <= hx_study_end_date)) \
+    .date.count_distinct_for_patient()
+
 # The following codes will be removed later when the importing CSV file function is ready. 
 # Use these codes to test this is working. 
 

tests/acceptance/external_studies/openprompt-long-covid-economics/analysis/variables.py

@@ -57,9 +57,10 @@ def add_hx_gp_visits(dataset, num_months):
 def add_hos_visits(dataset, from_date, num_months, end_date):
     # Number of Hospitalisation within `num_months` of `from_date`
     num_visits = hospital_admissions \
-        .where((hospital_admissions.admission_date >= from_date + days((num_months-1)*30)) &
-              (hospital_admissions.admission_date  < from_date + days(num_months*30)) &
-              (hospital_admissions.admission_date  <= end_date)) \
+        .where((hospital_admissions.discharge_date >= (hospital_admissions.admission_date + days(1))) &
+               (hospital_admissions.admission_date >= from_date + days((num_months-1)*30)) &
+               (hospital_admissions.admission_date < from_date + days(num_months*30)) &
+               (hospital_admissions.admission_date <= end_date)) \
         .admission_date.count_distinct_for_patient()
     setattr(dataset, f"hos_visit_m{num_months}", num_visits)
 
@@ -68,7 +69,7 @@ def add_hx_hos_visits(dataset, num_months):
     # Number of Hospitalisation within `num_months` of `from_date`
     num_visits = hospital_admissions \
         .where((hospital_admissions.admission_date >= hx_study_start_date + days((num_months-1)*30)) &
-              (hospital_admissions.discharge_date  <  hx_study_start_date + days(num_months*30))) \
+               (hospital_admissions.discharge_date  <  hx_study_start_date + days(num_months*30))) \
         .admission_date.count_distinct_for_patient()
     setattr(dataset, f"hx_hos_visit_m{num_months}", num_visits)
 
@@ -78,8 +79,8 @@ def add_ae_visits(dataset, from_date, num_months, end_date):
     # Number of A&E visits within `num_months` of `from_date`
     num_visits = emergency_care_attendances \
         .where((emergency_care_attendances.arrival_date >= from_date + days((num_months-1)*30)) &
-              (emergency_care_attendances.arrival_date  <  from_date + days(num_months*30)) &
-              (emergency_care_attendances.arrival_date  <= end_date)) \
+               (emergency_care_attendances.arrival_date  <  from_date + days(num_months*30)) &
+               (emergency_care_attendances.arrival_date  <= end_date)) \
         .arrival_date.count_distinct_for_patient()
     setattr(dataset, f"ae_visit_m{num_months}", num_visits)
 
@@ -339,6 +340,7 @@ def cost_opa_fn(dataset, from_date, num_months, end_date):
 def hos_stay_long_fn(dataset, from_date, end_date):
     hos_stay_long = hospital_admissions \
         .where((hospital_admissions.admission_date >= from_date) &
+               (hospital_admissions.discharge_date >= (hospital_admissions.admission_date + days(1))) &
                ((hospital_admissions.discharge_date > (hospital_admissions.admission_date + days(14)))) &
                ((hospital_admissions.admission_date + days(14)) <= end_date)) \
         .count_for_patient()
@@ -348,6 +350,7 @@ def hos_stay_long_fn(dataset, from_date, end_date):
 def hos_stay_short_fn(dataset, from_date, end_date):
     hos_stay_short = hospital_admissions \
         .where((hospital_admissions.admission_date >= from_date) &
+               (hospital_admissions.discharge_date >= (hospital_admissions.admission_date + days(1))) &
                ((hospital_admissions.discharge_date <= (hospital_admissions.admission_date + days(14)))) &
                ((hospital_admissions.discharge_date <= end_date))) \
         .count_for_patient()
@@ -356,41 +359,28 @@ def hos_stay_short_fn(dataset, from_date, end_date):
 
 # Function for adding all visit for medications. 
 # Count visits on the same day once:
-def total_drug_visit(dataset, from_date, num_months, end_date):
+def total_drug_visit(dataset, from_date, end_date):
     # Same date visits for prescriptions within `num_months` of `from_date`
     num_pres = medications \
-        .where((medications.date >= from_date + days((num_months-1)*30)) &
-              (medications.date  <  (from_date + days(num_months*30))) &
-              (medications.date  <= end_date)) \
-        .where((medications.dmd_code.is_in(total_drugs_dmd))) \
+        .where((medications.date >= from_date) &              
+               (medications.date  <= end_date)) \
         .date.count_distinct_for_patient()
-    setattr(dataset, f"all_drug_visits_{num_months}", num_pres)
+    setattr(dataset, "total_drug_visit", num_pres)
 
 # Temp: test generate data
 dataset = Dataset()
 dataset.define_population(age >= 18)
-# month1 = lc_dx.date + days(0*30)
-# month2 = lc_dx.date + days(1*30)
-# month3 = lc_dx.date + days(2*30)
-# month4 = lc_dx.date + days(3*30)
-# month5 = lc_dx.date + days(4*30)
-# month6 = lc_dx.date + days(5*30)
-# month7 = lc_dx.date + days(6*30)
-# month8 = lc_dx.date + days(7*30)
-# month9 = lc_dx.date + days(8*30)
-# month10 = lc_dx.date + days(9*30)
-# month11 = lc_dx.date + days(10*30)
-# month12 = lc_dx.date + days(11*30)
+
 # hx_outpatient_visit(dataset, lc_dx.date, num_months=2)
 
-# total_drug_visit(dataset, from_date = lc_dx.date, end_date=study_end_date, num_months=6)
+# total_drug_visit(dataset, from_date = lc_dx.date, end_date=study_end_date)
 # drug_12ent_number(dataset, lc_dx.date, num_months=2)
-# add_visits(dataset, lc_dx.date, num_months=1)
-# add_visits(dataset, lc_dx.date, num_months=2)
-# add_hos_visits(dataset, lc_dx.date, num_months=3)
-# add_hos_visits(dataset, lc_dx.date, num_months=4)
-# add_ae_visits(dataset, lc_dx.date, num_months=5)
-# add_ae_visits(dataset, lc_dx.date, num_months=6)
+# add_visits(dataset, lc_dx.date, num_months=1,end_date=study_end_date)
+# add_visits(dataset, lc_dx.date, num_months=2,end_date=study_end_date)
+# add_hos_visits(dataset, lc_dx.date, num_months=3,end_date=study_end_date)
+# add_hos_visits(dataset, lc_dx.date, num_months=4, end_date=study_end_date)
+
+# add_ae_visits(dataset, lc_dx.date, num_months=6, end_date=study_end_date)
 
 # outpatient_visit(dataset, from_date=lc_dx.date, num_months=1, end_date=study_end_date)
 # outpatient_lc_dx_visit(dataset, from_date=lc_dx.date, num_months=4, end_date=study_end_date)