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iaindillingham/dataset_definition.py

Last active October 2, 2023 16:56
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Dataset definition for the ehrQL tutorial
Raw
dataset_definition.py
from ehrql import case, codelist_from_csv, create_dataset, days, when
from ehrql.tables.beta.core import medications, patients
from ehrql.tables.beta.tpp import (
addresses,
clinical_events,
hospital_admissions,
practice_registrations,
)
index_date = "2023-10-01"
dataset = create_dataset()
dataset.configure_dummy_data(population_size=10)
# codelists
ethnicity_codelist = codelist_from_csv(
"codelists/opensafely-ethnicity.csv",
column="Code",
category_column="Grouping_6",
)
asthma_inhaler_codelist = codelist_from_csv(
"codelists/opensafely-asthma-inhaler-salbutamol-medication.csv",
column="code",
category_column="term",
)
# population variables
was_female_or_male = patients.sex.is_in(["female", "male"])
was_adult = (patients.age_on(index_date) >= 18) & (patients.age_on(index_date) <= 110)
was_alive = (
patients.date_of_death.is_after(index_date) | patients.date_of_death.is_null()
)
was_registered = practice_registrations.for_patient_on(index_date).exists_for_patient()
dataset.define_population(was_female_or_male & was_adult & was_alive & was_registered)
# demographic variables
dataset.age = patients.age_on(index_date)
dataset.sex = patients.sex
dataset.ethnicity = (
clinical_events.where(clinical_events.ctv3_code.is_in(ethnicity_codelist))
.sort_by(clinical_events.date)
.last_for_patient()
.ctv3_code.to_category(ethnicity_codelist)
)
imd_rounded = addresses.for_patient_on(index_date).imd_rounded
max_imd = 32844
dataset.imd_quintile = case(
when((imd_rounded >= 0) & (imd_rounded < int(max_imd * 1 / 5))).then(1),
when(imd_rounded < int(max_imd * 2 / 5)).then(2),
when(imd_rounded < int(max_imd * 3 / 5)).then(3),
when(imd_rounded < int(max_imd * 4 / 5)).then(4),
when(imd_rounded <= max_imd).then(5),
)
# exposure variable
dataset.num_asthma_inhaler_medications = (
medications.where(medications.dmd_code.is_in(asthma_inhaler_codelist))
.where(medications.date.is_on_or_between(index_date - days(30), index_date))
.count_for_patient()
)
# outcome variable
dataset.date_first_admitted = (
hospital_admissions.where(hospital_admissions.admission_date.is_after(index_date))
.sort_by(hospital_admissions.admission_date)
.first_for_patient()
.admission_date
)
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