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measures_test.py
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measures_test.py
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###################################################
# This script creates monthly counts/rates of opioid
# prescribing for any opioid prescribing by mode of administration
###################################################
from ehrql import Dataset, months, INTERVAL, Measures
from ehrql.tables.beta.tpp import (
patients,
medications,
practice_registrations)
import codelists
##########
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument("--start-date", type=str)
parser.add_argument("--intervals", type=int)
args = parser.parse_args()
start_date = args.start_date
intervals = args.intervals
##########
index_date = INTERVAL.start_date
dataset = Dataset()
# dataset.number_trans_rx = medications.where(
# medications.dmd_code.is_in(codelists.trans_opioid_codes)
# ).where(
# medications.date.is_on_or_between(index_date, INTERVAL.end_date)
# ).count_for_patient()
# dataset.number_opioid_rx = medications.where(
# medications.dmd_code.is_in(codelists.opioid_codes)
# ).where(
# medications.date.is_on_or_between(index_date, INTERVAL.end_date)
# ).count_for_patient()
number_par_rx = medications.where(
medications.dmd_code.is_in(codelists.par_opioid_codes)
).where(
medications.date.is_on_or_between(index_date, INTERVAL.end_date)
).count_for_patient()
number_diamorph_rx = medications.where(
medications.dmd_code.is_in(codelists.diamorph_opioid_codes)
).where(
medications.date.is_on_or_between(index_date, INTERVAL.end_date)
).count_for_patient()
diamorph_opioid_any = medications.where(
medications.dmd_code.is_in(codelists.diamorph_opioid_codes)
).where(
medications.date.is_on_or_between(index_date, INTERVAL.end_date)
).exists_for_patient()
par_opioid_any = medications.where(
medications.dmd_code.is_in(codelists.par_opioid_codes)
).where(
medications.date.is_on_or_between(index_date, INTERVAL.end_date)
).exists_for_patient()
par_notdiamorph_opioid_any = (
number_par_rx - number_diamorph_rx > 0
)
coprescribe_diamorph = (diamorph_opioid_any & par_notdiamorph_opioid_any)
measures = Measures()
measures.define_defaults(intervals=months(intervals).starting_on(start_date))
denominator = (
(patients.age_on(index_date) >= 18)
& (patients.age_on(index_date) < 110)
& ((patients.sex == "male") | (patients.sex == "female"))
& (patients.date_of_death.is_after(index_date) | patients.date_of_death.is_null())
& (practice_registrations.for_patient_on(index_date).exists_for_patient())
)
#########################
## Overall
# measures.define_measure(
# name="any_opioid",
# numerator=dataset.number_opioid_rx,
# denominator=denominator
# )
# measures.define_measure(
# name="par_opioid",
# numerator=dataset.number_par_rx,
# denominator=denominator
# )
# measures.define_measure(
# name="trans_opioid",
# numerator=dataset.number_trans_rx,
# denominator=denominator
# )
measures.define_measure(
name="diamorph_opioid",
numerator=number_diamorph_rx,
denominator=denominator
)
measures.define_measure(
name="par_opioid_any",
numerator=par_opioid_any,
denominator=denominator
)
measures.define_measure(
name="diamorph_opioid_any",
numerator=diamorph_opioid_any,
denominator=denominator
)
measures.define_measure(
name="par_notdiamorph_opioid_any",
numerator=par_notdiamorph_opioid_any,
denominator=denominator
)
measures.define_measure(
name="co_diamorph_opioid_any",
numerator=coprescribe_diamorph,
denominator=denominator
)