/
measures_demo_imd.py
166 lines (136 loc) · 4.06 KB
/
measures_demo_imd.py
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from ehrql import case, when, months, INTERVAL, Measures, minimum_of, maximum_of
from ehrql.tables.tpp import (
patients,
addresses,
practice_registrations,
clinical_events)
import codelists
from dataset_definition import make_dataset_lowerGI
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 = make_dataset_lowerGI(index_date=index_date, end_date=INTERVAL.end_date)
dataset.elig_cohort = dataset.entry_date.is_on_or_before(INTERVAL.end_date) & dataset.exit_date.is_after(index_date) & patients.date_of_birth.is_not_null()
period_entry = maximum_of(index_date, dataset.entry_date)
period_exit = minimum_of(INTERVAL.end_date, dataset.exit_date)
follow_up_days = (period_exit - period_entry).days
dataset.elig_follow_up_days = case(
when(dataset.elig_cohort).then(follow_up_days)
)
dataset.fit_any = case(
when(dataset.fit_test_any).then(1),
otherwise=0
)
dataset.ida = case(
when(dataset.ida_symp).then(1),
otherwise=0
)
dataset.cibh = case(
when(dataset.cibh_symp).then(1),
otherwise=0
)
dataset.abdomass = case(
when(dataset.abdomass_symp).then(1),
otherwise=0
)
dataset.prbleed_50 = case(
when(dataset.prbleed_symp_50).then(1),
otherwise=0
)
dataset.wl_50 = case(
when(dataset.wl_symp_50).then(1),
otherwise=0
)
dataset.abdopain_50 = case(
when(dataset.abdopain_symp_50).then(1),
otherwise=0
)
dataset.anaemia_60 = case(
when(dataset.anaemia_symp_60).then(1),
otherwise=0
)
dataset.fit_6 = case(
when(dataset.fit_6_all_lowerGI).then(1),
otherwise=0
)
##########
## Define demographic variables
imd = addresses.for_patient_on(dataset.entry_date).imd_rounded
imd5 = case(
when((imd >=0) & (imd < int(32844 * 1 / 5))).then("1 (most deprived)"),
when(imd < int(32844 * 2 / 5)).then("2"),
when(imd < int(32844 * 3 / 5)).then("3"),
when(imd < int(32844 * 4 / 5)).then("4"),
when(imd < int(32844 * 5 / 5)).then("5 (least deprived)"),
otherwise="unknown"
)
#########################
measures = Measures()
measures.configure_disclosure_control(enabled=False)
measures.define_defaults(intervals=months(intervals).starting_on(start_date))
measures.define_measure(
name="fit_test_rate",
numerator=dataset.fit_any,
denominator=dataset.elig_follow_up_days,
group_by={"imd": imd5}
)
measures.define_measure(
name="ida_symp_rate",
numerator=dataset.ida,
denominator=dataset.elig_follow_up_days,
group_by={"imd": imd5}
)
measures.define_measure(
name="cibh_symp_rate",
numerator=dataset.cibh,
denominator=dataset.elig_follow_up_days,
group_by={"imd": imd5}
)
measures.define_measure(
name="abdomass_symp_rate",
numerator=dataset.abdomass,
denominator=dataset.elig_follow_up_days,
group_by={"imd": imd5}
)
measures.define_measure(
name="prbleed_symp_50_rate",
numerator=dataset.prbleed_50,
denominator=dataset.elig_follow_up_days,
group_by={"imd": imd5}
)
measures.define_measure(
name="wl_symp_50_rate",
numerator=dataset.wl_50,
denominator=dataset.elig_follow_up_days,
group_by={"imd": imd5}
)
measures.define_measure(
name="abdopain_symp_50_rate",
numerator=dataset.abdopain_50,
denominator=dataset.elig_follow_up_days,
group_by={"imd": imd5}
)
measures.define_measure(
name="anaemia_symp_60_rate",
numerator=dataset.anaemia_60,
denominator=dataset.elig_follow_up_days,
group_by={"imd": imd5}
)
measures.define_measure(
name="fit_6_rate",
numerator=dataset.fit_6,
denominator=dataset.elig_follow_up_days,
group_by={"imd": imd5}
)
measures.define_measure(
name="ca_6_rate",
numerator=dataset.ca_6_all_lowerGI,
denominator=dataset.lowerGI_any_symp,
group_by={"imd": imd5}
)