measures_opioid_all.py

###########################################################
# This script creates weekly opioid prescribing rates
#   in the 6 months pre-waiting list, during waiting list and 
#   6 months post-waiting list for people with a completed RTT pathway
#   for orthopaedic surgery only
###########################################################

from ehrql import INTERVAL, create_measures, weeks, days, minimum_of, years, when, case
from ehrql.tables.tpp import (
    patients, 
    practice_registrations,
    medications,
    clinical_events,
    addresses,
    wl_clockstops)

import codelists


##########

from argparse import ArgumentParser

parser = ArgumentParser()
parser.add_argument("--codelist")

args = parser.parse_args()

codelist_name = args.codelist
codelist = getattr(codelists, codelist_name)

##########


# WL data - exclude rows with missing dates/dates outside study period/end date before start date
last_clockstops = wl_clockstops.where(
        wl_clockstops.referral_to_treatment_period_end_date.is_on_or_between("2021-05-01", "2022-04-30")
        & wl_clockstops.referral_to_treatment_period_start_date.is_on_or_before(wl_clockstops.referral_to_treatment_period_end_date)
        & wl_clockstops.week_ending_date.is_on_or_between("2021-05-01", "2022-04-30")
        & wl_clockstops.activity_treatment_function_code.is_in(["110","111"])
    ).sort_by(
        wl_clockstops.referral_to_treatment_period_start_date,
        wl_clockstops.pseudo_referral_identifier,
        wl_clockstops.pseudo_patient_pathway_identifier,
        wl_clockstops.pseudo_organisation_code_patient_pathway_identifier_issuer
    ).last_for_patient()


# RTT waiting list start date and end date
rtt_start_date = last_clockstops.referral_to_treatment_period_start_date
rtt_end_date = last_clockstops.referral_to_treatment_period_end_date
num_weeks = (rtt_end_date - rtt_start_date).weeks

wait_gp = case(
        when(num_weeks <= 18).then("<=18 weeks"),
        when(num_weeks <= 52).then("19-52 weeks"),
        otherwise=">52 weeks"
        )


# Set artificial start/end date for running Measures
#   this is to standardise dates, as every person's 
#   start is different (and Measures works on calendar dates only)
tmp_date = "2000-01-01"

# All opioid prescriptions during study period
all_opioid_rx = medications.where(
                medications.dmd_code.is_in(codelists.opioid_codes)
                & medications.date.is_on_or_between(rtt_start_date - days(365), rtt_end_date + days(365))
            )

# Standardise Rx dates relative to RTT start date for prescribing during WL 
all_opioid_rx.tmp_wait_date = tmp_date + days((all_opioid_rx.date - rtt_start_date).days)

# Standardise Rx dates relative to RTT end date for post-WL prescribing
all_opioid_rx.tmp_post_date = tmp_date + days((all_opioid_rx.date - (rtt_end_date + days(1))).days)

# Standardise Rx dates relative to RTT start date for pre-WL prescribing 
all_opioid_rx.tmp_pre_date = tmp_date + days((all_opioid_rx.date - (rtt_start_date - days(182))).days)


### Prescribing variables for numerator ####

# Num Rx during waiting list (up to 1 year)
count_opioid_wait = all_opioid_rx.where(
                all_opioid_rx.dmd_code.is_in(codelist)
                & all_opioid_rx.tmp_wait_date.is_during(INTERVAL)
            ).count_for_patient()

# Num Rx post waiting list (up to 6 months)
count_opioid_post = all_opioid_rx.where(
                all_opioid_rx.dmd_code.is_in(codelist)
                & all_opioid_rx.tmp_post_date.is_during(INTERVAL)
            ).count_for_patient()

# Num Rx pre waiting list (up to 6 months)
count_opioid_pre = all_opioid_rx.where(
                all_opioid_rx.dmd_code.is_in(codelist)
                & all_opioid_rx.tmp_pre_date.is_during(INTERVAL)
            ).count_for_patient()


## Censoring date
registrations = practice_registrations.spanning(
        rtt_start_date - days(182), rtt_start_date
    ).sort_by(
        practice_registrations.end_date
    ).last_for_patient()

reg_end_date = registrations.end_date
end_date = minimum_of(reg_end_date, patients.date_of_death, rtt_end_date + days(365))

# Standardise end date relative to RTT start and end dates
tmp_end_date_rtt_start = tmp_date + days((end_date - rtt_start_date).days)
tmp_end_date_rtt_end = tmp_date + days((end_date - rtt_end_date).days)

# Standardise RTT end date to RTT start date
tmp_rtt_end = tmp_date + days((rtt_end_date - rtt_start_date).days)


## Cancer diagnosis in past 5 years 
cancer = clinical_events.where(
        clinical_events.snomedct_code.is_in(codelists.cancer_codes)
    ).where(
        clinical_events.date.is_on_or_between(rtt_start_date - years(5), rtt_start_date)
    ).exists_for_patient()


### Grouping/stratification variables (Final list TBD) ###
prior_opioid_count = all_opioid_rx.where(
        all_opioid_rx.date.is_on_or_between(rtt_start_date - days(182), rtt_start_date - days(1))
    ).count_for_patient()

prior_opioid_rx = (prior_opioid_count >= 3)


# Demographics
age = patients.age_on(rtt_start_date)
sex = patients.sex



######


measures = create_measures()

measures.configure_dummy_data(population_size=500)

measures.configure_disclosure_control(enabled=False)

# Denominator 
denominator = (        
        # Adults with non-missing age/sex
        (age >= 18) 
        & (age < 110)
        & (sex.is_in(["male","female"]))

        # Registered for >6 months
        & registrations.exists_for_patient()

        # No cancer
        & ~cancer

        # Censoring date (death/deregistration) after start of waiting list
        & (end_date.is_after(rtt_start_date))

        # Routine priority type
        & (last_clockstops.priority_type_code.is_in(["routine"]))       
        
        # Admitted
        & (last_clockstops.waiting_list_type.is_in(["IRTT","PTLI","RTTI"]))

        # Alive at end of waiting list
        & ((patients.date_of_death >= rtt_end_date) | patients.date_of_death.is_null())
    )


# Prescribing during WL
measures.define_measure(
    name="count_wait",
    numerator=count_opioid_wait,
    # Denominator = only include people whose RTT end date and study end date are after interval end date
    #   IOW, exclude people who are no longer on waiting list or have been censored
    denominator=denominator & (tmp_end_date_rtt_start > INTERVAL.end_date) & (tmp_rtt_end > INTERVAL.end_date),
    intervals=weeks(52).starting_on("2000-01-01"),
    group_by={"prior_opioid_rx": prior_opioid_rx,
              "num_weeks": num_weeks}
    )

# Prescribing post WL
measures.define_measure(
    name="count_post",
    numerator=count_opioid_post,
    # Denominator = only include people whose RTT end date is after interval end date
    #   IOW, exclude people who have been censored
    denominator=denominator & (tmp_end_date_rtt_end > INTERVAL.end_date),
    intervals=weeks(52).starting_on("2000-01-01"),
    group_by={"prior_opioid_rx": prior_opioid_rx,
              "num_weeks": num_weeks}
    )

# Prescribing pre WL
measures.define_measure(
    name="count_pre",
    numerator=count_opioid_pre,
    # Denominator = only include people whose RTT end date is after interval end date
    #   IOW, exclude people who have been censored
    denominator=denominator,
    intervals=weeks(26).starting_on("2000-01-01"),
    group_by={"prior_opioid_rx": prior_opioid_rx,
              "num_weeks": num_weeks}
    )