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Refactor pf desc stats measure #93

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Jan 8, 2025
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Refactor pf desc stats measure #93

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148 changes: 74 additions & 74 deletions analysis/measures_definition_pf_descriptive_stats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,112 +8,112 @@
pharmacy_first_consultation_codelist,
pharmacy_first_conditions_codelist,
)
from config import start_date_measure_descriptive_stats, monthly_intervals_measure_descriptive_stats
from config import (
start_date_measure_descriptive_stats,
monthly_intervals_measure_descriptive_stats,
)

measures = create_measures()
measures.configure_dummy_data(population_size=1000)
measures.configure_dummy_data(population_size=100)
measures.configure_disclosure_control(enabled=True)

start_date = start_date_measure_descriptive_stats
monthly_intervals = monthly_intervals_measure_descriptive_stats

registration = practice_registrations.for_patient_on(INTERVAL.end_date)

# Function to retrieve consultation ids from clinical events that are PF consultations
pharmacy_first_ids = select_events(
clinical_events, codelist=pharmacy_first_consultation_codelist
).consultation_id
# Select clinical events and medications for measures INTERVAL
selected_events = clinical_events.where(
clinical_events.date.is_on_or_between(
INTERVAL.start_date,
INTERVAL.end_date,
)
)
selected_medications = medications.where(
medications.date.is_on_or_between(
INTERVAL.start_date,
INTERVAL.end_date,
)
)

# Select all Pharmacy First consultation events
pf_consultation_events = select_events(
selected_events,
codelist=pharmacy_first_consultation_codelist,
)

# Dates of pharmacy first consultations
pharmacy_first_dates = select_events(clinical_events, codelist=pharmacy_first_consultation_codelist).date
# Extract Pharmacy First consultation IDs and dates
pf_ids = pf_consultation_events.consultation_id
pf_dates = pf_consultation_events.date

# Function to retrieve selected events using pharmacy first ids
selected_clinical_events = select_events(
clinical_events, consultation_ids=pharmacy_first_ids
).where(clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date))
has_pf_consultation = pf_consultation_events.exists_for_patient()

# Med events linked to pharmacy first consultation IDs
selected_pfid_med_events = select_events(
medications, consultation_ids=pharmacy_first_ids).where(
medications.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date)
# Select Pharmacy First conditions by ID and date
selected_pf_id_conditions = selected_events.where(
selected_events.consultation_id.is_in(pf_ids)
).where(selected_events.snomedct_code.is_in(pharmacy_first_conditions_codelist))

selected_pf_date_conditions = (
selected_events.where(selected_events.consultation_id.is_not_in(pf_ids))
.where(selected_events.date.is_in(pf_dates))
.where(selected_events.snomedct_code.is_in(pharmacy_first_conditions_codelist))
)

# Med events that are not linked by ID but are linked to PF Med codelist
selected_med_events = medications.where(medications.dmd_code.is_in(pharmacy_first_med_codelist)
).where(medications.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date)
has_pf_id_condition = selected_pf_id_conditions.exists_for_patient()
has_pf_date_condition = selected_pf_date_conditions.exists_for_patient()

# Select Pharmacy First Medications by ID and date
selected_pf_id_medications = selected_medications.where(
selected_medications.consultation_id.is_in(pf_ids)
).where(selected_medications.dmd_code.is_in(pharmacy_first_med_codelist))

selected_pf_date_medications = (
selected_medications.where(selected_medications.consultation_id.is_not_in(pf_ids))
.where(selected_medications.date.is_in(pf_dates))
.where(selected_medications.dmd_code.is_in(pharmacy_first_med_codelist))
)

# Events linked to a PF clinical pathway, and not by PF ID
selected_clinical_pathways = select_events(
clinical_events, codelist=pharmacy_first_conditions_codelist
).where(clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date))

# Create variable which contains boolean values of whether pharmacy first event exists for patient
has_pf_consultation = select_events(
selected_clinical_events, codelist=pharmacy_first_consultation_codelist).exists_for_patient()

# PF consultations with PF clinical condition
has_pf_condition = select_events(
selected_clinical_events, codelist=pharmacy_first_conditions_codelist).exists_for_patient()

# Specify whether a patient has been prescribed a PF medication on the same day as a PF consultation code
has_pfmed_on_pfdate = selected_med_events.where(medications.date.is_in(pharmacy_first_dates)).exists_for_patient()

# Specify whether a patient has a PF condition
has_pfpathway_on_pfdate = selected_clinical_pathways.where(
selected_clinical_pathways.date.is_in(pharmacy_first_dates)
).exists_for_patient()

# PF consultations with prescribed PF medication
has_pf_medication = selected_pfid_med_events.where(
selected_pfid_med_events.dmd_code.is_in(pharmacy_first_med_codelist)
).exists_for_patient()

# Define the denominator as the number of patients registered
denominator = (
registration.exists_for_patient()
& patients.sex.is_in(["male", "female"])
& has_pf_consultation
has_pf_id_medication = selected_pf_id_medications.exists_for_patient()
has_pf_date_medication = selected_pf_date_medications.exists_for_patient()

# Define measures
measures.define_defaults(
denominator=(
registration.exists_for_patient()
& patients.sex.is_in(["male", "female"])
& has_pf_consultation
),
intervals=months(monthly_intervals).starting_on(start_date),
)
measures.define_defaults(denominator=denominator)

# Measures for PF consultations with PF medication
# Measures linked by Pharmacy First consultation ID
measures.define_measure(
name="pf_with_pfmed",
numerator=has_pf_medication,
intervals=months(monthly_intervals).starting_on(start_date),
name="pfmed_with_pfid",
numerator=has_pf_id_medication,
)
# Measures for PF consultations with PF condition

measures.define_measure(
name="pf_with_pfcondition",
numerator=has_pf_condition,
intervals=months(monthly_intervals).starting_on(start_date),
name="pfcondition_with_pfid",
numerator=has_pf_id_condition,
)

# Measures for PF consultations with both PF medication and condition
measures.define_measure(
name="pf_with_pfmed_and_pfcondition",
numerator=has_pf_condition & has_pf_medication,
intervals=months(monthly_intervals).starting_on(start_date),
name="pfmed_and_pfcondition_with_pfid",
numerator=has_pf_id_medication & has_pf_id_condition,
)

# Measures for PF medications prescribed on the same day as PF consultation
# Measures linked by Pharmacy First consultation date
measures.define_measure(
name="pfmed_on_pfdate",
numerator=has_pfmed_on_pfdate,
intervals=months(monthly_intervals).starting_on(start_date),
numerator=has_pf_date_medication,
)

# Measures for PF conditions diagnosed on the same day as PF consultation
measures.define_measure(
name="pfpathway_on_pfdate",
numerator=has_pfpathway_on_pfdate,
intervals=months(monthly_intervals).starting_on(start_date),
name="pfcondition_on_pfdate",
numerator=has_pf_date_condition,
)

# Measures for PF conditions diagnosed and PF med prescribed on the same day as PF consultation
measures.define_measure(
name="pfmed_and_pfpathway_on_pfdate",
numerator=has_pfmed_on_pfdate & has_pfpathway_on_pfdate,
intervals=months(monthly_intervals).starting_on(start_date),
name="pfmed_and_pfcondition_on_pfdate",
numerator=has_pf_date_medication & has_pf_date_condition,
)
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