study_definition_prevax_extf.py

# Import statements

## Set seed
import numpy as np
np.random.seed(123456)

## Cohort extractor
from cohortextractor import (
  StudyDefinition,
  patients,
  codelist_from_csv,
  codelist,
  filter_codes_by_category,
  combine_codelists,
)

## Codelists from codelist.py (which pulls them from the codelist folder)
from codelists import *

## Datetime functions
from datetime import date

## Study definition helper
import study_definition_helper_functions as helpers
# Specify index date for MH prevax
## Import common variables function
from common_variables import generate_common_variables
(
    dynamic_variables
) = generate_common_variables(index_date_variable="index_date_cohort", exposure_end_date_variable="end_date_exposure", outcome_end_date_variable="end_date_outcome")

## Variables for deriving JCVI groups
from grouping_variables import (
    study_dates,
    jcvi_variables, 
    start_date,
    end_date,
    pandemic_start
)

study = StudyDefinition(

    # Specify study dates
        index_date_cohort = patients.with_value_from_file(
            f_path = 'output/index_dates.csv.gz', 
            returning = 'index_prevax', 
            returning_type = 'date', 
            date_format = 'YYYY-MM-DD',
        ),
        end_date_exposure = patients.with_value_from_file(
            f_path = 'output/index_dates.csv.gz', 
            returning = 'end_prevax', 
            returning_type = 'date', 
            date_format = 'YYYY-MM-DD',     
        ),
        end_date_outcome = patients.with_value_from_file(
            f_path = 'output/index_dates.csv.gz', 
            returning = 'end_prevax_extf', 
            returning_type = 'date', 
            date_format = 'YYYY-MM-DD',     
        ),

    # Configure the expectations framework
        default_expectations={
            "date": {"earliest": study_dates["earliest_expec"], "latest": "today"},
            "rate": "uniform",
            "incidence": 0.5,
        },

    # Define the study population 
    # NB: all inclusions and exclusions are performed in stage 1
        population = patients.all(),

    # Define sex 
    # NB: this is required for JCVI variables hence is defined here
        cov_cat_sex = patients.with_value_from_file(
            f_path = 'output/index_dates.csv.gz',
            returning = 'cov_cat_sex',
            returning_type = 'str',  
        ),
    
    ## Any covid vaccination, identified by target disease
        vax_date_covid_1 = patients.with_value_from_file(
            f_path = 'output/index_dates.csv.gz',
            returning = 'vax_date_covid_1',
            returning_type = 'date'          
        ),

    # Define vaccine eligibility variables
        **jcvi_variables, 

    # Define common variables (e.g., exposures, outcomes, covariates) that require dynamic dates
        **dynamic_variables
        
)