training/src/processing/misc/process_validation_adm.py

from utils.adm_common import (initialize_adm_data, correct_stays,
                              track_copd_resp)


def main():

    # Load in data
    adm_file = "<YOUR_DATA_PATH>/EXAMPLE_STUDY_DATA/SMR01_Cohort3R.csv"
    adm = initialize_adm_data(adm_file)

    # Fill null STAY data and combine transfer admissions
    adm = correct_stays(adm)

    # Track COPD and respiratory events
    adm = track_copd_resp(adm)

    # Select relevant columns
    adm_reduced = adm[['SafeHavenID', 'ADMDATE', 'copd_event', 'resp_event']]

    # Track events
    adm_reduced['copd_resp_event'] = adm_reduced['copd_event'] | adm_reduced['resp_event']
    adm_reduced['adm_event'] = 1

    # Save data
    adm_reduced.to_pickle('<YOUR_DATA_PATH>/Model_E_Extracts/validation_adm_proc-og.pkl')


main()