1  ENACT

1.1 Data preparation process

The data preparation process is as follows:

  1. Run loyalty cohort using settings on 2020-01-01 and a 3-year lookback.
    * More information about loyalty cohort algorithm

  2. Download the CCSR_PASC_ACT_Mapping_022024.csv

  3. Pall patients with a COVID positive lab test or a COVID diagnosis, pull loyalty scores for these patients and cut the initial patient sets to those with a loyalty score > 0.3.
    * Query script: ExportCases.sql

  4. Pull patient data and demographics for the updated cases starting on 2017-01-01.
    * Query script: ExportDemCases.sql

1.2 Table example

Tables we need should have these columns:

Patient data (should be saved as cases.csv)

patient_num start_date concept_cd c_fullname phenx
num date (yyyy-mm-dd) char char char

Demographic data (should be saved as dems_cases.csv)

patient_num age sex_cd race_cd ethnicity_cd CHARLSON_INDEX
num num char (F/M) char char num

1.3 Directory guide

Recommended directory tree on the server/device where docker is running in the next step:

  • PASC

    • data

      • cases

        • cases.csv
        • dems_cases.csv

    • output