CLIF Table One Generator

Generate “Table One” summary (by year + overall) from CLIF parquet data files for all encounters with at least one ICU stay.

Requirements

• Required table filenames should be clif_patient, clif_hospitalization, clif_adt, clif_vitals, clif_labs, clif_medication_admin_continuous, clif_respiratory_support, clif_patient_assessments
• Within each table, the following variables and categories are required.

Table Name	Required Variables	Required Categories
patient	patient_id, race_category, ethnicity_category, sex_category, death_dttm	-
hospitalization	patient_id, hospitalization_id, admission_dttm, discharge_dttm,discharge_dttm, age_at_admission	-
adt	hospitalization_id, hospital_id,in_dttm, out_dttm, location_category	-
vitals	hospitalization_id, recorded_dttm, vital_category, vital_value	weight_kg
labs	hospitalization_id, lab_result_dttm,lab_order_dttm lab_category, lab_value_numeric	creatinine, bilirubin_total, po2_arterial, platelet_count
medication_admin_continuous	hospitalization_id, admin_dttm, med_name, med_category, med_dose, med_dose_unit	norepinephrine, epinephrine, phenylephrine, vasopressin, dopamine, angiotensin(optional)
respiratory_support	hospitalization_id, recorded_dttm, device_category, mode_category, fio2_set, lpm_set, resp_rate_set, peep_set, resp_rate_obs, tidal_volume_set, pressure_control_set, pressure_support_set,	-
patient_assessments	hospitalization_id, recorded_dttm , assessment_category, numerical_value	gcs_total
crrt_therapy	hospitalization_id, recorded_dttm	-

Configuration

1. Navigate to the config/ directory.
2. Rename config_template.json to config.json.
3. Update the config.json with site-specific settings.

Note: For multi-hospital sites that have created a hospitalization_joined_id to track patients transferring between hospitals, set id_column to hospitalization_joined_id. For single-hospital sites, use hospitalization_id as the id_column.

Environment setup and project execution

The environment setup code is provided in the generate_table_one.sh file for macOS and generate_table_one.bat for Windows.

For macOS:

1. Make the script executable and run it

chmod +x generate_table_one.sh
./generate_table_one.sh

For Windows:

1. Run the script in the command prompt:

generate_table_one.bat

Output

Upload table_one_<site_name>.csv to the box folder.