CLIF Project Title

CLIF VERSION

[major].[minor]

Objective

Describe the project objective

Required CLIF tables and fields

Please refer to the CLIF data dictionary, CLIF Tools, ETL Guide, and specific table contacts for more information on constructing the required tables and fields.

List all required tables for the project here, and provide a brief rationale for why they are required.

Example: The following tables are required:

1. patient: patient_id, race_category, ethnicity_category, sex_category
2. hospitalization: patient_id, hospitalization_id, admission_dttm, discharge_dttm, age_at_admission
3. vitals: hospitalization_id, recorded_dttm, vital_category, vital_value
   • vital_category = 'heart_rate', 'resp_rate', 'sbp', 'dbp', 'map', 'resp_rate', 'spo2'
4. labs: hospitalization_id, lab_result_dttm, lab_category, lab_value
   • lab_category = 'lactate'
5. medication_admin_continuous: hospitalization_id, admin_dttm, med_name, med_category, med_dose, med_dose_unit
   • med_category = "norepinephrine", "epinephrine", "phenylephrine", "vasopressin", "dopamine", "angiotensin", "nicardipine", "nitroprusside", "clevidipine", "cisatracurium"
6. respiratory_support: hospitalization_id, recorded_dttm, device_category, mode_category, tracheostomy, fio2_set, lpm_set, resp_rate_set, peep_set, resp_rate_obs

For Python users, the clifpy package provides essential utilities for working with CLIF data, including:

• Key features: outlier handling, encounter stitching, wide data creation, and more
• Advanced features: SOFA score computation, respiratory support waterfall, medication unit conversion, and more

See the clifpy user guide for detailed documentation.

Cohort identification

Describe study cohort inclusion and exclusion criteria here

Expected Results

Describe the output of the analysis. The final project results should be saved in the output/final directory.

Detailed Instructions for running the project

1. Update config/config.json

Follow instructions in the config/README.md file for detailed configuration steps.

Note: if using the 01_run_cohort_id_app.R file, this step is not necessary as the app will create the config file for the user

2. Set up the project environment

Describe the steps to setup the project environment.

Example for R: Run 00_renv_restore.R in the code to set up the project environment

Example for Python:

Preferred method using uv:

uv init project-name
cd project-name

Note: uv automatically creates virtual environments and manages dependencies. It generates required files like uv.lock for reproducible builds. For more details, see the CLIF uv guide by Zewei Whiskey Liao.

Alternative method using python3:

python3 -m venv .mobilization
source .mobilization/bin/activate
pip install -r requirements.txt 

3. Run code

Detailed instructions on the code workflow are provided in the code directory

Example Repositories

• CLIF Adult Sepsis Events for R
• CLIF Eligibility for mobilization for Python
• CLIF Variation in Ventilation

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