- Access to MIMIC-IV. Learn more here.
- Project ID of a Google Project, make sure to have the necessary IAM permissions to run queries on Big Query.
Important Note: The google account enabled to access the MIMIC-IV must the be same as the one associated with the Google Project.
- run
pip install "git+https://github.com/jhn-nt/dpsdc.git"
- to test the installation, run
python3 -m unittest dpsdc.tests
- dry run, completed in a couple of minutes:
python3 -m dpsdc -p <your project-id> --dry
- to run the whole experiment (ca 2 hours), use:
python3 -m dpsdc -p <your project-id>
The above code will run the experiment for a cohort of ventilated patients using weight as a disparity axis and frequency of turnings as a proxy. To test it on a different group run:
python3 -m dpsdc -p <your project-id> -i /path/to/info.json -dp /path/to/proxy.sql -c /path/to/cohort.sql
where:
info.json
is json containing three keyscohort.sql
is a BigQuery query returning a list of patients ids of the cohort under investigationproxy.sql
A proxy quantity that one wants to investigate. Each rows shoould contain also a patient id