covid19_CDSS

Work in progress

Setup

Perform all steps listed here to complete setup

Requirements:

pip install -r requirements.txt

Create Credentials

1. Login on https://data.castoredc.com
2. Create an API Client ID and Client Secret in your Castor account settings
3. Save the client_id (string with dashes) in a file called 'client'
4. Save the client_secret (long alphanumerical string) in a file called 'secret'
5. Put these two files in one seperate private folder

Create Config file

1. Fill in paths to API-credentials and/or path to files in covid19_createconfig.py. Do not push this file filled in to master.
2. Run covid19_createconfig.py

Running analysis

1. Change parameters at the bottom of covid19_ICU_admission.py __main__ to set:

   • The prediction goal (goal)
   • Variables to include in the prediction (variables_to_include). These are based on the variables names used in Castor and data_struct
   • The model to use, these are classes stored in .\Classifiers.

2. Run the file from an editor or command line python covid19_ICU_admission.py

Adding new model

Add new models by using the blueprint in .\Classifiers\classifier_blueprint.py. Read the comments within the file carefully and do NOT change the prewritten variables. DO NOT edit the blueprint file but copy it.

Using castor_api (standalone)

See https://github.com/wouterpotters/castor-python

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For questions:

API: Wouter Potters

Pipeline: Maarten Ottenhoff