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FIBER

The fiber package.

  • Free software: MIT license

Installation

From source:

git clone https://gitlab.hpi.de/fiber/fiber && \
cd fiber && \
pip install -e .

Quickstart

For a quick start, checkout this iPython notebook. We demonstrate the most important Features in there.

Configuration of the database connection

Check out .env-example to setup the HANA or MySQL connection.

Features

Cohort

Basic Functions:

  • occurs(target, event) All target occurrences in relation to an event.
  • values_for(target, event) All target values in relation to an event.

For each event, all relevant target entries are returned with a relative timedelta in days.

Postprocessing Functions:

  • has_co_occurrence(df, time_windows) Binary occurrence for different time windows relative to the event.
  • aggregate_values(df, time_windows) Aggregate values for different time windows relative to the event.

Convenience Functions:

Wrappers around has_co_occurrence for frequently used

  • has_onset(time_windows=[(0, 1), (0, 7), (0, 14), (0, 28)])
  • has_precondition(time_windows=[(-inf, 0)])

Stores

YAMLStore

  • Retrieve lists of codes for ICD-10, ICD-9 and other schemes. Can be used for example for diagnosis, procedures or vital signs. 
    import fiber.storage.yaml as fiber_yaml
fiber_yaml.get_condition(Procedure, 'heart surgery', ['ICD-10', 'ICD-9'])