This package helps to convert clinical data into Medical Coding Sequences.

TemporalSequencer

Convert timestamped coding data into temporal sequences. The temporal sequencer supports shuffling codes within a specified level of temporal precision, e.g., shuffling all codes that occur on the same day. Can also add include metadata (e.g., person_id, age, sex, etc) which get serialized at the beginning.

Usage

Examples

Code:

from MedicalCodingSequence import *
from datetime import datetime
ts = TemporalSequencer(metadata={'person_id': 42})
ts.add_data(timestamp=datetime(1955, 11, 12, 22, 4, 0, 0), code=4198400)
ts.add_data(timestamp=datetime(2015, 10, 21, 0, 0, 0, 123456), code=4060282)
ts.add_data(timestamp=datetime(1985, 7, 3, 1, 2, 3, 456789), code=37606318)
print(ts.serialize())

Output:

{"person_id": 42}	(1955-11-12_22:04:00.000000, 4198400)	(1985-07-03_01:02:03.456789, 37606318)	(2015-10-21_00:00:00.123456, 4060282)

See example_temporalsequence_omop.py for an example of sequencing patient data from an OMOP database.

Notes

1. Timestamps retain full precision in serialized output regardless of shuffle_level setting
2. Metadata must be JSON serializable. For example, for DOB, convert Python datetime objects to string first since datetime objects are not JSON serializable.