fiber-utils

Utility methods for FIBER that do not belong into the core module. Like for visualizations, cohort filters, or time series transformation.

• Free software: MIT license

Installation

From source:

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

Categories of Utility Functions

• Cohort utilities
  • Remove duplicated codings & filter cohorts based on information density
    • days_between_cohort_condition_occurrences
    • deduplicate_cohort
    • cohort_condition_occurrence_heatmap
    • cohort_condition_occurrence_filter
  • Compare cohorts
    • cohort_overlap
  • Time series handling
    • pivot_time_series
• Condition utilities
  • Condition incidence and occurrence exploration and plotting
    • most_common_condition_codes_for_cohort
    • number_condition_occurrences_per_patient
    • condition_occurrence_distribution
    • compare_condition_incidence_in_cohort
    • plot_condition_first_occurrence_on_day_hist
    • plot_condition_last_occurrence_on_day_hist
  • Quantiles & days until quantiles
    • condition_occurrence_quantiles_for_days
    • condition_occurrence_number_days_for_quantiles
• Time series utilities (symbolic and sparse symbolic representation)
  • sax_transform
  • ssr_transform

The implementation of Sparse Symbolic Representation is based on https://github.com/fbagattini/sparse_symbolic_representation. Usage granted through Creative Commons License in https://doi.org/10.1186/s12911-018-0717-4.