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comorbidipy

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comorbidipy is a Python package for calculating comorbidity scores and clinical risk scores from ICD codes. It is a modernized rewrite of the excellent R library comorbidity with additional calculators.

Features

  • 🏥 Charlson Comorbidity Index – Multiple mapping variants (Quan, Swedish, Australian, SHMI) and weighting schemes
  • 📊 Elixhauser Comorbidity Index – van Walraven and Swiss weights
  • 👴 Hospital Frailty Risk Score (HFRS) – For patients ≥75 years
  • ♿ Disability & Sensory Impairments – Learning disabilities, visual/hearing impairments

Performance

Built with Polars for exceptional performance:

  • ⚡ Process millions of rows efficiently
  • 🧠 Memory-efficient operations with lazy evaluation
  • 📁 Support for CSV, Parquet, JSON, and Avro formats

Quick Start

Installation

pip install comorbidipy

Python API

import polars as pl
from comorbidipy import comorbidity, hfrs, disability

# Sample data
df = pl.DataFrame({
    "id": ["P001", "P001", "P002", "P002"],
    "code": ["I21", "E112", "I50", "J44"],
    "age": [65, 65, 72, 72],
})

# Calculate Charlson Comorbidity Index
result = comorbidity(df, id="id", code="code", age="age")
print(result)

Command Line

# Calculate Charlson score
comorbidipy charlson input.csv output.parquet --mapping quan --weights charlson

# Calculate Elixhauser score
comorbidipy elixhauser input.csv output.csv --weights van_walraven

# Calculate HFRS
comorbidipy hfrs-cmd patients.parquet results.parquet

# Show available options
comorbidipy info

Why comorbidipy?

Feature comorbidipy Other packages
DataFrame library Polars (fast) pandas (slower)
Large datasets ✅ Streaming support ❌ Memory-bound
CLI ✅ Full-featured ❌ Limited/None
Multiple formats CSV, Parquet, JSON, Avro CSV only
Type hints ✅ Complete Partial

License

MIT License - see LICENSE for details.

Credits