pycomorb

Python package to calculate comorbidity and frailty scores using ICD codes and polars DataFrames.

Overview

pycomorb provides fast, flexible, and reproducible calculation of clinical risk scores from ICD-coded data. It supports multiple comorbidity and frailty indices, including several international variants.

It is inspired by the R package comorbidity by Alessandro Gasparini and the corresponding Python rewrite comorbidipy by Vishnu V Chandrabalan.

As a special feature, it also implements the history of the German Modification of the ICD-10 (ICD-10-GM) coding system, allowing users to apply the correct mappings and weights based on the year of diagnosis.

Included Indices / Scores

• Charlson Comorbidity Index (multiple mappings and weights)
• Elixhauser Comorbidity Index (multiple mappings and weights)
• Combined Comorbidity Score (Gagne et al.)
• Hospital Frailty Risk Score (HFRS)

Supported Variants

See common/README.md for more details and references.

Charlson Comorbidity Index

• Mappings:
  • Quan et al. 2005 (Quan 2005)
  • Deyo et al. 1992 (Deyo 1992)
  • Romano et al. 1993 (Romano 1993)
  • Australia (Sundararajan et al. 2004, ICD-10-AM) (Sundararajan 2004)
  • Sweden (Ludvigsson et al. 2021, ICD-10) (Ludvigsson 2021)
  • UK SHMI (NHS Digital, v1.55)
• Weights:
  • Charlson et al. 1987 (Charlson 1987)
  • Quan et al. 2011 (Quan 2011)
  • SHMI (NHS Digital, v1.55)
  • Modified SHMI (NHS Digital, v1.55)

Elixhauser Comorbidity Index

• Mappings:
  • Quan et al. 2005 (Quan 2005)
  • Original Elixhauser et al. 1998 (ICD-9) (Elixhauser 1998)
• Weights:
  • van Walraven et al. 2009 (van Walraven 2009)
  • Thompson et al. 2015 (Thompson 2015)
  • AHRQ (Moore et al. 2017, AHRQ Comorbidity Software)

Combined Comorbidity Score

• Gagne et al. 2011 (Gagne 2011), with ICD-9 and ICD-10 support (Sun 2017)

Hospital Frailty Risk Score

• Gilbert et al. 2018, ICD-10 (Gilbert 2018)

Installation

You can install pycomorb via pip:

pip install pycomorb

Usage

import polars as pl
from pycomorb import comorbidity

# Example: Calculate Charlson score
df = pl.DataFrame({
    "id": [1, 2, 3],
    "code": ["I21", "E119", "C349"],
    "age": [65, 72, 80]
})

charlson = comorbidity(
    score="charlson",
    df=df,
    id_col="id",
    code_col="code",
    age_col="age",
    icd_version="icd10",
    implementation="quan",
    return_categories=True
)

See the docstrings in each module for details on arguments and supported variants.

License and Documentation

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• Free software: MIT license
• Documentation: (TODO)
• Die Erstellung erfolgt unter Verwendung der maschinenlesbaren Fassung des Bundesinstituts für Arzneimittel und Medizinprodukte (BfArM).