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

Categories are: Myocardial infarction, Congestive heart failure, Peripheral vascular disease, Cerebrovascular disease, Dementia, Chronic pulmonary disease, Rheumatic disease, Peptic ulcer disease, Mild liver disease, Diabetes without chronic complication, Diabetes with chronic complication, Hemiplegia or paraplegia, Renal disease, Any malignancy, including lymphoma and leukemia, except malignant neoplasm of skin, Moderate or severe liver disease, Metastatic solid tumor, AIDS/HIV. The Danish/Thygesen variant instead keeps Any tumor, Leukemia, and Lymphoma as three separate categories, as in the original 1987 Charlson paper.

• Mappings:
  • Deyo et al. 1992 (Deyo 1992) – ICD-9-CM (implementation="deyo")
  • Romano et al. 1993 (Romano 1993) – ICD-9-CM (implementation="romano")
  • D'Hoore et al. 1996 (D'Hoore 1996) – ICD-9-CM (implementation="dhoore")
  • Australia, Sundararajan et al. 2004 (Sundararajan 2004) – ICD-10-AM (implementation="australia")
  • Quan et al. 2005 (Quan 2005) – ICD-9-CM and ICD-10 (implementation="quan")
  • RCS, Armitage and van der Meulen 2010 (Armitage & van der Meulen 2010) – ICD-10 (always used with RCS weights) (implementation="rcs")
  • Denmark, Thygesen et al. 2011 (Thygesen 2011) – ICD-10 (implementation="thygesen")
  • Sweden, Ludvigsson et al. 2021 (Ludvigsson 2021) – ICD-9 and ICD-10 (implementation="sweden")
  • UK SHMI, NHS Digital v1.60 (June 2026) – ICD-10 (always used with SHMI weights) (implementation="uk_shmi")
  • Germany, Sokołowski et al. 2026 (Sokołowski 2026) – ICD-10-GM (year-specific; requires year_col) (implementation="sokolowski")
• Weights:
  • Charlson et al. 1987 (Charlson 1987) (weights="charlson")
  • Schneeweiss et al. 2003 (Schneeweiss 2003) (weights="schneeweiss")
  • RCS, Armitage and van der Meulen 2010 (Armitage & van der Meulen 2010) (weights="rcs")
  • Quan et al. 2011 (Quan 2011) (weights="quan")
  • UK SHMI, NHS Digital v1.60 (June 2026) (negative totals are floored at zero) (weights="uk_shmi")

Elixhauser Comorbidity Index

Categories are: Congestive heart failure, Cardiac arrhythmias, Valvular disease, Pulmonary circulation disorders, Peripheral vascular disorders, Hypertension uncomplicated, Hypertension complicated, Paralysis, Other neurological disorders, Chronic pulmonary disease, Diabetes uncomplicated, Diabetes complicated, Hypothyroidism, Renal failure, Liver disease, Peptic ulcer disease excluding bleeding, AIDS/HIV, Lymphoma, Metastatic cancer, Solid tumor without metastasis, Rheumatoid arthritis/collagen vascular diseases, Coagulopathy, Obesity, Weight loss, Fluid and electrolyte disorders, Blood loss anemia, Deficiency anemia, Alcohol abuse, Drug abuse, Psychoses, Depression.

• Mappings:
  • Elixhauser et al. 1998 (Elixhauser 1998) – ICD-9-CM (implementation="elixhauser")
  • Quan et al. 2005 (Quan 2005) – ICD-9-CM and ICD-10 (implementation="quan")
  • AHRQ v3.7 (AHRQ Comorbidity Software) – ICD-9-CM (implementation="ahrq_icd9")
  • AHRQ Refined v2026.1 (AHRQ Comorbidity Software) – ICD-10-CM (year-specific; requires year_col) (implementation="ahrq_icd10")
• Weights:
  • van Walraven et al. 2009 (van Walraven 2009) (weights="van_walraven")
  • Thompson et al. 2015 (Thompson 2015) (weights="thompson_30" or weights="thompson_29")
  • AHRQ v3.7, Moore et al. 2017 (Moore 2017) – ICD-9-CM (weights="ahrq"; always used with implementation="ahrq_icd9")
  • AHRQ Refined v2026.1 (AHRQ Comorbidity Software) – ICD-10-CM (weights="ahrq"; always used with implementation="ahrq_icd10")
  • Swiss, Sharma et al. 2021 (Sharma 2021) (weights="swiss")

Combined Comorbidity Score

Categories are: Alcohol abuse, Any tumor, Cardiac arrhythmias, Chronic pulmonary disease, Coagulopathy, Complicated diabetes, Congestive heart failure, Deficiency anemia, Dementia, Fluid and electrolyte disorders, Hemiplegia, HIV/AIDS, Hypertension, Liver disease, Metastatic cancer, Peripheral vascular disease, Psychosis, Pulmonary circulation disorders, Renal failure, Weight loss.

• Mappings:
  • Gagne et al. 2011 (Gagne 2011) – ICD-9-CM (score="combined", icd_version="icd9"; Charlson conditions after Romano 1993, Elixhauser conditions after Quan 2005)
  • Sun et al. 2017 (Sun 2017) – ICD-10-CM (score="combined", icd_version="icd10")
• Weights:
  • Gagne et al. 2011 (Gagne 2011) (score="combined")

Hospital Frailty Risk Score

• Mappings:
  • Gilbert et al. 2018 (Gilbert 2018) – ICD-10 (score="hfrs")
• Weights:
  • Gilbert et al. 2018 (Gilbert 2018) (score="hfrs")

Installation

You can install pycomorb via pip:

pip install pycomorb

R Installation

To install the R version of the package (rcomorb), you first need to install the polars dependency from the R-multiverse repository, and then install the package locally:

Sys.setenv(NOT_CRAN = "true") # Enable installation with pre-built Rust library binary
install.packages("polars", repos = "https://community.r-multiverse.org")
devtools::install("rcomorb")

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).