Charlson Comorbidity Index

The Charlson Comorbidity Index (CCI) is a method of categorizing comorbidities of patients based on ICD diagnosis codes. Each comorbidity category has an associated weight based on the adjusted risk of mortality or resource use.

Overview

The original Charlson index was developed in 1987 and has been updated several times with different mapping schemes for ICD-9 and ICD-10 codes.

Supported Mappings

Mapping	ICD-9	ICD-10	Description
quan	✅	✅	Quan et al. (2005) - Most widely used
swedish	❌	✅	Swedish National Patient Register
australian	❌	✅	Australian IHW adaptation
shmi	❌	✅	UK Summary Hospital-level Mortality Indicator

Weighting Schemes

Weighting	Description
charlson	Original 1987 weights (1-6 scale)
quan	Quan et al. updated weights
shmi	UK SHMI weights
shmi_modified	Modified SHMI weights

Comorbidity Categories

The Charlson index identifies 17 comorbidity categories:

Abbreviation	Condition	Original Weight
ami	Acute myocardial infarction	1
chf	Congestive heart failure	1
pvd	Peripheral vascular disease	1
cevd	Cerebrovascular disease	1
dementia	Dementia	1
copd	Chronic obstructive pulmonary disease	1
rheumd	Rheumatoid disease	1
pud	Peptic ulcer disease	1
mld	Mild liver disease	1
diab	Diabetes without complications	1
diabwc	Diabetes with complications	2
hp	Hemiplegia or paraplegia	2
rend	Renal disease	2
canc	Cancer (any malignancy)	2
msld	Moderate or severe liver disease	3
metacanc	Metastatic solid tumor	6
aids	AIDS/HIV	6

Usage

Python API

import polars as pl
from comorbidipy import comorbidity, ScoreType, MappingVariant, WeightingVariant

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

# Basic calculation
result = comorbidity(
    df,
    id_col="id",
    code_col="code",
    score=ScoreType.CHARLSON,
)

# With age adjustment
result = comorbidity(
    df,
    id_col="id",
    code_col="code",
    age_col="age",
    score=ScoreType.CHARLSON,
    weighting=WeightingVariant.CHARLSON,
)

# Using Swedish mapping
result = comorbidity(
    df,
    id_col="id",
    code_col="code",
    score=ScoreType.CHARLSON,
    variant=MappingVariant.SWEDISH,
)

CLI

# Basic Charlson calculation
comorbidipy charlson input.csv output.csv

# With specific mapping and weights
comorbidipy charlson input.csv output.parquet \
    --mapping quan \
    --weights charlson \
    --age-col age

# Using Swedish mapping
comorbidipy charlson input.csv output.csv --mapping swedish

Age Adjustment

When age is provided with the original Charlson weights, the score includes an age component:

• Age 40-49: +1 point
• Age 50-59: +2 points
• Age 60-69: +3 points
• Age 70+: +4 points

The output includes: - comorbidity_score: Base score without age adjustment - age_adj_comorbidity_score: Score with age adjustment - survival_10yr: Estimated 10-year survival probability

Assign Zero Logic

By default (assign0=True), when a more severe form of a condition is present, the less severe form is set to 0:

• mld (mild liver disease) → 0 if msld (moderate/severe) present
• diab (diabetes) → 0 if diabwc (diabetes with complications) present
• canc (cancer) → 0 if metacanc (metastatic cancer) present

To keep both forms:

result = comorbidity(df, assign0=False)

Output

The output DataFrame includes: - Patient ID column - Binary columns (0/1) for each of the 17 comorbidity categories - comorbidity_score: Weighted sum of comorbidities - age_adj_comorbidity_score: (if age provided with Charlson weights) - survival_10yr: (if age provided with Charlson weights)

References

1. Charlson ME, et al. A new method of classifying prognostic comorbidity in longitudinal studies. J Chronic Dis. 1987;40(5):373-383.
2. Quan H, et al. Coding algorithms for defining comorbidities in ICD-9-CM and ICD-10 administrative data. Med Care. 2005;43(11):1130-1139.