An R package for working with ICD codes and comorbidity assessments.
The medicalcoder package was intentionally designed and built to have zero dependencies beyond R version 3.5.0 (needed due to a change in data serialization) and zero imports. The package is completely self-contained for the purposes of installation and use.
This design choice was made for several reasons.
Ease of installation:
Only requirement is R >= 3.5.0.
No need for external files, downloads, or other packages for the ICD database.
Works well with different data paradigms
Base R data.frames,
tidyverse tibbles, and
data.tables from the data.table package.
One of the reasons for focusing on building a self-contained package with no need for additional namespaces is to make installation and use in a pseudo-air-gapped system easier. The author of this package routinely works on machines with extremely limited access to the world-wide web. As such, relying on any system dependencies or other R packages can become difficult as the machine may or may not have the needed software. So long as R >= 3.5.0 is available, medicalcoder will work.
A great deal of thought went into performance of the methods and the size of the package. The internal data sets, for example, are not stored in a structure that is easy to use for end users. When the package namespace is loaded, the needed internal lookup tables are generated and cached.
Maintainer: Peter DeWitt peter.dewitt@cuanschutz.edu (ORCID) [cover designer]
Other contributors:
Tell Bennett tell.bennett@cuanschutz.edu (ORCID) [contributor]
Seth Russell seth.russell@cuanschutz.edu (ORCID) [contributor]
Meg Rebull meg.rebull@cuanschutz.edu (ORCID) [contributor]
Vincent Rubinetti vincent.rubinetti@cuanschutz.edu (ORCID) [cover designer]
medicalcoder is a lightweight, base-R package for working with ICD-9 and ICD-10 diagnosis and procedure codes. It provides fast, dependency-free tools to look up, validate, and manipulate ICD codes, while also implementing widely used comorbidity algorithms such as Charlson, Elixhauser, and the Pediatric Complex Chronic Conditions (PCCC). Designed for portability and reproducibility, the package avoids external dependencies—requiring only R >= 3.5.0—yet offers a rich set of curated ICD code libraries from the United States' Centers for Medicare and Medicaid Services (CMS), Centers for Disease Control (CDC), and the World Health Organization (WHO).
The package balances performance with elegance: its internal caching, efficient joins, and compact data structures make it practical for large-scale health data analyses, while its clean design makes it easy to extend or audit. Whether you need to flag comorbidities, explore ICD hierarchies, or standardize clinical coding workflows, medicalcoder provides a robust, transparent foundation for research and applied work in biomedical informatics.
comorbidities(), get_icd_codes(), is_icd(),
Vignette for working with ICD codes:
Vignettes for applying comorbidities: