medicalcoder: a unified and longitudinally aware framework for International Classification of Diseases code-based comorbidity assessment in R

Abstract

Abstract Objectives Comorbidity algorithms derived from International Classification of Diseases (ICD) codes are central to risk adjustment and cohort characterization, but existing software inconsistently handles mixed ICD-9/10 data and typically operates at the encounter level. We developed medicalcoder to address these limitations. Materials and Methods medicalcoder is an R package with an internal ICD database and unified interface for applying variants of the Charlson, Elixhauser, and Pediatric Complex Chronic Conditions (PCCC) algorithms. It supports full and compact ICD codes, mixed ICD versions, present-on-admission (POA) and primary diagnosis indicators, and encounter-level and cumulative longitudinal flagging. Results The medicalcoder package requires only R ≥ 3.5.0; no additional packages, internet access, or external data are required. Outputs are consistent with published reference implementations. Longitudinal flagging identifies additional comorbidity flags under a carry-forward assumption while accounting for POA or technology-dependent logic. Conclusions medicalcoder provides a unified, reproducible framework for ICD-based comorbidity assessment in modern clinical datasets.