Facilitates probabilistic record linkage between infectious disease surveillance datasets (notifiable disease registers, outbreak line-lists), vaccination registries, and hospitalization records using methods based on Fellegi and Sunter (1969) tools:::Rd_expr_doi("10.1080/01621459.1969.10501049") and Sayers et al. (2016) tools:::Rd_expr_doi("10.1093/ije/dyv322"). The package provides core functions for data preparation, linkage, and analysis: clean_the_nest() standardizes variable names and formats across heterogeneous datasets; murmuration() performs machine learning-based record linkage using blocking variables and similarity metrics; molting() deidentifies datasets for secure sharing; homing() re-identifies previously deidentified datasets; plumage() identifies and categorizes comorbidities; and preening() creates analysis-ready variables including age categories and temporal groupings. Designed for epidemiological research linking acute and post-acute disease outcomes to vaccination status and healthcare utilization. Supports multiple linkage scenarios including case-to-vaccination, case-to-hospitalization, and event-based vaccination status determination (e.g., outbreak attendees, flight passengers, exposure site visitors).
Maintainer: Nicolas Smoll nrsmoll@gmail.com (ORCID)