Link Infectious Disease Cases to Vaccination and Hospitalization
Records
Description
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) and
Sayers et al. (2016) . 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).