starling: Link Infectious Disease Cases to Vaccination and Hospitalization
Records
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) <doi:10.1080/01621459.1969.10501049> and
Sayers et al. (2016) <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).
| Version: |
0.6.5 |
| Depends: |
R (≥ 3.5.0) |
| Imports: |
dplyr, lubridate, janitor, stringr, tidyr, reclin2, datawizard, digest, rlang, magrittr |
| Suggests: |
testthat (≥ 3.0.0), knitr, gtsummary, rmarkdown |
| Published: |
2026-01-26 |
| DOI: |
10.32614/CRAN.package.starling (may not be active yet) |
| Author: |
Nicolas Smoll 
[aut, cre] |
| Maintainer: |
Nicolas Smoll <nrsmoll at gmail.com> |
| License: |
GPL (≥ 3) |
| NeedsCompilation: |
no |
| Language: |
en-US |
| CRAN checks: |
starling results |
Documentation:
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