vax_data

A sample dataset containing vaccination records in long format for multiple
individuals, with some having multiple vaccination entries.

datasets

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).

Nicolas Smoll

starling

Link Infectious Disease Cases to Vaccination and Hospitalization
Records

vax_data function

A data frame with 15 rows and 9 variables:<dl>
 <dt>patient_id</dt>
<dd>Patient identifier</dd> <dt>firstname</dt>
<dd>Patient's first name</dd> <dt>last_name</dt>
<dd>Patient's last name</dd> <dt>birth_date</dt>
<dd>Patient's date of birth</dd> <dt>medicare_number</dt>
<dd>Medicare number</dd> <dt>gender</dt>
<dd>Gender (Male/Female)</dd> <dt>postcode</dt>
<dd>Postcode of residence</dd> <dt>vaccine_delivered</dt>
<dd>Type of vaccine administered</dd> <dt>service_date</dt>
<dd>Date of vaccination</dd>
</dl>

Format

Example Vaccination Dataset — vax_data

A data frame with 15 rows and 9 variables:<dl>
 <dt>patient_id</dt>
<dd>Patient identifier</dd>

 <dt>firstname</dt>
<dd>Patient's first name</dd>

 <dt>last_name</dt>
<dd>Patient's last name</dd>

 <dt>birth_date</dt>
<dd>Patient's date of birth</dd>

 <dt>medicare_number</dt>
<dd>Medicare number</dd>

 <dt>gender</dt>
<dd>Gender (Male/Female)</dd>

 <dt>postcode</dt>
<dd>Postcode of residence</dd>

 <dt>vaccine_delivered</dt>
<dd>Type of vaccine administered</dd>

 <dt>service_date</dt>
<dd>Date of vaccination</dd>


</dl>

vax_data: Example Vaccination Dataset

Description

Usage

Arguments

Format

Examples