manifest_data

A sample dataset containing passenger manifest for flight QF123 on
2024-03-15, used to demonstrate event-based vaccination linkage.

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

manifest_data function

A data frame with 8 rows and 8 variables:<dl>
 <dt>passenger_id</dt>
<dd>Passenger identifier</dd> <dt>first_name</dt>
<dd>Passenger's first name</dd> <dt>surname</dt>
<dd>Passenger's surname</dd> <dt>date_of_birth</dt>
<dd>Passenger's date of birth</dd> <dt>gender</dt>
<dd>Gender (M/F)</dd> <dt>seat_number</dt>
<dd>Seat assignment</dd> <dt>flight_number</dt>
<dd>Flight number</dd> <dt>flight_date</dt>
<dd>Date of flight</dd>
</dl>

Format

Example Flight Manifest Dataset — manifest_data

A data frame with 8 rows and 8 variables:<dl>
 <dt>passenger_id</dt>
<dd>Passenger identifier</dd>

 <dt>first_name</dt>
<dd>Passenger's first name</dd>

 <dt>surname</dt>
<dd>Passenger's surname</dd>

 <dt>date_of_birth</dt>
<dd>Passenger's date of birth</dd>

 <dt>gender</dt>
<dd>Gender (M/F)</dd>

 <dt>seat_number</dt>
<dd>Seat assignment</dd>

 <dt>flight_number</dt>
<dd>Flight number</dd>

 <dt>flight_date</dt>
<dd>Date of flight</dd>


</dl>

manifest_data: Example Flight Manifest Dataset

Description

Usage

Arguments

Format

Examples