linelist_data

A sample dataset containing measles outbreak cases associated with a music
festival on 2024-06-01.

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

linelist_data function

A data frame with 10 rows and 10 variables:<dl>
 <dt>case_id</dt>
<dd>Case identifier</dd> <dt>first_name</dt>
<dd>Patient's first name</dd> <dt>surname</dt>
<dd>Patient's surname</dd> <dt>date_of_birth</dt>
<dd>Patient's date of birth</dd> <dt>medicare_no</dt>
<dd>Medicare number</dd> <dt>gender</dt>
<dd>Gender (M/F)</dd> <dt>postcode</dt>
<dd>Postcode of residence</dd> <dt>onset_date</dt>
<dd>Date of symptom onset</dd> <dt>notification_date</dt>
<dd>Date case was notified</dd> <dt>case_classification</dt>
<dd>Case classification (Confirmed/Probable)</dd>
</dl>

Format

Example Outbreak Linelist Dataset — linelist_data

A data frame with 10 rows and 10 variables:<dl>
 <dt>case_id</dt>
<dd>Case identifier</dd>

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

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

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

 <dt>medicare_no</dt>
<dd>Medicare number</dd>

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

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

 <dt>onset_date</dt>
<dd>Date of symptom onset</dd>

 <dt>notification_date</dt>
<dd>Date case was notified</dd>

 <dt>case_classification</dt>
<dd>Case classification (Confirmed/Probable)</dd>


</dl>

linelist_data: Example Outbreak Linelist Dataset

Description

Usage

Arguments

Format

Examples