hosp_data

A sample dataset containing hospitalization records for 10 individuals,
with 3 overlapping with dx_data.

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

hosp_data function

A data frame with 10 rows and 11 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 with check digit</dd> <dt>sex</dt>
<dd>Sex (1=Male, 2=Female)</dd> <dt>zip_codes</dt>
<dd>Postcode</dd> <dt>cultural_heritage</dt>
<dd>Indigenous status</dd> <dt>icd_codes</dt>
<dd>ICD-10 diagnosis code</dd> <dt>date_of_admission</dt>
<dd>Hospital admission date</dd> <dt>date_of_discharge</dt>
<dd>Hospital discharge date</dd>
</dl>

Format

Example Hospitalization Dataset — hosp_data

A data frame with 10 rows and 11 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 with check digit</dd>

 <dt>sex</dt>
<dd>Sex (1=Male, 2=Female)</dd>

 <dt>zip_codes</dt>
<dd>Postcode</dd>

 <dt>cultural_heritage</dt>
<dd>Indigenous status</dd>

 <dt>icd_codes</dt>
<dd>ICD-10 diagnosis code</dd>

 <dt>date_of_admission</dt>
<dd>Hospital admission date</dd>

 <dt>date_of_discharge</dt>
<dd>Hospital discharge date</dd>


</dl>

hosp_data: Example Hospitalization Dataset

Description

Usage

Arguments

Format

Examples