DESA: An R Package for Detecting Epidemics using a School-Absenteeism Surveillance Framework

TL;DR

DESA is an R package that models and detects influenza epidemics early through school absenteeism data, providing a comprehensive tool for researchers and public health officials.

Contribution

Introduces DESA, an R package that models, detects, and evaluates epidemics using absenteeism data, with simulation capabilities for research and early warning.

Findings

Provides a complete workflow demonstration with simulated data.

Enables early detection and alerting of influenza epidemics.

Accessible via CRAN for the R community.

Abstract

Absenteeism of elementary school children has been shown to be effective in the early detection of an incoming influenza epidemic within a given population. This paper introduces DESA, an R package designed to: 1) model an epidemic using school absenteeism data, 2) raise an alert for an incoming epidemic using school absenteeism data, 3) evaluate the timeliness of the raised alert using different metrics, and 4) simulate community-level household populations, epidemics, and school absenteeism to facilitate research in related fields. This paper provides an overview of the functions in the package and demonstrates its complete workflow using simulated data generated within the package. DESA offers researchers and public health officials a tool for improving early detection of seasonal influenza epidemics or epidemics of other diseases. The package is available on CRAN, making it readily accessible to the R user community.