Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

A powerful tool for automating the early detection of seasonal epidemic onsets in time series data. It offers the ability to estimate growth rates across consecutive time intervals, calculate the sum of cases (SoC) within those intervals, and estimate seasonal onsets within user defined seasons. With use of a disease-specific threshold it also offers the possibility to estimate seasonal onset of epidemics. Additionally it offers the ability to estimate burden levels for seasons based on historical data. It is aimed towards epidemiologists, public health professionals, and researchers seeking to identify and respond to seasonal epidemics in a timely fashion.

aedseo

Description

The Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels (aedseo) package provides a powerful tool for automating the early detection of seasonal epidemic onsets in time series data. It offers the ability to estimate growth rates for consecutive time intervals. With use of the average observations within those intervals and an estimated disease-specific threshold it also offers the possibility to estimate seasonal onset of epidemics. Additionally it offers the ability to estimate burden levels for seasons based on historical data. It is aimed towards epidemiologists, public health professionals, and researchers seeking to identify and respond to seasonal epidemics in a timely fashion.

Installation

# Install aedseo from CRAN
install.packages("aedseo")

Development version

You can install the development version of aedseo from GitHub with:

# install.packages("devtools")
devtools::install_github("ssi-dk/aedseo")

Getting started

To quickly get started with aedseo, follow these steps:

1. Install the package using the code provided above.
2. Load the package with library(aedseo).
3. Create a time series data object (tsd) from your data using the to_time_series() function or generate_seasonal_data() functions.
4. Apply the combined_seasonal_output() function to get a comprehensive seasonal analysis with seasonal onset and burden levels.

Vignette

For a more detailed introduction to the workflow of this package, see the Get Started vignette or run;

vignette("aedseo")

Citation

The AEDSEO method is described and externally evaluated in:

Otero Sofia Myrup, Emborg Hanne-Dorthe, Telkamp Kasper Schou, Moustsen-Helms Ida Rask, Søborg Bolette, Christiansen Lasse Engbo. [Evaluation of the Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels (AEDSEO) method for respiratory surveillance using data from 21 European countries]. Eurosurveillance. 2026;31(30):2500896. https://doi.org/10.2807/1560-7917.ES.2026.31.30.2500896

To cite the aedseo package and method, run:

citation("aedseo")

Contributing

We welcome contributions to the aedseo package. Feel free to open issues, submit pull requests, or provide feedback to help us improve.