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United4Surveillance / signal-detection-tool

A tool for detection of signals in infectious disease surveillance data.
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SignalDetectionTool

Overview

A shiny app for automated detection of signals in infectious disease surveillance data. A signal is an anomaly in an infectious disease surveillance time series.
This app allows the user to investigate generated signals and corresponding surveillance time series. It includes upload of csv or Excel files, data checks, possibility to set parameters for signal detection, visualisation of results and generation of reports. The tool is interactive and flexible so that it can be used in different contexts and customised to the user’s needs.

Installation

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

# install.packages("devtools")
devtools::install_github("United4Surveillance/signal-detection-tool")

Usage

The shiny application is structured into a Help, Data, Input parameters, Signals and Report tab.
You can try the shiny application yourself using test data provided with the package. The test data is found in dev/data/input/input.csv.

Help

The Help tab provides more information to the user how to use the app and details about settings in the individual tabs and signal detection algorithms.

Data

In the Data tab the user can upload the surveillance data for which the signal detection should be performed. The input format is a line list of infectious disease cases and the tool accepts data in the predefined format described in dev/data/input/description.md. A data format check is automatically run once the data file has been uploaded. You can also view the required input format using

library(SignalDetectionTool)
View(input_metadata)

Input parameters

In the Input parameters tab you can configure the signal detection you want to perform. You can specify filters, stratification variables, time periods and the signal detection algorithm which should be used.

Signals

The Signals tab can look like this when using the test data and stratificaton by age group, county and sex.

Report

In the Report tab HTML and Word reports can be generated showing the results of the Signals Tab.

Development Process and Contribution

The tool development is an open source development process.

The participants of Work Package 2.2 of the United4Surveillance project will be the maintainers of the repository and can contribute directly, third parties can contribute via pull requests.

The maintainers will meet regularly and discuss pull request, issues and add new issues according to the collected requirements.

Maintainers and contributers can work indepedently on issues.

For more information on how to contribute, please see our contributing guidelines.

Roadmap

The first version 0.1.0 of the tool was provided to european public health institutes for piloting in April 2024. The piloting phase ends in November 2024.
Our goal is to get as much feedback from the piloting countries as possible. Therefore, we adopt an agile development approach with the aim to ship improved versions as often and as early as possible. Some of the current features we want to develop are: