EpiSignalDetection tool

Tool

EpiSignalDetection is a tool for detection of epidemiological signals. Public health experts and epidemiologists can use the tool to detect signals for outbreaks, based on changes in disease incidence.

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EpiSignalDetectionReport tool - graph

EpiSignalDetection is an R package, which analyses surveillance data to identify any fluctuations in disease incidence, which might indicate early warning signs for outbreaks.  Statistical methods are applied to analyse observed infectious diseases surveillance data collected by ECDC at the EU/EEA or country level. The tool includes:

  • Signal Detection tool, an interactive 'shiny' application in which the user can import external data and perform basic signal detection analyses;
  • An automated report in HTML format, presenting the results of the time series analysis in tables and graphs. The report can also be stratified by population characteristics (see 'Population' variable).

Installation

The software is available as an R package under European Union Public Licence v.1.2 EUPL © the European Union 2007, 2016.

R was chosen as the computing platform, to make the tool as broadly available as possible, as it is free, open source, and runs on any modern operating system.

To use an R package, R must first be downloaded and installed on your computer.

The R package of the EpiSignalDetection tool can be downloaded for free using the following options: from the ECDC website, from the CRAN website, as well as from GitHub.

Instructions:

For detailed instructions for installing the R package, read the manual and the vignette.

Option 1: Download from the ECDC website

Public health experts and epidemiologists can download the software from the ECDC website.

Steps: To install from the ECDC website

1. Download the package: EpiSignalDetection tool: Source package
2. Open R.
3. Open the Packages menu.
4. Select Install package(s) from local zip files.
5. Navigate to where you have saved the ECDC Zip.
6. Select filename and click Open.

The package must be downloaded to your computer before you can open it in R. DO NOT unpack the downloaded Zip file, it only needs to be saved on your computer.

To verify the integrity of the original zip file (version 0.1.1):

 MD5 checksum
593e41346b69abb5d71516f0b9474260

SHA1 checksum
6e5996a08e47c710163950b9a15dbafb142d7783

Option 2: Download from CRAN

For R users, an R package was released on the CRAN repository:

Option 3: Download from GitHub

GitHub users can download directly from the ECDC GitHub page:

Disclaimer

ECDC accepts no responsibility or liability whatsoever (including but not limited to any direct or consequential loss or damage it might occur to you and/or any other third party) arising out of or in connection with the installation and/or usage of this software.

Suggested citation

EpiSignalDetection: Signal Detection Analysis, R package, [software application] Version 0.1.1 Stockholm: European Centre for Disease Prevention and Control; 2018