The Moving Epidemic Method Web Application

The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) , , allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week. 'memapp' is a web application created in the Shiny framework for the 'mem' R package.


Overview

memapp is a web application created to serve as a graphical user interface for the R mem package. It was created using Shiny, a web application framework for R.

Installation

The stable package can be installed from the official R repositories (CRAN) using the built-in install function (or from the package manager in some GUIs for R):

# install the memapp CRAN version
install.packages("memapp")

To install the development version of memapp use the devtools package.

# install the devtools package
install.packages("devtools")
# install the memapp development version from GitHub
devtools::install_github("lozalojo/memapp")

When installing this version also you are intalling development versions of some sensitive packages that are used by memapp (including the mem package).

Usage

To run the memapp application, just use the function:

# run the app:
memapp::runmemapp()

You can specify other parameters passed to shiny::runApp, such as display = normal, or
launch.browser = TRUE.

Notes

In order to use the Surveillance/Animation graph, magick package must be installed:

install.packages("magick")

Or alternatively, for low specs machines, the animation package:

install.packages("animation")

Along with one of the following programs: GraphicsMagick or ImageMagick:

www.imagemagick.org www.graphicsmagick.org

The installers can be downloaded from their webpages or can be installed directly from R:

# check if installr is installed, and install it otherwise
if(!require("installr")) install.packages('installr')
library("installr")
# install GraphicsMagic
install.GraphicsMagick()
# install ImageMagick
install.ImageMagick()

Localization

Starting with version 2.6, memapp enabled an option to localize the app. If your language is not listed in the Languages section and you want to see the app translated please, open the semicolon separated values file at github:

https://github.com/lozalojo/memapp/blob/master/inst/shinyapp/lang/en-GB.txt

With a text editor, translate the second column to your language and send it to the maintainer.

References

Vega T, Lozano JE, Ortiz de Lejarazu R, Gutierrez Perez M. Modelling influenza epidemic—can we detect the beginning and predict the intensity and duration? Int Congr Ser. 2004 Jun;1263:281–3.

Vega T, Lozano JE, Meerhoff T, Snacken R, Mott J, Ortiz de Lejarazu R, et al. Influenza surveillance in Europe: establishing epidemic thresholds by the moving epidemic method. Influenza Other Respir Viruses. 2013 Jul;7(4):546–58. DOI:10.1111/j.1750-2659.2012.00422.x.

Vega T, Lozano JE, Meerhoff T, Snacken R, Beaute J, Jorgensen P, et al. Influenza surveillance in Europe: comparing intensity levels calculated using the moving epidemic method. Influenza Other Respir Viruses. 2015 Sep;9(5):234–46. DOI:10.1111/irv.12330.

Lozano JE. lozalojo/mem: Second release of the MEM R library. Zenodo [Internet]. [cited 2017 Feb 1]; Available from: https://zenodo.org/record/165983. DOI:10.5281/zenodo.165983

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Reference manual

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