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robin-thompson edited this page Jul 7, 2019 · 37 revisions

Welcome to EpiEstim App!

EpiEstim App can be used to estimate disease transmissibility during an infectious disease outbreak from incidence time series and information about the serial interval.

Our online software interface for running EpiEstim App immediately and entirely online is now here! https://shiny.dide.imperial.ac.uk/epiestim/

It is also possible to download R and launch the application manually - this is very easy to do and can be completed in a few easy steps, which we describe here.

Getting started

  1. Download R from http://cran.us.r-project.org

  2. In R, install devtools using the command install.packages("devtools").

  3. In R, install the app using the command devtools::install_github("jstockwin/EpiEstimApp", force = TRUE).

  4. In R, run EpiEstim App using the command EpiEstimApp::runEpiEstimApp(). The app should then open in a web browser automatically, but if this does not happen then look for Listening on http://127.0.0.1:xxxx in your R console and open that page in a web browser manually.

Examples

As described in the paper (see reference at the bottom of this page), we have put together examples that can be used to reproduce the analysis in Figure 2 of the paper. To do this using the easy-to-use app, click here. To do this using R code, please click here.

Documentation

For help using EpiEstim App, see our interactive documentation pages. Sample data for use with EpiEstim App can be found with the publication below.

Issues

If you have any issues, please contact robin.thompson@chch.ox.ac.uk

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