20 November 2019

This repository is for the development and maintenance of R teaching material for use in the EPIET (European Programme of Intervention Epidemiology Training) and UK FETP (United Kingdom Field Epidemiology Training Programme) Outbreak Investigation (OI) module.

The module includes two computer-based outbreak investigation case studies and a GIS mapping exercise; the help guides for these exercises have been translated from the STATA version into R.

This repository contains a folder for each of the following resources:

• Copenhagen case study R practical guide
• Campylobacter case study R practical guide
• GIS mapping exercise R practical guide and template code

This material is based on equivalent practical guides for STATA and ArcGIS, respectively. Each guide is presented as an R markdown document; please see the title pages for copyright details and a list of authors and contributors.

Each exercise requires the use of one or more teaching datasets, which are included in this repository.

To run the R markdown guides or R templates, participants and facilitators will need to install the following software:

• R (download and install the latest version from CRAN here)
• RStudio (download the latest version as an installer or ready-to-use .zip file here)
• Rtools (download and install the latest version from CRAN here)

A list of required R packages and functions, as well as code to install them has been included in the first chunk of each R markdown document.

After installing the above software, clone this repository either by clicking on the green Clone or download button on this page, or by entering the following command into git bash:

git clone https://github.com/EPIET/OutbreakInvestigation.git

Then:

• Open the .Rproj file in RStudio
• Navigate to the Files tab within RStudio and open the relevant case study folder
• Click on the relevant R markdown document to open it

To provide a printed copy of the R markdown practical guide for participants:

• Open the relevant R markdown document in RStudio (as above)
• Click on the Knit button and select Knit to pdf
• This will save a .pdf version of the document in your working directory, which can then be printed.

This project is currently being maintained by Amy Mikhail.

Contributions are welcome: please contact the maintainer to request access.

To report bugs or make feature requests, please post an issue here.