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Brief introduction to R for Epidemiologists

20 November 2019

Background:

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) introductory course (IC).

The module now includes a brief demonstration session to introduce participants to R.

An R markdown document demonstrates how to perform key tasks for epidemiologists:

  • Setting up an R project file in RStudio
  • Create an R script
  • Create an R markdown / notebook file
  • Installing and loading packages
  • Setting the working directory using the here package
  • Importing and viewing a dataset
  • Exploring an imported dataset
  • Recoding variables
  • Creating new variables with conditional logic (e.g. a case definition)
  • Performing descriptive analysis (epicurve of symptom onset dates and age sex profile of cases)
  • Calculating risk ratios for exposures (raw and stratified)

Acknowledgements:

This material is based on an equivalent introductory guide to STATA for epidemiologists, written by Alicia Barrasa, for the EPIET/EUPHEM programme introductory course. The document demonstrates how to perform the same steps in R.

Requirements:

This demonstration uses a STATA .dta teaching dataset from an outbreak of gastrointestinal infection that occured at a school dinner. The dataset is included in this repository.

To run this demonstration, the demonstrator will need the following software installed on their machine:

  • 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)

In addition, the following packages are required (the first chunk in the R markdown document will automatically install them if needed when run on the demonstrator’s machine):

  • here: locates your working directory in the folder where you created your .Rproj file
  • haven: imports STATA .dta datasets and other less common file types into R
  • data.table: data cleaning, recoding, reshaping and creating summary tables
  • lubridate: performing calculations with dates
  • epitrix: create 2x2 epitables and other functions for cleaning epidemiological data
  • ggplot2: create graphs
  • epitools: calculate risk ratios
  • EpiFunc: create descriptive epidemiology figures (age sex pyramids and epicurves)
  • devtools: used to install and build the EpiFunc package from Github

How to use:

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/IntroductoryCourse.git

Then:

  • Open the .Rproj file in RStudio
  • Navigate to the Files tab within RStudio
  • Click on 20191015_Brief introduction to R_script_AM.Rmd R markdown document to open it
  • Run each chunk separately in the live demonstration, explaining what is happening as you go.

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

  • Open the 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.

Maintenance:

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.