README.Rmd

---
title: "Brief introduction to R for Epidemiologists"
date: "`r format(Sys.time(), '%d %B %Y')`"
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```


### 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](https://cran.r-project.org/))
 - RStudio (download the latest version as an installer or ready-to-use `.zip` file [here](https://rstudio.com/products/rstudio/download/))
 - Rtools (download and install the latest version from CRAN [here](https://cran.r-project.org/bin/windows/Rtools/))


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:

```{r, eval=FALSE}

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](https://github.com/AmyMikhail).  

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

To report bugs or make feature requests, please post an issue [here](https://github.com/EPIET/IntroductoryCourse/issues).