RECON Introduction to Outbreak Analysis Using R

/// Short course on outbreak analytics organised by RECON
/// - with EAN: Malta, Mater Dei Hospital, 19-20 November 2018
/// - with TEPHINET: Atlanta, Georgia, USA, 27-28 October 2019

Learning Goals

By the end of this module, the students should:

• be able to neatly organise data, scripts, and reports in R
• be able to write and render RMarkdown documents
• be able to read in and write data in flat text files
• be able to read help files effectively
• be able to perform single variable and stratified descriptive epidemiological analysis using 2x2 contingency tables
• be familiar with functions and lapply

Instructions

1. Install the {usethis} R package: install.packages("usethis", repos = "https://cran.rstudio.com")
2. Open RStudio and run usethis::create_from_github("reconhub/introduction-to-r-stegen"). This template will be downloaded to your computer's desktop and RStudio will open a new window to this project. Continue in there.
3. Using RStudio's file pane at the bottom right, open the "00-refresher.R" file to follow along. Don't move to the next step until you finish.
4. Open the first practical on RECON learn: https://www.reconlearn.org/post/stegen.html (also located in the materials/ folder)
5. Click on File > New File > New R Script and save it as "01-my-script.R"
6. Follow the practical by typing lines of code from the practical into your R script. Don't forget to add comments.

If you get stuck, an automated report is located in the 99-stegen-solutions.R file.