ETC5513: Collaborative and Reproducible Practices

Workshop 2

Author

Michael Lydeamore

Published

3 April 2025

  1. To complete this tutorial, you’ll need the pre-built RStudio project. Go to Moodle, under Week 2, download the Tutorial 2 RStudio Project zip.
    Save this file on your computer and unzip it. You can open the .Rproj file and that should launch RStudio.
  2. To render into a PDF, you will need to install the tinytex package. There are two methods to do this:
    Either install.packages("tinytex") or at your command line type quarto install tinytex. Your tutors can help with this if you get stuck.

Exercise 1: RStudio Projects

  1. Create a new RStudio project. You can call it whatever you like, but something that will help you remember later will be advantageous.
  2. Inside the project, create a folder called data.
  3. Place the avian influenza data from Moodle into this folder.
  4. Create a new Quarto documengt
  5. Write your name as an author in the YAML
  6. Change the HTML theme to cerulean.
  7. Set the document to render as HTML and PDF.

Exercise 2: YAML and R Chunk Options

  1. Create a new R chunk that loads the following libraries: rmarkdown, knitr, tidyverse, readr, kableExtra, ggplot2
  2. Change the R chunk option from to message: false and warning: false. What happens when you render the file?
  3. Create a new section called Introduction and type using markdown the following:
    “In this tutorial we are looking at the Avian Influenza cases detected globally since 1997.”
    Hint: Think about the # character.
  4. In the R chunk you made in Question 1, add the chunk option echo: false. What does this do?
  5. Using markdown, link the words “US CDC” to the website https://www.cdc.gov/bird-flu/php/avian-flu-summary/chart-epi-curve-ah5n1.html