Reproducible R

 

These exercises follow the material in Reproducible R.

Exercise 1 - Rmarkdown basics

• Open up markdownExampleDefaultStyles.Rmd and compare each section to the rendered output: Example HTML Default style.. Review how each piece of markdown controls the final rendered document. There are several examples we have not covered in the slides.

• Open up markdownExample.Rmd in the scripts directory and compare to the rendered output: Example HTML with extra style.. What has changed?

# Different Styles in YAML
# Updated table of contents in YAML
# Set Up chunk - we can use this to control defaults for code chunk arguments. In this case we have turned echo off for every chunk. 

Exercise 2 - Convert a Rmarkdown

• Open scriptToConvertToRMarkdown.r in scripts directory and save as new name.
• Convert this script to an Rmarkdown document inside RStudio.
• Update YAML to reflect author, date, title etc.
• Break the code down into chunks. Add some code chunk arguments to control figure sizes and/or echo of code.
• Add appropriate annotation and session information.
• Try making both interactive and non-interactive versions of the tables and plots.
• Render the document.

Exercise 3 - Make a Rmarkdown - Make your own Rmarkdown document from scratch - Include YAML parameters like date - Read in file “readThisTable.csv” - Run some summary stats and plots - Use chunk arguments: fig.height/fig.width/fig.path/dev to save plots in pdf and png format

Exercise 4 - Quarto - Convert your Rmd from exercise 2 into a Quarto document - Keep the parameters the same. Render and review the result. Compare it to the Rmd output. - Try and update all code arguments

Additional Exercise - Take some of your own scripts. They can either be python or R. Try and convert them into an Rmarkdown/Quarto format so you can create a nice report summary of that piece of work.