Pre-tutorial instructions

Getting ready for D-Day

Need help before the tutorial in Salzburg ?

Christophe will be around on Monday 8th July in the morning - you can reach out to meet if you have any problems to share ahead of the tutorial.

He can be contacted beforehand - See profile at @cderv.

Before the tutorial, please follow these steps:

Before Tutorial day

Setting up your environment:

• Download and install the latest versions of R, RStudio and Quarto:

  • A recent version of R (4.4 or higher)

  • The latest version of RStudio (2024.04.2-764 or higher)

  • The latest version of Quarto 1.5 available at https://quarto.org/docs/download/

• Install the following packages:

  # For the exercises 
  # (dplyr and ggplot2 should be sufficient if you don't want the entire tidyverse)
  pkg_list <- c("rmarkdown", "palmerpenguins", "gt", "tidyverse") 
  # R base
  install.packages(pkg_list)
  # or using pak
  pak::pkg_install(pkg_list)

If you prefer to have the files locally in advance:

• Download exercises.zip. This compressed folder contains various resources that may be useful for the exercises. Unzip it on your desktop or in a location that you can easily locate on your computer. You will be able to simply copy and paste the files you need throughout the tutorial.

• Download examples-correction.zip. This is the equivalent of exercise solutions - Do not look in advance if you really want to practice on the day. This compressed folder contains various resources used as examples and demonstrations. Unzip it on your desktop or in a location that you can easily locate on your computer. You will be able to simply copy and paste the files you need throughout the tutorial.

Advice

Create a dedicated folder on your environment for the tutorial to store the exercises, your notes and to be able to do the exercises in a healthy environment.

Don’t create an RStudio folder because we’ll be creating different projects for the exercises, and creating RStudio sub-projects doesn’t work well.

Example of organization:

> tuto-quarto-user-2024
|-- notes/
|-- exercises/
  |-- rstudio-project1/
  |-- quarto-project1/
|-- README.md (to note the context of these files)

What you need to know (or revise) to feel at ease

Assumption for the tutorial: You know R Markdown and you know Markdown syntax.

• Markdown syntax for Pandoc

  • This is the same as R Markdown:
    https://bookdown.org/yihui/rmarkdown/markdown-syntax.html

  • It is also documented on Quarto website:
    https://quarto.org/docs/authoring/markdown-basics.html

• Include R code with knitr

  • R code chunks:
    https://bookdown.org/yihui/rmarkdown/r-code.html

  • What is an R Markdown file?
    https://bookdown.org/yihui/rmarkdown-cookbook/rmarkdown-anatomy.html

Check your setup

Here are a few tips for checking your installation if you’ve installed quarto yourself:

• quarto check install must operate without error

  $ quarto check install
  
  Quarto 1.5.53
  [>] Checking Quarto installation......OK
        Version: 1.5.53
        Path: C:\Users\chris\scoop\apps\quarto\current\bin
        CodePage: 1252
  
  [>] Checking tools....................OK
        TinyTeX: v2024.07.03
        Chromium: 869685
  
  [>] Checking LaTeX....................OK
        Using: TinyTex
        Path: C:\Users\chris\AppData\Roaming\TinyTeX\bin\windows\
        Version: 2024
  
  [>] Checking basic markdown render....OK

  It is better if you have TinyTeX installed to work with Quarto (https://quarto.org/docs/output-formats/pdf-engine.html#installing-tex), but not mandatory for this tutorial.

• quarto check knitr must work without error

  $ quarto check knitr
  
  Quarto 1.5.53
  (-) Checking R installation...........
  
  [>] Checking R installation...........OK
        Version: 4.4.0
        Path: C:/PROGRA~1/R/R-44~1.0
        LibPaths:
          - C:/Users/chris/AppData/Local/R/win-library/4.4
          - C:/Program Files/R/R-4.4.0/library
        knitr: 1.47
        rmarkdown: 2.27
  
  [>] Checking Knitr engine render......OK