install.packages(c(
  "broom",
  "fs",
  "here",
  "knitr",
  "naniar",
  "quarto",
  "rmarkdown",
  "skimr",
  "spelling",
  "tidyverse",
  "tinytex",
  "usethis",
  "visdat"
))

1.5 A note on PDF

Quarto documents can be compiled to PDF, which is a great feature. In order to convert the documents to PDF, they use a software called LaTeX (pronounced la-tek or lay-tek).

You need to install LaTeX yourself. Quarto doesn’t come with it. I recommend that you use TinyTeX, the steps are below.

Once TinyTeX is installed, Quarto takes care of the rest. Its built-in LaTeX engine runs LaTeX for you, and installs any missing LaTeX packages as it goes.

1.5.1 Installing TinyTeX

Installing LaTeX can be a pain, but thankfully Yihui Xie has put a lot of time and energy into making an easier way to install it - tinytex. tinytex is an R package that installs a sane, lightweight (<200Mb) version of LaTeX.

To install TinyTeX, run the following in R. It takes a few minutes:

tinytex::install_tinytex()

If you get the following error, this is good! As it means that TeX has already been installed:

Error: Detected an existing tlmgr at /usr/local/bin/tlmgr. It seems TeX Live has been installed (check tinytex::tinytex_root()). You have to uninstall it, or use install_tinytex(force = TRUE) if you are sure TinyTeX can override it (e.g., you are a PATH expert or installed TinyTeX previously).

Alternatively, you can run the following from the terminal

quarto install tinytex
# follow the prompts from here

1.5.2 Problem solving with LaTeX

If you have any problems with installing tinytex, I recommend you check out the tinytex FAQ page.

1.6 Test Script

You should be able to run the following code on your machine

library(broom)
library(fs)
library(here)
library(knitr)
library(naniar)
library(quarto)
library(rmarkdown)
library(skimr)
library(spelling)
library(tidyverse)
library(tinytex)
library(usethis)
library(visdat)

1.7 Downloading the exercises

The exercises and data for the course live in their own repository, qmd4sci-exercises. This code from usethis will automagically download them, and open up an RStudio project. We will talk more about those later.

usethis::use_course("njtierney/qmd4sci-exercises")

If this doesn’t work on your machine, the same files are in this zip - clicking this link should download it for you: https://github.com/njtierney/qmd4sci-exercises/archive/refs/heads/main.zip

Alternatively you can go to https://github.com/njtierney/qmd4sci-exercises and download them there by navigating to the “Download Zip” link - see below for a screenshot: