Enough Markdown to Write a Thesis


Richard J Telford


November 13, 2022

1 Introduction

The traditional way to write a report, manuscript or thesis is to run the analyses in R or some other software and then copy the figures, tables etc. into a word processor. Then you find an error in the code or data and need to repeat the process. Repeatedly.

This is very inefficient and error prone: there is a better way.

Quarto lets you have the code and the text in one document. If the code or the data are updated, new versions of the figures and tables are automatically generated and inserted into the corrected document. This is a much more reproducible process.

This book is written with Quarto.


Perkel (2022) Cut the tyranny of copy-and-paste with these coding tools, Nature 603, 191-192 doi: https://doi.org/10.1038/d41586-022-00563-z

1.1 Organisation of this book

First Steps with Quarto shows you how to create a quarto document, edit it, add figures and tables, and render it as a finished document.

Towards a Thesis shows you how author a manuscript, report or thesis in quarto by adding citations and cross-references to figures and tables.

Fixing Problems The final section has some trouble shooting suggestions.

Quarto and R markdown

Quarto is based on R markdown. If you know how to use R markdown, you know how to use quarto as almost any R markdown document should also work with quarto.

There are several improvements in quarto over R markdown which make it easier to use.

  • No need to remember different behaviour and capabilities of rmarkdown vs bookdown etc.

  • Simplified cross-references

  • Better support for multiple programming languages

Before you start

You will need to have installed

  • RStudio (version 2022.2 or newer)
  • R
  • quarto
  • quarto R package (install.packages("quarto"))

If you cannot install quarto on your computer (perhaps because of permission problems), either use the Rmarkdown tutorial, or use rstudio.cloud.