Quarto for Scientists
Dr Nick Tierney
For a scientific report to be completely credible, it must be reproducible. The full computational environment used to derive the results, including the data and code used for statistical analysis should be available for others to reproduce.
Quarto is a tool that allows you integrate your code, text and figures in a single file in order to make high quality, reproducible reports. A paper published with an included Quarto file and data sets can (in principle) be reproduced by anyone with a computer.
This is a course on how to use Quarto, with the target audience being for scientists. This was first developed as a short workshop on rmarkdown, as the book rmarkdown for scientists. The general structure will be the same, and it will grow and change over time as a living book.
https://qmd4sci.njtierney.com/
Learning Outcomes
After completing this course, you will know how to:
- Create your own Quarto document
- Create figures and tables that you can reference in text, and update with - your data
- Export your Quarto document to PDF, HTML, and Microsoft Word
- Use keyboard shortcuts to improve workflow
- Cite research articles and generate a bibliography
We may, depending on time, also cover the following areas:
- Change the size and type of your figures
- Create captions for your figures, and reference them in text
- Cite research articles and generate a bibliography
- Debug and handle common errors
Pre-workshop preparation
See the installation chapter for details on software to be installed.
Working materials will be made available at https://github.com/njtierney/qmd4sci-materials.
Schedule
| Duration1 | Topic |
|---|---|
| 15min | Get started with your own Quarto document |
| 20min | Workflow when using Quarto documents and projects |
| 20min | Exporting Quarto documents to PDF, HTML, and Microsoft Word |
| 10min | Break |
| 30min | Managing captions, figures, tables |
| 15min | Managing equations and bibliographies |
| 30min | Break |
| 30min | How to debug and handle common errors |
| 30min | Other Quarto formats |
| 10min | Break |
| 60min | Other Quarto formats |
About the Presenter
Dr Nick Tierney has an bachelors and honours degree in Psychological Science, and completed his PhD in Statistics (under Kerrie Mengersen) in 2018. He works as a research software engineer, with Nick Golding on the greta R package for statistical modelling, and implementing novel statistical methods for infectious diseases like COVID19 and malaria. He works at The Kids Research Institute, which is based in Perth, Western Australia, but works remotely from Launceston, Tasmania.
He is a strong advocate for free and open source software, and has written several R packages to improve data analysis. These can be seen on his software page.
Licence
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Footnotes
times are approximate↩︎