Introduction to quantitative methods with
Chapter 6: Introduction to reproducible publications with quarto
Introduction
- Exercises associated with this chapter here
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Challenges
- Produce reproducible studies by integrating code and text in the same document
- The complete generation of the study is contained in a single project
- Limit the risk of errors due to manual actions
- Native management of different formats for the final document (pdf, html, odt, etc.)
R Markdown
R Markdown is an R package that allows linking
- Text in
Markdown format
- Code in
R that can be executed and whose outputs can be integrated into the text
- Separation of content and form of the document
- A document is compiled in two steps
- knit: the
knitr package transforms the text and R outputs into a standard Markdown document
- convert: the
pandoc software transforms the .md document into a standard output format (html, pdf, etc.)
Quarto
Quarto is the successor to R Markdown
Quarto supports different computation engines (knitr, Jupyter, Observable…) which makes it natively multi-language (R, Python, JavaScript…)
- The functioning of both systems remains very similar
Anatomy of a reproducible document
