This would produce an HTML output with a floating table of contents ( toc: true, toc_float: true), numbered sections, and the “cerulian” theme (see e.g. title: "My title" author: "Mr My full Name" date: "December 21, 2020" output: html_document: toc: true toc_float: true number_sections: true theme: cerulian bibliography: references.bib biblio-style: apalike. If you click on the knit button, just above the file, you will be prompted to save the file, and then the file will be parsed and the output document generated. A new R Markdown document will be generated. You can fill in the title of your document, your name, and choose the output format (HTML, PDF, or Word). To get started with R Markdown, you can create a template from within RStudio, by clicking on the menu File > New File > R Markdown. This chapter includes parts of the latter book. ![]() Another source showcasing the many possibilities of R Markdown is R Markdown: The Definitive Guide. A good reference to R Markdown is the R Markdown cookbook. As an introduction, there are many things left unsaid, so you will quite likely have to consult other sources to get properly acquainted with all the possibilities of R Markdown. This chapter provides a brief introduction to R Markdown, as well as the papaja package to produce output in the APA style. For instance, this book was completely written in R Markdown, with help from the additional bookfown package ( ). R Markdown is extremely flexible and useful. Anyone with the R Markdown file would be able to reproduce everything in a scientific paper. Including all analysis in the same document allows for completely reproducible research. A big benefit of this is that can keep your analysis and write-up in one place, so you don’t have to copy-paste results from one place to another (which often results in errors and issues). Markdown documents can be “parsed” to produce documents in a variety of formats, including HTML, PDF, Open Document Type, Microsoft Word, you name it… R Markdown integrates Markdown with R, allowing you to use R to include figures, tables, and R output (as well as the corresponding code, if you wish) directly in the document. Markdown itself is a lightweight markup language, with a plain-text formatting syntax. One of the many things that makes R extremely useful as a data analysis platform is its ability to generate high-quality reproducible reports and documents via R Markdown.
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