List of Tables List of Figures Preface About the Author Introduction Motivation Get started Usage Two rendering approaches Some tips Components Markdown syntax Inline formatting Block-level elements Math expressions Markdown extensions by bookdown Number and reference equations Theorems and proofs Special headers Text references R code Figures Tables Cross-references Custom blocks Citations Index HTML widgets Web pages and Shiny apps Output Formats HTML GitBook style Bootstrap style Tufte style LaTeX/PDF E-Books EPUB MOBI A single document Customization YAML options Theming Templates Configuration Internationalization Editing Build the book Preview a chapter Serve the book RStudio IDE Collaboration Publishing RStudio Connect GitHub Publishers Appendix Software Tools R and R packages Pandoc LaTeX Software Usage 103 knitr R Markdown FAQ 109 Bibliography 111 Index 113
Yihui Xie is a software engineer at RStudio. He is the author of several R packages, and interested in statistical computing, data visualization, and web technologies. He founded the largest online community for statistics "Capital of Statistics" in China in 2006. After publishing a few journal papers, a PhD thesis, and the book Dynamic Documents with R and knitr, the frustration with LaTeX eventually led to the creation of bookdown.
If you have written about statistics and included examples that are implemented in a programming language, you have struggled with the challenge of weaving together these two distinct forms of communication. Donald Knuth laid out a model of "literate programming" (1992) that prioritizes the clarity of computer code by embedding snippets of code within explanatory text. A new tool for authoring large-scale dynamic documents in this paradigm is the bookdown package, described by a book of the same name, and it stands as the most comprehensive and extensible tool available for R users... R Markdown...had limitations as well. There was no method to cross-reference figures in one chapter from another chapter of the book. The figures were not numbered successively. These problems, and many others, were solved by the release of the bookdown package...Xie has revolutionized the publishing of statistical reports using the knitr and rmarkdown packages and this is surely the next step in that revolution. His idea of books being versions instead of editions is ground-breaking. I look forward to the continual improvements to this bookdown package and this book in the years to come."~The American Statistician There could be a lot of interesting and unexpected ways that bookdown could be used to generate content. For example, automated software tests for clinical data analysis programs can be scheduled to run overnight and used knitr to create PDFs to show to auditors. The issue is that hundreds of files could be created. Bookdown could generate a much more organized and cross-referenced package to show to regulators during audits. ~ Max Kuhn I definitely recommend publication, and as quickly as possible. People are waiting for this. The R/bookdown/knitr system is better than GitBook for scientific work with code and formulas, especially if combined with R Studio. ~ Jan de Leeuw, UCLA I would whole-heartedly recommend this book for publication. I think the ability to render long documents in a variety of formats, with text intermingled with code, will only grow in importance in future years. This book and associated package are clearly a major step towards being able to achieve this. The book was very well written, and notwithstanding the few suggestions I had for improvements, I think there is little modification that needs to be done before publication. I am sure it will prove interesting and useful to many readers. ~ Michael Grayling, U. of Cambridge Bookdown is hugely useful for long-form documents: books, course notes, theses/dissertations. And I expect it to be widely adopted for those purposes...The book is quite nicely written: clear and concise. ~ Karl Broman, U. of Wisconsin The audience would absolutely include R users who are comfortable with Word but not LaTeX (for example, in my department, most of the graduate students have used R Markdown, but only a couple know LaTeX)...One huge advantage of bookdown is that you can have a current version of a book online as you develop it. ~ Brooke Anderson, Colorado State U. Simply amazing! Six hours, basic R and R Markdown knowledge, and I created a book using bookdown. ~ Lars Schoebitz