• https://yihui.org
• first language: Chinese
• second language: R (10 years)
• third language: English

• code + narratives = report

• i.e. computing languages + authoring languages

  We built a linear regression model.
  
  ```{r}
  fit <- lm(dist ~ speed, data = cars)
  b   <- coef(fit)
  plot(fit)
  ```
  
  The slope of the regression is `r b[1]`.

• an example

• an R package (install.packages('knitr'))
• document formats
  • .Rnw (R + LaTeX)
  • .Rmd (R + Markdown)
  • any computing language + any authoring language (in theory)
• editors
  • RStudio
  • LyX
  • …
• resources
  • https://yihui.org/knitr
  • Dynamic Documents with R and knitr (Chapman & Hall, 2013)

• LaTeX: precise control, full complexity, horrible readability
• Markdown: simple, simple, simple

\section{Introduction}

We did a \emph{cool} study,
and our main findings:


\begin{enumerate}
\item You can never remember
  how to escape backslashes.
\item A dollar sign is \$,
  an ampersand \&, and
  a \textbackslash{}.
\item How about ~? Use $\sim$.
\end{enumerate}

# Introduction

We did a _cool_ study, and
our main findings:

1. You do not need to remember
  a lot of rules.
2. A dollar sign is $,
  an ampersand is &, and
  a backslash \.
3. A tilde is ~.

Write content instead of
markup languages.

• http://rpubs.com

• primarily for HTML
• paragraphs, # headers, > blockquotes
• phrase _emphasis_
• - lists
• [links](url)
• ![images](url)
• code blocks

• LaTeX is for printing
• HTML is not as powerful in terms of typsetting (not bad either!), but is excellent for interaction
• examples
  • the docco_classic style
  • gitbook

Now we go to Pandoc and solve the problem directly.

• tables
• LaTeX math $\sum_{i=1}^n \alpha_i$ = \(\sum_{i=1}^n \alpha_i\)
• YAML metadata

• raw HTML/LaTeX

  <div class="my-class">
    ![image](url)
  </div>
  
  _emphasis_ and \emph{emphasis}

• footnotes ^[A footnote here.]

• citations [@joe2014]

• LaTeX/PDF
• beamer
• HTML
• ioslides
• reveal.js
• Word (MS Word, OpenOffice)
• E-books
• …

• do you want to mess with
  • Pandoc's 73 command line arguments?
  • knitr's 49 chunk options?
• rmarkdown provides wrappers that produce reasonably beautiful output by default
  • Bootstrap 3 and themes
  • highlight.js

• http://rmarkdown.rstudio.com
• rmarkdown and Pandoc are currently shipped with RStudio preview version

• can be used as a standalone package as well (require separate Pandoc installation)

  library(rmarkdown)
  render('input.Rmd')
  render('input.Rmd', pdf_document())
  render('input.Rmd', word_document())
  render('input.Rmd', beamer_presentation())
  render('input.Rmd', ioslides_presentation())

---
title: "Sample Document"
output:
  html_document:
    toc: true
    theme: united
---

This is equivalent to:

rmarkdown::render('input.Rmd',
    html_document(toc = TRUE, theme = 'united'))

• new markdown document wizard
• setting YAML metadata
• one-click compilation
• navigation between Rmd source and slides

• an R package for interactive web applications
• http://shiny.rstudio.com
• shiny::runExample('01_hello')

• a document is both dynamic and interactive
• knitr: R Markdown –> Markdown
• rmarkdown: Markdown –> HTML
• shiny: HTML <–> R
• demo