• https://yihui.org
• first language: Chinese
• second language: R (10 years)
• third language: English
• graduated from Iowa State Univ (Stats, 2013)
• joined RStudio
• (co-)author and maintainer of some R packages (e.g. animation, knitr, cranvas, formatR, testit, highr, Rd2roxygen, fun, servr, tikzDevice, shiny, evaluate, markdown)
• initiated the Chinese R Conference in 2008 (7th this year)
• Capital of Statistics (http://cos.name)

• 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
  • Emacs/ESS
  • …

• 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.

• the docco_classic style
• gitbook
• the challenges do not really make much sense
  • LaTeX is for printing
  • HTML is not as powerful in terms of typsetting (not bad either!), but is excellent for interaction

We used to tell them "go to Pandoc".

Now we go to Pandoc and solve the problem directly.

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

• markdown extensions
  • 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]

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

• we used to call knitr and Pandoc separately

  # in R
  library(knitr)
  knit('input.Rmd')
  # in command line
  pandoc -to beamer -o output.pdf --smart input.md

• 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'))

str(rmarkdown::html_document(), 2)

## List of 5
##  $ knitr           :List of 3
##   ..$ opts_knit : NULL
##   ..$ opts_chunk:List of 5
##   ..$ knit_hooks: NULL
##  $ pandoc          :List of 5
##   ..$ to      : chr "html"
##   ..$ from    : chr "markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures"
##   ..$ args    : chr [1:8] "--smart" "--email-obfuscation" "none" "--self-contained" ...
##   ..$ keep_tex: logi FALSE
##   ..$ ext     : NULL
##  $ clean_supporting: logi TRUE
##  $ pre_processor   :function (...)  
##  $ post_processor  :function (metadata, input_file, output_file, clean, verbose)  
##  - attr(*, "class")= chr "rmarkdown_output_format"

title: "Sample Document"
output:
  my_nice_document:
    fig_width: 8
    toc: true

my_nice_document() is your own function that returns a list of knitr and Pandoc options.

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

• the new chunk option render = knit_print by default
• currently in the development version (will appear in knitr 1.6 on CRAN): https://github.com/yihui/knitr
• an S3 generic function
• you can define how to "print" your objects
• by default it is approximately equal to print()

library(knitr)
# define a method for objects of the class data.frame
knit_print.data.frame = function(x, options) {
    res = paste(c("", "", kable(x, output = FALSE)), collapse = "\n")
    asis_output(res)
}

• 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

Don't just believe everything I said…