• 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]`.

• 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.

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://www.rstudio.com/ide/download/preview
• https://github.com/rstudio/rmarkdown
• 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 3
##   ..$ to  : chr "html"
##   ..$ from: chr "markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures"
##   ..$ args: chr [1:5] "–section-divs" "–smart" "–self-contained" "–template" …
##  $ clean_supporting: logi TRUE
##  $ format_filter   :function (output_format, files_dir, input_lines)
##  $ post_processor  : NULL
##  - 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