Outline for Knitr tutorial at UseR 2016

See Etherpad for notes during the tutorial, or to ask questions.

Part 1: An intro to R Markdown

0. Reminder about literate programming and Markdown

1. Pandoc's markdown syntax

   • YAML metadata
   • LaTeX math
   • syntax highlighting
   • raw HTML/LaTeX
   • tables
   • footnotes
   • citations

2. R Markdown output formats

   • HTML, PDF, Word, presentations, ...
   • Process: Rmd -> (knitr) -> md -> (pandoc) -> output
   • rmarkdown package does the whole thing

3. Customizing output

   • Basic format options: TOC, numbered sections, self-contained, fig_height, themes, ...
   • Customize CSS for HTML output
     • ioslides example re slide numbers
   • Customize LaTeX preample for PDF output
   • Pandoc templates
   • Customize Word templates (header/footer, font styles, ...)

Part 2: New output formats

1. Closer look at structure of output format object

   • knitr options (chunk options, hooks, etc)
   • pandoc options
   • pre/post-processor functions

2. Examples of new output formats

   • html_vignette, rtf_document
   • tufte package (tufte::tufte_html(), tufte::tufte_handout())
   • Long-form documents using bookdown
     • cross-references of figures/tables/sections
     • separate HTML pages for chapters

Part 3: Other applications

1. Journal articles (rticles)

2. Build websites

3. HTML widgets

4. Shiny apps within R Markdown

5. Run code from other languages (C, C++, Python, ...)