R Markdown

What is rMarkdown?

R Markdown documents are fully reproducible. Use a productive notebook interface to weave together narrative text and code to produce elegantly formatted output. Use multiple languages including R, Python, and SQL. – rmarkdown official site

R Markdown supports dozens of static and dynamic output formats including HTML, PDF, MS Word, Beamer, HTML5 slides, Tufte-style handouts, books, dashboards, shiny applications, scientific articles, websites, and more. – rmarkdown official site

In Action – One source, many faces with high reproducibility.

to PDF and html files

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---

title: "Embryo Cryopreservation Project"

output:

pdf_document:

highlight: zenburn

includes:

in_header: header.tex

pandoc_args: --number-sections

toc: yes

html_document:

theme: united

toc: yes

---

...code here

to revealjs presentation

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---

title: "Embryo Cryopreservation Project"

output:

revealjs::revealjs_presentation:

self_contained: false

reveal_plugins: ["search", "zoom", "notes"]

theme: default

center: true

incremental: true

css: present_style.css

pandoc_args: [

"--title-prefix", "Foo",

"--id-prefix", "Bar"

]

---

Emacs ESS mode with R markdown

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;;markdown mode required

(add-to-list 'load-path "/home/tan/config/emacs/extend/markdown-mode/")

(require 'markdown-mode)

;;; Markdown mode

(autoload 'markdown-mode "markdown-mode" "Major mode for editing Markdown files" t)

(setq auto-mode-alist (cons '("\\.markdown" . markdown-mode) auto-mode-alist))

(setq auto-mode-alist (cons '("\\.md" . markdown-mode) auto-mode-alist))

(setq auto-mode-alist (cons '("\\.ronn?" . markdown-mode) auto-mode-alist))

;;http://stackoverflow.com/questions/14231043/emacs-markdown-mode-error-on-preview-bin-bash-markdown-command-not-found

(setq load-path

(append (list "/home/tan/config/emacs/extend/polymode/" "/home/tan/config/emacs/extend/polymode/modes")

load-path))

(require 'poly-R)

(require 'poly-markdown)

;;; MARKDOWN

(add-to-list 'auto-mode-alist '("\\.Rmd" . poly-markdown+r-mode))

(add-to-list 'auto-mode-alist '("\\.md" . poly-markdown+r-mode))

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