rmarkdown Introduction David Dalpiaz STAT 430, Fall 2017 1

Announcements • Homework 00 has been released • Be sure to read homework policies document! • Optional but highly recommended • Begin Quiz review problems • Solutions not provided, be sure to take notes! • Reading and Videos • Read! Watch! Review! 2

Markdown • Markdown allows you to write a file format independent document using an easy-to-read and easy-to-write plain text format. • Instead of marking up text so that is easy for a computer to read. . . • e.g. HTML: <html><body><b>Name</b></body></html> • The goal is to mark down text so that is human readable: • e.g. **Name** 3

Example Markdown Document 4

Supported Output Files As a result of Markdown being structured so loosely, any file format can be generated using pandoc. That is to say, from one Markdown document you can generate any of the following: • docx • PDF • HTML • ODT • RTF The downside is that there is slightly less control over formatting, but it is well worth it. 5

RMarkdown RMarkdown developed by RStudio takes what Markdown has established and extends it significantly by: • Allowing R code and its results to be merged with Markdown; • Ensuring that RMarkdown documents are fully reproducible; • Enabling extra modifications to original markdown specification. 6

Creating an RMarkdown Document To create an RMarkdown or .Rmd Document within RStudio: Click the Enter Document Title White Plus Select R Markdown 7

Initial RMarkdown View 8

Compiling RMarkdown Document Use either: • An RStudio shortcut • Windows: Ctrl + Shift + K • macOS: Command + Shift + K • The “Knit ..” button on the source editor window • Or, compile the document via rmarkdown::render() • more on this later. . . 9

Sample Render of Default RMarkdown View 10

Sections of an RMarkdown Document There are principally three sections to an RMarkdown document. • YAML header • Code chunks • Copious amounts of text! 11

Options. . . Options. . . Options. . . Some of RMarkdown’s output options can be configured via a GUI in RStudio 1 1 To see all the options granted by RMarkdown, check out the package website at: http://rmarkdown.rstudio.com/ . 12

Dynamic Code Chunks To initiate a code chunk within RMarkdown, all one needs to do is use: ```{r chunk_label} # Code here ``` Example: Here we will embed the output of obtaining 10 random numbers. ```{r chunk_demo} x = runif(10) print(x) ``` 13

Examples of Markdown syntax Writing text with emphasis in *italics*, **bold** and `code style`. Line breaks create a new paragraph. Links can be hidden e.g. [illinois](www.illinois.edu) or not <http://illinois.edu> . Sample Image: ![Illinois](img/wordmark_vertical.png) 14

Rendered Example of Markdown syntax Writing text with emphasis in italics , bold and code style . Line breaks create a new paragraph. Links can be hidden e.g. illinois or not http://illinois.edu . Sample Image: 15

Examples of Markdown syntax (Con’t) > "Never gonna give you up, never gonna let you down..." > > --- Rick Astley - generic - bullet point - listing 1. Ordered number list 1. is numbered 42. correctly Inline math $a^2 + b^2 = c^2$ Display math (centered math) $$1 - x = y$$ 16

Rendered Example of Markdown syntax (Con’t) “Never gonna give you up, never gonna let you down. . . ” — Rick Astley • generic • bullet point • listing 1. Ordered number list 2. is numbered 3. correctly Inline math a 2 + b 2 = c 2 Display math (centered math) 1 − x = y 17

Why? Literate Programming Reproducible Research 18

rmarkdown Live Coding Let’s try it! 19

rmarkdown Introduction David Dalpiaz STAT 430, Fall 2017 1 - PowerPoint PPT Presentation

rmarkdown Introduction David Dalpiaz STAT 430, Fall 2017 1 Announcements Homework 00 has been released Be sure to read homework policies document! Optional but highly recommended Begin Quiz review problems Solutions not

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