R Markdown!The Basics!

ThiswastheoriginalworkflowinRStudiousing

Rscriptfiles(*.R)

RNotebooksbringtogetherprose,code,andresults.Theyaregreatfor•  CommunicaCngresults

tothosewhodonotneedtoseethecode

•  CollaboraCngwithotherdatascienCstsinterestedintheresultsandthecode

•  Actuallydoingdatascience

R Markdown

Components of an R Notebook

TextusingMarkdown(andLaTeX)

CodeusingR(orotherlanguages)

YAMLheader

Text Using Markdown

Headers

# Header 1

## Header 2

### Header 3

#### Header 4

##### Header 5

###### Header 6

Header 1 Header 1 Header 1 Header 1 Header 1 Header 1

Use#’stocreateheadersfor

chapters,secCons,subsecCons,etc.

Text

italics

bold

code

Text

Text

_italics_

_ _bold_ _

`code`

Textisrenderedasplaintext.Useunderscores(_)tomakeitalics,twounderscores(__)tomakebold,backCckstomakecode.

Addtwospacesattheendofalinetostartanewline

Lists

Bullet points* item 1* item 2

Numbered lists1. item 12. item 2

Bullet points•  item 1•  item 2

Numbered lists1.  item 12.  item 2

Useasteriskstomakebulletpoints.Usenumberstomakenumberedlists.

Hyperlinks

This is a [link](www.ship.edu).

This is a link.

Usebracketstodenotealink.PlacetheURLinparentheses.

EquationsAccording to Einstein, $E=mc^2$.

According to Einstein, E = mc2.

WriteequaConswithLaTeXcommandsandsurroundthemin$’s.

Equation Blocks

According to Einstein, $$E=mc^2$$.

According to Einstein,

E = mc2.Usetwo$’stomakecenteredequaConblocks.

TheRStudiologo.

Images

 The RStudio logo.

Usealinkprecededbyan!toinsertanimage.LinkshouldbeaURLorfilepath.

Code Chunks

Code Chunks

InfinalkniTeddocument(html,pdf,etc.)InRnotebook

Chunk Options

Forcode:evaldeterminesifthecodeisevaluated

Chunk Options

Forresults:echodeterminesiftheoutputisshown,messageandwarningdetermine

iftheseareshown.

Chunk Options

Forplots:fig.heightandfig.widthcontrolthesizeoftheplot,andfig.aligncontrols

itsposiCon

Inline CodeToday is`r Sys.Date()`.

Today is 2018-02-06.

Placecodeinasentencewith`r#code`.RMarkdownwillreplacethecodewithitsresults.

Output Format

Preview

WhilewriCngyourdocument,youcanperiodicallyPreviewit.

Knit Youcanknittohtml,pdf,orwordbyclicking

onthetriangle

YAML Header

TheYAMLheaderkeepstrackoftheoutputtypes

andtheiropCons

YAML Header

IftheabilitytoPreviewthenotebookdisappears,addthislinetotheYAML

The setup code chunk

Chunk OptionsThesetupcodechunkisalwaysrunonce

beforeanyotherchunks.Inthiscourse,thiswillbethefirstcodechunkthatwillcontainthepackagesyouareusing.Youcanhidethewarningsandmessagesforloadingpackages

Eventually…

Interactive Webpages

Websites

Books

Journal Articles