R Markdown - Shippensburg University of...
Transcript of R Markdown - Shippensburg University of...
![Page 1: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/1.jpg)
R Markdown!The Basics!
![Page 2: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/2.jpg)
ThiswastheoriginalworkflowinRStudiousing
Rscriptfiles(*.R)
![Page 3: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/3.jpg)
RNotebooksbringtogetherprose,code,andresults.Theyaregreatfor• CommunicaCngresults
tothosewhodonotneedtoseethecode
• CollaboraCngwithotherdatascienCstsinterestedintheresultsandthecode
• Actuallydoingdatascience
![Page 4: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/4.jpg)
R Markdown
![Page 5: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/5.jpg)
Components of an R Notebook
![Page 6: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/6.jpg)
TextusingMarkdown(andLaTeX)
CodeusingR(orotherlanguages)
YAMLheader
![Page 7: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/7.jpg)
Text Using Markdown
![Page 8: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/8.jpg)
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.
![Page 9: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/9.jpg)
Text
italics
bold
code
Text
Text
_italics_
_ _bold_ _
`code`
Textisrenderedasplaintext.Useunderscores(_)tomakeitalics,twounderscores(__)tomakebold,backCckstomakecode.
Addtwospacesattheendofalinetostartanewline
![Page 10: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/10.jpg)
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.
![Page 11: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/11.jpg)
Hyperlinks
This is a [link](www.ship.edu).
This is a link.
Usebracketstodenotealink.PlacetheURLinparentheses.
![Page 12: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/12.jpg)
EquationsAccording to Einstein, $E=mc^2$.
According to Einstein, E = mc2.
WriteequaConswithLaTeXcommandsandsurroundthemin$’s.
![Page 13: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/13.jpg)
Equation Blocks
According to Einstein, $$E=mc^2$$.
According to Einstein,
E = mc2.Usetwo$’stomakecenteredequaConblocks.
![Page 14: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/14.jpg)
TheRStudiologo.
Images
![](logo.png) The RStudio logo.
Usealinkprecededbyan!toinsertanimage.LinkshouldbeaURLorfilepath.
![Page 15: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/15.jpg)
![Page 16: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/16.jpg)
Code Chunks
![Page 17: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/17.jpg)
Code Chunks
InfinalkniTeddocument(html,pdf,etc.)InRnotebook
![Page 18: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/18.jpg)
Chunk Options
Forcode:evaldeterminesifthecodeisevaluated
![Page 19: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/19.jpg)
Chunk Options
Forresults:echodeterminesiftheoutputisshown,messageandwarningdetermine
iftheseareshown.
![Page 20: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/20.jpg)
Chunk Options
Forplots:fig.heightandfig.widthcontrolthesizeoftheplot,andfig.aligncontrols
itsposiCon
![Page 21: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/21.jpg)
![Page 22: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/22.jpg)
Inline CodeToday is`r Sys.Date()`.
Today is 2018-02-06.
Placecodeinasentencewith`r#code`.RMarkdownwillreplacethecodewithitsresults.
![Page 23: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/23.jpg)
Output Format
![Page 24: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/24.jpg)
Preview
WhilewriCngyourdocument,youcanperiodicallyPreviewit.
![Page 25: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/25.jpg)
Knit Youcanknittohtml,pdf,orwordbyclicking
onthetriangle
![Page 26: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/26.jpg)
YAML Header
TheYAMLheaderkeepstrackoftheoutputtypes
andtheiropCons
![Page 27: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/27.jpg)
YAML Header
IftheabilitytoPreviewthenotebookdisappears,addthislinetotheYAML
![Page 28: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/28.jpg)
The setup code chunk
![Page 29: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/29.jpg)
Chunk OptionsThesetupcodechunkisalwaysrunonce
beforeanyotherchunks.Inthiscourse,thiswillbethefirstcodechunkthatwillcontainthepackagesyouareusing.Youcanhidethewarningsandmessagesforloadingpackages
![Page 30: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/30.jpg)
Eventually…
![Page 31: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/31.jpg)
Interactive Webpages
![Page 32: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/32.jpg)
Websites
![Page 33: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/33.jpg)
Books
![Page 34: R Markdown - Shippensburg University of Pennsylvaniawebspace.ship.edu/lebryant/mat219/pdf/slides-05-rmarkdown-basics.pdfR Markdown! The Basics! This was the original workflow in RStudio](https://reader030.fdocuments.net/reader030/viewer/2022040900/5e705a159093f37f61385674/html5/thumbnails/34.jpg)
Journal Articles