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R Markdown

R Markdown allows users to embed R code and output into documents like HTML, PDFs, and Word files. It makes R work reproducible since the source code is rerun every time, so changes to data or code will be reflected in the output. Users can create R Markdown files in RStudio, add titles, text, code chunks, and formatting. Knitting the file generates the output document. LaTeX is required to knit PDF slideshows and takes up significant storage space to download and install.

Uploaded by

Ketki Muzumdar
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© © All Rights Reserved
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Download as PDF, TXT or read online on Scribd
85 views

R Markdown

R Markdown allows users to embed R code and output into documents like HTML, PDFs, and Word files. It makes R work reproducible since the source code is rerun every time, so changes to data or code will be reflected in the output. Users can create R Markdown files in RStudio, add titles, text, code chunks, and formatting. Knitting the file generates the output document. LaTeX is required to knit PDF slideshows and takes up significant storage space to download and install.

Uploaded by

Ketki Muzumdar
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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R Markdown

The Johns Hopkins Data Science Lab

August 26, 2016


Introduction

R Markdown is built into RStudio and allows you to create


documents like HTML, PDF, and Word documents from R. With R
Markdown, you can embed R code into your documents.

Why use R Markdown?

I Turn work in R into more accessible formats


I Incorporate R code and R plots into documents
I R Markdown documents are reproducible the source code
gets rerun every time a document is generated, so if data
change or source code changes, the output in the document
will change with it.
Getting Started

I Create a new R Markdown file in RStudio by going to


File > New File > R Markdown. . .
I Click the presentation tab
I Enter a title, author, and select what kind of slideshow you
ultimately want (this can all be changed later)
Getting Started

The beginning of an R Markdown file looks like this: ---


title: "Air Quality"
author: "JHU"
date: "May 17, 2016"
output: html_document
--- The new document youve created will contain example text and
code below this delete it for a fresh start.
Making Your First Slide

I Title your first slide using two # signs: ## Insert Title


Here
I To make a slide without a title, use three asterisks: ***
I You can add subheadings with more # signs: ###
Subheading or #### Smaller Subheading
I To add a new slide, just add another Title: ## New Slide
Title
Adding Text

I Add bullet points to a slide using a hyphen followed by a space:


- bullet point
I Add sub-points using four spaces and a plus sign: +
sub-point
I Add an ordered list by typing the number/letter: 1. first
point a) sub-sub-point
I Add bullet points that appear one by one (on click) with: >-
iterated bullet point
Formatting Text

Text Code in R Markdown

plain text plain text


italics *italics*
bold **bold**
link [link](http://www.jhsph.edu)
verbatim code code here
Embedding R Code

This is a chunk of R code in R Markdown: {r}


head(airquality)
The code gets run, and both the input and output are displayed.

head(airquality)

## Ozone Solar.R Wind Temp Month Day


## 1 41 190 7.4 67 5 1
## 2 36 118 8.0 72 5 2
## 3 12 149 12.6 74 5 3
## 4 18 313 11.5 62 5 4
## 5 NA NA 14.3 56 5 5
## 6 28 NA 14.9 66 5 6
Embedding R Code

To hide the input code, use echo=FALSE. {r, echo=FALSE}


head(airquality)

## Ozone Solar.R Wind Temp Month Day


## 1 41 190 7.4 67 5 1
## 2 36 118 8.0 72 5 2
## 3 12 149 12.6 74 5 3
## 4 18 313 11.5 62 5 4
## 5 NA NA 14.3 56 5 5
## 6 28 NA 14.9 66 5 6

This can be useful for showing plots.


Embedding R Code

To show the input code only, use eval=FALSE. {r, eval=FALSE}


head(airquality)

head(airquality)
Embedding R Code

To run the code without showing input or output, use


include=FALSE. {r, include=FALSE} library(ggplot2)
Generating Slideshows

I Click the Knit button at the top of the R Markdown document


to generate your new document.
I You may be asked to install required packages if you dont
already have them installed hit Yes and RStudio will install
them for you
I You can change the type of document generated by changing
the output line in the header, or by selecting an output from
the Knit buttons pull-down menu.
Generating Slideshows

I HTML: two options with different looks


I output: ioslides_presentation
I output: slidy_presentation
I PDF: output: beamer_presentation
I Note: You can specify multiple outputs at the beginning of the
R Markdown file if you will need to generate multiple filetypes.
PDFs and LaTeX

I To knit a PDF slideshow, you will need to install LaTeX on


your computer
I LaTeX is a typesetting system that is needed to convert R
Markdown into formatted text for PDFs

Downloading and Installing LaTeX

I LaTeX is free
I LaTeX takes up a lot of space (almost ~2.6 GB download and
takes up ~5 GB when installed)
I Visit https://www.tug.org/begin.html to download
LaTeX for your operating system
I Depending on your internet connection, it may take a while to
download due to its size
Conclusion

For more information about R Markdown visit


http://rmarkdown.rstudio.com/

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