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R Markdown

On your marks, get set, ready, go!


Thiyanga S. Talagala

December 28, 2020

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Packages

install.packages("rmarkdown")

install.packages("knitr")

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Packages

install.packages("rmarkdown")

install.packages("knitr")

Additional packages

install.packages("tidyverse")

install.packages("reticulate")

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Creating an R Markdown document

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Select a folder to save the document

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Give a name to the document

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Demo

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R Markdown pipeline

Image source: here

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Customizing your R Markdown document: text

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Change Header

Code

# Header 1
## Header 2
### Header 3

Output

Header 1

Header 2

Header 3

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Add content

Code

# Header 1
This is section 1.
## Header 2
This is section 1.2
### Header 3
This is section 1.2.1

Output

Header 1

This is section 1.

Header 2

This is section 1.2

Header 3

This is section 1.2.1

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Text formatting

Code

text

Output

M1: This text is in italics.

M2: This is also italics.

M3: This text is in bold.

M4: This is also bold.

This text is strikethrough.

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Include R codes

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Anatomy of R Markdown

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Anatomy of R Markdown

code chunk

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Anatomy of R Markdown

Text

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Anatomy of R Markdown

YAML

HTML Document

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Anatomy of R Markdown

YAML

PDF Document

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Anatomy of R Markdown

YAML

Word Document

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Chunk options

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fig.width/ fig.height

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fig.width/ fig.height

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echo [TRUE/ FALSE]

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eval [TRUE/ FALSE]

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Chunk options

  • eval = FALSE - prevent the code from being evaluated

  • include = FALSE - run the code but doesn't show it in the final document

  • echo = FALSE - prevent the code but not the results from appearing

  • message = FALSE - prevent messages from appearing in the finished file

  • results = "hide" - hide the printed output

  • error = TRUE - cause the render to continue even if the code returns an error

  • comment=NA - remove # from the output

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Chunk options

  • eval = FALSE - prevent the code from being evaluated

  • include = FALSE - run the code but doesn't show it in the final document

  • echo = FALSE - prevent the code but not the results from appearing

  • message = FALSE - prevent messages from appearing in the finished file

  • results = "hide" - hide the printed output

  • error = TRUE - cause the render to continue even if the code returns an error

  • comment=NA - remove # from the output

Without comment=NA

a <- 1:5; a
## [1] 1 2 3 4 5

With comment=NA

a <- 1:5; a
[1] 1 2 3 4 5
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Mathematical Equations

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How to type Greek letters?

Please read my blog post here:

https://thiyanga.netlify.app/post/greekletters/

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Styling your R Markdown document

YAML

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toc: true

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toc_float: true

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number_sections

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Styling your R Markdown document

theme

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Styling your R Markdown document

highlight

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Themes

  • default

  • cerulean

  • journal

  • flatly

  • darkly

  • readable

  • spacelab

  • united

  • cosmo

  • lumen

  • paper

  • sandstone

  • simplex

  • yeti

Highlight

  • default

  • tango

  • espresso

  • zenburn

  • haddock

  • breezedark

  • kate

  • monochrome

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Styling your R Markdown document

Tabbed Sections

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R Markdown to R script

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R script to R Markdown

Method 1 (Using Rstudio)

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R script to R Markdown

Method 2 (Using R console)

rmarkdown::render('11-Demo.R')
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Document your Analysis

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Include Latex tables

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Include images

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Python and R together

install.packages("reticulate")

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Parameterized R Markdown

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Acknowledgements:

Yihui Xie, RStudio

Emi Tanaka, Monash University, Australia

All contributors

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Thank you

Make some VOICE using R Makrkdown!

Slides are available at https://talks-thiyanga.netlify.app/rmarkdown_rladies/rmarkdownrladies_tst#1

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

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Packages

install.packages("rmarkdown")

install.packages("knitr")

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