+ - 0:00:00
Notes for current slide
Notes for next slide
These slides are viewed best by Chrome and occasionally need to be refreshed if elements did not load properly. See here for PDF .
1/52

R Markdown Workshop



R Markdown Basics with
rmarkdown & knitr

Presented by Emi Tanaka

School of Mathematics and Statistics


dr.emi.tanaka@gmail.com @statsgen

1st Dec 2019 @ Biometrics by the Botanic Gardens | Adelaide, Australia

1/52

What you can do with R Markdown?

2/52

What you can do with R Markdown?


These slides are made using R Markdown.
2/52

What you can do with R Markdown?


This dynamic report is made using R Markdown.
3/52

What you can do with R Markdown?


This manuscript is made using R Markdown.
4/52

What you can do with R Markdown?


This online book is made using R Markdown.
Available at https://otexts.com/fpp2/
The pdf book version is also made using R Markdown.
5/52

What you can do with R Markdown?


This thesis (online and pdf) is made using R Markdown.
Available at https://thesis.earo.me/
6/52

What you can do with R Markdown?


These blog posts are made using R Markdown.
7/52

What you can do with R Markdown?

Possibilities are endless...

  • Microsoft Word document (.doc, .docx)
  • Open Document Text (.odt)
  • Rich text format (.rtf)
  • Power point slides (.ppt, .pptx)
  • Posters (as .html or .pdf)
  • Resume (as .html or .pdf)
  • Interactive R Notebooks (.html)
  • Markdown documents (.md)
  • Dashboard (.html)


Check out Xie et al. (2018) R Markdown: The Definite Guide.

8/52

Before R Markdown (and Sweave)


9/52

R Markdown in a nutshell 🥜

R Markdown integrates text + code in one source document with ability to knit to many output formats (via Pandoc).

10/52

🔍 Open and inspect the file

first-rmarkdown.Rmd

11/52

R Markdown Basics

12/52

Knitting: Rmd    md    html

13/52

Knitting: Rmd    md    pdf

14/52

How does it all work?


15/52

R Markdown under the hood: html_document

knitr 📦 does the hard work of converting Rmd    md 

---
title: "My Report"
output: html_document
---
# Hello
```{r}
1 + 1
```
---
title: "My Report"
output: html_document
---
# Hello
```r
1 + 1
```
```
## [1] 2
```
Rmd
md
16/52

R Markdown under the hood: html_document

Then rmarkdown 📦 prepares md for pandoc to convert to html . 

---
title: "My Report"
output: html_document
---
# Hello
```r
1 + 1
```
```
## [1] 2
```
<body>
<div class="container-fluid main-container">
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">My Report</h1>
</div>
<div id="hello" class="section level1">
<h1>Hello</h1>
<pre class="r"><code>1 + 1</code></pre>
<pre><code>## [1] 2</code></pre>
</div>
</div>
</body>
This html file is missing some elements due to restriction of space.
md
html
17/52

R Markdown under the hood: pdf_document

Same as before: knitr 📦 converts Rmd    md 

---
title: "My Report"
output: pdf_document
---
# Hello
```{r}
1 + 1
```
---
title: "My Report"
output: pdf_document
---
# Hello
```r
1 + 1
```
```
## [1] 2
```
Rmd
md
18/52

R Markdown under the hood: pdf_document

Then rmarkdown 📦 prepares md for pandoc to convert to tex pdf . 

---
title: "My Report"
output: html_document
---
# Hello
```r
1 + 1
```
```
## [1] 2
```
\begin{document}
\maketitle
\hypertarget{hello}{%
\section{Hello}\label{hello}}
\begin{Shaded}
\begin{Highlighting}[]
\DecValTok{1} \OperatorTok{+}\StringTok{ }\DecValTok{1}
\end{Highlighting}
\end{Shaded}
\begin{verbatim}
## [1] 2
\end{verbatim}
\end{document}
md
tex
This tex document is missing elements before \begin{document} due to restriction of space.
19/52

Meta data with YAML


20/52

YAML - YAML Ain't Markup Language

Basic format

---
key: value
---

Example

---
title: "R Markdown Workshop"
subtitle: "The Basics"
author: "Emi Tanaka"
date: "`r Sys.Date()`"
output: html_document
---

There must be a space after ":"!

21/52

Default (minimal) html output

<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta name="author" content="Emi Tanaka" />
<meta name="date" content="2019-11-19" />
<title>R Markdown Workshop</title>
</head>
<body>
<h1 class="title toc-ignore">R Markdown Workshop</h1>
<h3 class="subtitle">The Basics</h3>
<h4 class="author">Emi Tanaka</h4>
<h4 class="date">2019-11-19</h4>
</body>
</html>

html meta data

Default html template add special YAML key values to file automatically

22/52

YAML structure

  • White spaces indicate structure in YAML - don't use tabs though!
  • Same as R, you can comment lines by starting with #.
  • YAML is case sensitive.
  • A key can hold multiple values. 
key: 
  - value1
  - value2
key: [value1, value2]
23/52

YAML with multiple key values

---
title: "R Package & R Markdown Workshop"
author: 
  - "Damjan Vukcevic"
  - "Emi Tanaka"
output: html_document
---

html raw file

<body>
<h1 class="title toc-ignore">R Package & R Markdown Workshop</h1>
<h4 class="author">Damjan Vukcevic</h4>
<h4 class="author">Emi Tanaka</h4> 
</body>

24/52

Values spanning multiple lines

---
title: >
  this is a  
  **single line**
abstract: |
  this value spans  
  *many lines* and  
  appears as it is  
output: pdf_document
---

Note that there are two spaces after each line in the above YAML values. This is necessary to create a new line for markdown.

25/52

🔍 Open and inspect the file

second-rmarkdown.Rmd

26/52

key can contain keys

---
output: 
  html_document:
    toc: true
    toc_float: true 
    code_download: true 
    code_folding: "hide"
---

What does each of the above keys do?

04:00
27/52

ymlthis 📦

  • If you installed ymlthis then go to RStudio > Addins > YMLTHIS
  • It will launch a shiny app with various YAML options
  • See also helper functions at https://ymlthis.r-lib.org/
28/52

🔧 Open and inspect the file

challenge-05-yaml.Rmd

29/52

Text


30/52

Text in Markdown: Headers


# Header 1
## Header 2
### Header 3
#### Header 4
##### Header 5
###### Header 6

Header 1

Header 2

Header 3

Header 4

Header 5
Header 6
Go to RStudio > Help > Markdown Quick Reference
31/52

Text in Markdown: Formatting


 **This text is bold** 
 __This text is also bold__  
 *This text is italic* 
 _This text is also italic_  
 **_You can combine both_**


This text is bold

This text is also bold

This text is italic

This text is also italic

You can combine both

Go to RStudio > Help > Markdown Quick Reference
32/52

Text in Markdown: Lists

 1. Breakfast
   * Cereal
   * Milk
 1. Lunch
   * Pizza
 * Tissue box 
   * Soft 
   * Hard
 * Soy sauce
  1. Breakfast
    • Cereal
    • Milk
  2. Lunch
    • Pizza
  • Tissue box
    • Soft
    • Hard
  • Soy sauce
Go to RStudio > Help > Markdown Quick Reference
33/52

Markdown: lightweight markup language
Focus on writing - add flair later

markdown

# Section 
Bla bla.
Then **bold**.

html

<h1>Section</h1>
Bla bla.
Then <b>bold</b>.

latex

\section{Section}
Bla bla.
Then \textbf{bold}.

docx

Section

Bla bla.
Then bold.

34/52

🔧 Open and go through:

challenge-06-table.Rmd

05:00
35/52

Code chunk


36/52

Keyboard shortcut for inserting code chunk


In RStudio .Rmd press


  • Mac: ⌘ + ⌥ + i
  • PC: Ctrl + Alt + i


to insert a chunk of R code

```{r}
```
37/52

Chunk options: echo & eval

```{r, echo = FALSE}
plot(speed ~ dist, cars)
```

```{r, eval = FALSE}
plot(speed ~ dist, cars)
```
plot(speed ~ dist, cars)
38/52

Valid chunk options


  • Chunk options must be written in one line, i.e. no line break.
  • All option values must be valid R expressions. Exception is the chunk name. E.g.
    • fig.path = figures/ is not valid but
      fig.path = "figures/" is valid
    • eval = true is not valid but
      eval = runif(1) > 0.5 is valid
39/52

Chunk names (or labels)


The chunk below is called plot1.

```{r plot1}
ggplot(cars, aes(dist, speed)) + geom_point()
```

All chunks have a label regardless of whether it is explicitly supplied or not.

Do not include spaces, "_" or punctuation marks in your chunk name!

40/52

🔧 Pick your challenge:


  • challenge-07-include.Rmd
  • challenge-08-global-option.Rmd
  • challenge-09-figures.Rmd
  • challenge-10-cache.Rmd
  • challenge-11-names.Rmd
25:00
41/52

Inline code


42/52

Inline R Commands


Text can contain inline R commands where output is evaluated but code is not echoed.



Text

Updated last: `r Sys.Date()`

Output

Updated last: 2019-12-03

Text

The value of $\pi$ is `r pi`.

Output

The value of π is 3.1415927.

43/52

Accessing YAML meta data inline

All YAML meta data are stored in rmarkdown::metadata as a list.

---
title: "R Markdown Workshop"
output: html_document
---
rmarkdown::metadata$title
  [1] "R Markdown Workshop"

All key values of params is stored as a list in params. 

---
params: 
   data: datav1.csv
output: pdf_document
---
params$data
  [1] "datav1.csv"
44/52

Stack your Rmd components as you want but only one YAML piece and it needs to be on the top!


For workflow, you'd probably want to keep your tower's height manageable.

45/52

R Markdown is not just for R

```{python, echo = FALSE}
a = [1, 2, 3]
a[0]
```
  1
```{bash, echo = FALSE}
date +%B
```
  December
46/52

Sharing your html documents

47/52

RPubs

After knitting, find this Publish button:

and select RPubs if there is a choice:

48/52

Netlify: without Git

  • Rename your output html file as index.html
  • Go to https://app.netlify.com/
  • If you are logged in, go to the bottom of Sites to find
  • Drag and drop the folder that contains the index.html
  • 🎉 it's alive!
  • You probably want to change the site name - to do this go to site > site settings > change site name.
49/52

Netlify: with Git

  • Rename your output html file as index.html
  • Git commit your folder (or html file alone if no dependency)
  • Host it on GitHub (my preference), GitLab or Bitbucket
  • Go to https://app.netlify.com/ and create a new site from the repo
  • 🎉🎉🎉🎉🎉
  • Again, you probably want to change the site name - to do this go to site > site settings > change site name.
50/52

Happy sharing!

That's it for the basics!

51/52

Session Information

devtools::session_info()
  ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   setting  value                       
   version  R version 3.6.0 (2019-04-26)
   os       macOS Mojave 10.14.6        
   system   x86_64, darwin15.6.0        
   ui       X11                         
   language (EN)                        
   collate  en_AU.UTF-8                 
   ctype    en_AU.UTF-8                 
   tz       Australia/Adelaide          
   date     2019-12-03                  
  ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   package     * version    date       lib source                              
   anicon        0.1.0      2019-05-28 [1] Github (emitanaka/anicon@377aece)   
   assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                      
   backports     1.1.4      2019-04-10 [1] CRAN (R 3.6.0)                      
   broom         0.5.2      2019-04-07 [1] CRAN (R 3.6.0)                      
   callr         3.3.1      2019-07-18 [1] CRAN (R 3.6.0)                      
   cellranger    1.1.0      2016-07-27 [1] CRAN (R 3.6.0)                      
   cli           1.1.0      2019-03-19 [1] CRAN (R 3.6.0)                      
   colorspace    1.4-1      2019-03-18 [1] CRAN (R 3.6.0)                      
   countdown     0.2.0      2019-05-30 [1] Github (gadenbuie/countdown@c8e8710)
   crayon        1.3.4      2017-09-16 [1] CRAN (R 3.6.0)                      
   desc          1.2.0      2018-05-01 [1] CRAN (R 3.6.0)                      
   devtools      2.0.2      2019-04-08 [1] CRAN (R 3.6.0)                      
   digest        0.6.22     2019-10-21 [1] CRAN (R 3.6.0)                      
   dplyr       * 0.8.3      2019-07-04 [1] CRAN (R 3.6.0)                      
   emo           0.0.0.9000 2019-06-03 [1] Github (hadley/emo@02a5206)         
   evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.0)                      
   forcats     * 0.4.0      2019-02-17 [1] CRAN (R 3.6.0)                      
   fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                      
   generics      0.0.2      2018-11-29 [1] CRAN (R 3.6.0)                      
   ggplot2     * 3.2.1      2019-08-10 [1] CRAN (R 3.6.0)                      
   glue          1.3.1.9000 2019-10-24 [1] Github (tidyverse/glue@71eeddf)     
   gtable        0.3.0      2019-03-25 [1] CRAN (R 3.6.0)                      
   haven         2.1.0      2019-02-19 [1] CRAN (R 3.6.0)                      
   hms           0.5.1      2019-08-23 [1] CRAN (R 3.6.0)                      
   htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.0)                      
   httr          1.4.1      2019-08-05 [1] CRAN (R 3.6.0)                      
   icon          0.1.0      2019-05-28 [1] Github (ropenscilabs/icon@a510f88)  
   jsonlite      1.6        2018-12-07 [1] CRAN (R 3.6.0)                      
   knitr         1.25       2019-09-18 [1] CRAN (R 3.6.0)                      
   lattice       0.20-38    2018-11-04 [1] CRAN (R 3.6.0)                      
   lazyeval      0.2.2      2019-03-15 [1] CRAN (R 3.6.0)                      
   lifecycle     0.1.0      2019-08-01 [1] CRAN (R 3.6.0)                      
   lubridate     1.7.4      2018-04-11 [1] CRAN (R 3.6.0)                      
   magrittr      1.5        2014-11-22 [1] CRAN (R 3.6.0)                      
   Matrix        1.2-17     2019-03-22 [1] CRAN (R 3.6.0)                      
   memoise       1.1.0      2017-04-21 [1] CRAN (R 3.6.0)                      
   modelr        0.1.4      2019-02-18 [1] CRAN (R 3.6.0)                      
   munsell       0.5.0      2018-06-12 [1] CRAN (R 3.6.0)                      
   nlme          3.1-140    2019-05-12 [1] CRAN (R 3.6.0)                      
   pillar        1.4.2      2019-06-29 [1] CRAN (R 3.6.0)                      
   pkgbuild      1.0.3      2019-03-20 [1] CRAN (R 3.6.0)                      
   pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 3.6.0)                      
   pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.6.0)                      
   prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.6.0)                      
   processx      3.4.1      2019-07-18 [1] CRAN (R 3.6.0)                      
   ps            1.3.0      2018-12-21 [1] CRAN (R 3.6.0)                      
   purrr       * 0.3.2      2019-03-15 [1] CRAN (R 3.6.0)                      
   R6            2.4.0      2019-02-14 [1] CRAN (R 3.6.0)                      
   Rcpp          1.0.2      2019-07-25 [1] CRAN (R 3.6.0)                      
   readr       * 1.3.1      2018-12-21 [1] CRAN (R 3.6.0)                      
   readxl        1.3.1      2019-03-13 [1] CRAN (R 3.6.0)                      
   remotes       2.0.4      2019-04-10 [1] CRAN (R 3.6.0)                      
   reticulate    1.12       2019-04-12 [1] CRAN (R 3.6.0)                      
   rlang         0.4.0.9000 2019-08-03 [1] Github (r-lib/rlang@b0905db)        
   rmarkdown     1.16       2019-10-01 [1] CRAN (R 3.6.0)                      
   rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.6.0)                      
   rstudioapi    0.10       2019-03-19 [1] CRAN (R 3.6.0)                      
   rvest         0.3.4      2019-05-15 [1] CRAN (R 3.6.0)                      
   scales        1.0.0      2018-08-09 [1] CRAN (R 3.6.0)                      
   sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.6.0)                      
   stringi       1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                      
   stringr     * 1.4.0      2019-02-10 [1] CRAN (R 3.6.0)                      
   testthat      2.2.1      2019-07-25 [1] CRAN (R 3.6.0)                      
   tibble      * 2.1.3      2019-06-06 [1] CRAN (R 3.6.0)                      
   tidyr       * 1.0.0      2019-09-11 [1] CRAN (R 3.6.0)                      
   tidyselect    0.2.5      2018-10-11 [1] CRAN (R 3.6.0)                      
   tidyverse   * 1.2.1      2017-11-14 [1] CRAN (R 3.6.0)                      
   usethis       1.5.0      2019-04-07 [1] CRAN (R 3.6.0)                      
   vctrs         0.2.0.9000 2019-08-03 [1] Github (r-lib/vctrs@11c34ae)        
   whisker       0.3-2      2013-04-28 [1] CRAN (R 3.6.0)                      
   withr         2.1.2      2018-03-15 [1] CRAN (R 3.6.0)                      
   xaringan      0.9        2019-03-06 [1] CRAN (R 3.6.0)                      
   xfun          0.10       2019-10-01 [1] CRAN (R 3.6.0)                      
   xml2          1.2.0      2018-01-24 [1] CRAN (R 3.6.0)                      
   yaml          2.2.0      2018-07-25 [1] CRAN (R 3.6.0)                      
   zeallot       0.1.0      2018-01-28 [1] CRAN (R 3.6.0)                      
  [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

These slides are licensed under

52/52

R Markdown Workshop



R Markdown Basics with
rmarkdown & knitr

Presented by Emi Tanaka

School of Mathematics and Statistics


dr.emi.tanaka@gmail.com @statsgen

1st Dec 2019 @ Biometrics by the Botanic Gardens | Adelaide, Australia

1/52
Paused

Help

Keyboard shortcuts

↑, ←, Pg Up, k Go to previous slide
↓, →, Pg Dn, Space, j Go to next slide
Home Go to first slide
End Go to last slide
Number + Return Go to specific slide
b / m / f Toggle blackout / mirrored / fullscreen mode
c Clone slideshow
p Toggle presenter mode
t Restart the presentation timer
?, h Toggle this help
Esc Back to slideshow