R Markdown Workshop

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# <span style="text-shadow: 2px 2px 30px white;">R Markdown Workshop</span>

<br><br>
## <span style="color:yellow;text-shadow: 2px 2px 30px black;">Pretty Presentations with `xaringan` <img src='images/xaringan.png' height = '50px'></span>

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Presented by Emi Tanaka

School of Mathematics and Statistics

<img src="assets/USydLogo-white.svg" style="width:200px"><br>
<span><i class="fas  fa-envelope faa-float animated "></i></span>  dr.emi.tanaka@gmail.com
<span><i class="fab  fa-twitter faa-float animated faa-fast "></i></span>  @statsgen

.bottom_abs.width100.bg-black[
1st Dec 2019 @ Biometrics by the Botanic Gardens | Adelaide, Australia
]

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# HTML Slides from Rmd

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* There are a number of ways to make html slides in Rmd including `ioslides` and `slidy`. 
* My favorite one is `xaringan` 📦!
* It's highly customisable.
* These slides are made by `xaringan`!
* `xaringan` uses `remark.js` to render the final html instead of `pandoc` (which means some `pandoc` features don't work)

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https://slides.yihui.name/xaringan

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# `xaringan` slides

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```markdown
---
title: "My first xaringan slide"
subtitle: "Not!"
author: "Emi Tanaka"
date: "4th October 2019"
output: 
  xaringan::moon_reader
---

# Slide after title slide

*---

# Next slide

We can use **markdown**!

*---

```
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YAML information used for title slide

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No spaces after `---`!

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To fully customise `xaringan` slides, <br>you need to know some HTML/CSS

<br>

We'll have a short intro 💻

---

# HTML/CSS

<br>

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```
]

::: {.output background-color:red!important; }

This creates a box 
with red background.

:::

---

# HTML/CSS II

But the box and text look too squished.

I increase the padding here.

<br>

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:::

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```
]

::: {.output background-color:red!important;padding:20px; }

This creates a box 
with red background.

:::

---

# HTML/CSS III

But a white text suits better.

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:::

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```
]

::: {.output background-color:red!important;padding:20px; color: white; }

This creates a box 
with red background.

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---

# HTML/CSS IV

In contrast to `div`, `span` is "inline".

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```
]

::: { .output padding-bottom: 20px;}

<span style="background-color:red!important;padding:20px; color: white;"> This creates a box with red background.</span>

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---

# `remark.js`: div and span classes

`remark.js` makes it easier to write `div` and `span` elements.

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::: { .item border-right: dashed 3px black; }

Text in new line

```markdown
.bg-red[
Some text
]
```

is converted to

```markdown
<div class="bg-red">
Some text
</div>
```

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Placing `[` `]` in the same line

```markdown
.bg-red[Some text]
```

results in

```markdown
<span class="bg-red">
Some text
</span>
```

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---

# Specifying CSS

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You can specify the css file in the YAML:

```
output: 
  xaringan::moon_reader: 
    css: 
      - "default" # in-built theme
      - "default_fonts" # in built theme
      - "custom.css" # your own 
```

then define all custom classes in `custom.css`, e.g.

```css

.bg-red {
  background-color: red;
}

```

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---

# Apply class to the whole slide

::: paddings

```markdown

# Slide 1

---

*class: bg-red

# Slide 2

This slide will have a red background

---

# Slide 3

```

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---

::: paddings

Alternatively, you can use `xaringanthemer` to customise the look of a `xaringan`.

<br>

<br>

<br>

By the way, can you figure out what `xaringan::inf_mr()` does?

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# Resources

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* Thanks for coming!
* There are more to Tidyverse + R Markdown than can be taught in a one day workshop and some helpful resources are on the right to ask questions.

<br>

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All source files to this workshop <br>can be found at

https://github.com/emitanaka/biometrics2019

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## Learn with the *community*

* Your local R-Ladies Meetup: [Melbourne](https://www.meetup.com/en-AU/rladies-melbourne/), [Sydney](https://www.meetup.com/rladies-sydney/), [Canberra](https://www.meetup.com/rladies-canberra/), [Perth](https://www.meetup.com/en-AU/rladies-perth/), [Adelaide](https://www.meetup.com/en-AU/rladies-adelaide/), [Brisbane](https://www.meetup.com/en-AU/rladies-brisbane/)
* [R4DS Community Slack](https://www.rfordatasci.com/)
* [Twitter with hastag #rstats](https://twitter.com/search?q=%23rstats)
* [RStudio Community](https://community.rstudio.com/)
* [Stackoverflow](https://stackoverflow.com/questions/tagged/r) (I answer questions tagged with `xaringan` often)

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background-color: #e5e5e5

# Session Information

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```r
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)                    
   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)                    
   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)                    
   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)      
   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
```

<p></p>
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These slides are licensed under <br><center><a href="https://creativecommons.org/licenses/by-sa/3.0/au/"><img src="images/cc.svg" style="height:2em;"/><img src="images/by.svg" style="height:2em;"/><img src="images/sa.svg" style="height:2em;"/></a></center>