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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Writing dynamic and reproducible documents</title>
<meta charset="utf-8" />
<meta name="author" content="Olivier Gimenez" />
<script src="assets/libs/header-attrs-2.3/header-attrs.js"></script>
<link href="assets/libs/font-awesome-5.3.1/css/fontawesome-all.min.css" rel="stylesheet" />
<link rel="stylesheet" href="assets/css/rutgers-rmarkdown.css" type="text/css" />
<link rel="stylesheet" href="assets/css/rutgers-fonts_og.css" type="text/css" />
</head>
<body>
<textarea id="source">
class: center, middle, inverse, title-slide
# Writing dynamic and reproducible documents
## An introduction to R Markdown
### Olivier Gimenez
### November 2020
---
# Credits
- Garrett Grolemund [RStudio webinar](https://github.com/garrettgman/webinars/tree/master/12-Getting-started-with-R-Markdown)
- Ulrik Lyngs [workshop material](https://github.com/ulyngs/rmarkdown-workshop-2019)
---
class: inverse, center, middle
# Motivation
---
<iframe width="1300" height="600" src="https://www.youtube.com/embed/s3JldKoA0zw" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
Credit: [Ignasi Bartomeus, PhD](https://bartomeuslab.com/)
---
#
.center[]
---
# How can you reproduce results?
.center[]
---
# What do we need to make research reproducible?
- Something to integrate text, figures and code
* `R`, `Python`, etc
- Something that can be continuously edited and updated
* Living or dynamic document
- Something that can be easily used in versioning tools
* Git
---
.center[]
---
# R Markdown workflow
.center[]
---
# Structure of a R Markdown document
.center[
https://yongfu.name/2019-fju-rmd-talk/slide/#1
]
---
class: inverse, center, middle
# Demo
Open RStudio
Create a new Rmd file
Identify 3 components (frontmatter, content, chunks)
---
.center[]
---
.center[]
---
# Structure of a R Markdown document
.center[]
---
# Structure of a R Markdown document
.center[]
---
class: inverse, center, middle
# Format your text with Markdown
---
# What is Markdown?
- A way to write stuff
- Mostly plain words, with some formating
.center[]
---
# Websites that use Markdown
- GitHub <https://github.com/>
- StackOverflow <https://stackoverflow.com/>
- HackMD <https://hackmd.io>
- Many more
---
# Headers
- Use # to create headers
- Multiple #'s create lower level headers
.center[]
---
# Text
- Text is rendered as plain text
.center[]
---
# Lists
- Use asterisks to make bullet points
- Use numbers to make numbered lists
- Use 4 spaces or 1 tab for indentation
.center[]
---
# Hyperlinks
- To add a hyperlink, put your text between brackets
- Then place the URL between parentheses
.center[]
---
# Equations
- Write equations with Latex syntax
.center[]
---
# Equation blocks
.center[]
---
# Images
- Use a link preceded by an ! to insert an image
- The link text should be
- a URL if the image is hosted online
- a file path if the image is saved on your computer
.center[]
---
# Tables
```md
| header A | header B |
|---------:|:---------|
| data | data |
Table:title
```
- A bit of a hassle...
- Use a [generator of Tables for Markdown](https://www.tablesgenerator.com/markdown_tables)
- Wait for next section to learn how to generate tables from `R`
---
# R Markdown Reference Guide
<https://rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf>
.center[]
---
# Structure of a R Markdown document
.center[]
---
# Structure of a R Markdown document
.center[]
---
class: inverse, center, middle
## Code, figures and tables
---
# Embed code
- Insert chunk of `R` code
- R Markdown runs code and includes results.
.center[]
---
# Inline code
- Place code in a sentence with
- R Markdown replaces code with results
.center[]
---
# Chunk options
- By default, R markdown includes both code and results
.center[]
---
# echo
- Add options between brackets after `r`.
- `echo = FALSE` hides code.
.center[]
---
# echo
- Add options between brackets after `r`.
- `echo = FALSE` hides code.
.center[]
---
# eval
- `eval = FALSE` prevents code from being run
- No results is displayed, only code
.center[]
---
# fig.height, fig.width
- Specify dimension of plots (in inches) with fig.width and fig.height
- Separate multiple arguments with commas.
.center[]
---
# message
- `message = FALSE` prevents messages from appearing
in output
.center[]
---
# Default chunk options
- Repeating chunk options can be painful
- If you have `echo = FALSE` in every single chunk, how to set the default chunk option to `echo = FALSE` ?
- Use `knitr::opts_chunk$set(echo = FALSE)`
- You may overwrite the default for each chunk
- For chunk options, check out <https://yihui.name/knitr/options/>
---
# Including tables
```r
# cars is a built-in-to-R data set of cars
# and their stopping distances
cars %>%
head(5) %>%
knitr::kable(format = "html", caption = "A kable table")
```
<table>
<caption>A kable table</caption>
<thead>
<tr>
<th style="text-align:right;"> speed </th>
<th style="text-align:right;"> dist </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:right;"> 4 </td>
<td style="text-align:right;"> 2 </td>
</tr>
<tr>
<td style="text-align:right;"> 4 </td>
<td style="text-align:right;"> 10 </td>
</tr>
<tr>
<td style="text-align:right;"> 7 </td>
<td style="text-align:right;"> 4 </td>
</tr>
<tr>
<td style="text-align:right;"> 7 </td>
<td style="text-align:right;"> 22 </td>
</tr>
<tr>
<td style="text-align:right;"> 8 </td>
<td style="text-align:right;"> 16 </td>
</tr>
</tbody>
</table>
- The [`kable`](https://www.rdocumentation.org/packages/knitr/versions/1.21/topics/kable) package is often used with the [`kableExtra`](https://cran.r-project.org/web/packages/kableExtra/vignettes/awesome_table_in_html.html) package
- A number of other packages are available for making pretty tables, see [rmarkdown.rstudio.com](https://rmarkdown.rstudio.com/lesson-7.html)
---
# R Markdown Reference Guide
<https://rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf>
.center[]
---
# Structure of a R Markdown document
.center[]
---
# Structure of a R Markdown document
.center[]
---
class: inverse, center, middle
# YAML Yet Another Markup Language
---
# YAML in brief
- Contains the metadata of the document
- Starts and ends by three dashes
- Comes first in the document
---
# Simplest example
.center[]
---
# Output formats
.center[]
---
# Knit
<div style="width:100%;height:0;padding-bottom:61%;position:relative;"><iframe src="https://giphy.com/embed/3oEhmHmWP3Y9wQxoli" width="100%" height="100%" style="position:absolute" frameBorder="0" class="giphy-embed" allowFullScreen></iframe></div><p>
---
# Output formats
.center[]
---
# Appearance and style
- In HTML output, you can use `theme` or a custom **.css** style sheet
- `theme` options ([bootswatch.com](https://bootswatch.com/)) : *“cerulean”, “journal”, “flatly”, “darkly”, “readable”, “spacelab”, “united”, “cosmo”, “lumen”, “paper”, “sandstone”, “simplex”, “yeti”*
- You may also use LaTeX templates with R Markdown, and write [reproducible scientific paper](https://github.com/rstudio/rticles)
- You can also [use Word templates in R Markdown](http://rmarkdown.rstudio.com/articles_docx.html) (see also [this short video](https://vimeo.com/110804387))
---
# Managing bibliography
--
<ol>
<li> Put references in a plain text file with the extension **.bib**, in **BibTex** format (my advice: use [Zotero](https://www.zotero.org))
</ol>
```bibtex
*@article{Shea2014,
author = {Shea, Nicholas and Boldt, Annika},
journal = {Trends in Cognitive Sciences},
pages = {186--193},
title = {{Supra-personal cognitive control}},
volume = {18},
year = {2014},
doi = {10.1016/j.tics.2014.01.006},
}
```
--
<ol start = 2>
<li>Reference this file in your YAML header
</ol>
```yaml
---
title: "Citation test"
*bibliography: example.bib
output: html_document
---
```
---
# Citations
<ol start = 3>
<li>In your text, citations go inside brackets and separated by semicolons
</ol>
--
.pull-left[
### This...
Blah blah [@Shea2014; @Lottridge2012].
]
.pull-right[
### turns into this...
Blah blah (Shea et al. 2014; Lottridge et al. 2012).
]
---
class: larger-body
# Citations
<ol start = 3>
<li>In your text, citations go inside brackets and separated by semicolons
</ol>
.pull-left[
### This...
Blah blah [@Shea2014; @Lottridge2012].
@Shea2014 says blah.
Blah blah [see @Shea2014, pp. 33-35; also @Wu2016, ch. 1].
]
.pull-right[
### turns into this...
Blah blah (Shea et al. 2014; Lottridge et al. 2012).
Shea et al. (2014) says blah.
Blah blah (see Shea et al. 2014, 33–35; also Wu 2016, ch. 1).
]
---
class: larger-body
# Citations
<ol start = 3>
<li>In your text, citations go inside brackets and separated by semicolons
</ol>
.pull-left[
### This...
Blah blah [@Shea2014; @Lottridge2012].
@Shea2014 says blah.
Blah blah [see @Shea2014, pp. 33-35; also @Wu2016, ch. 1].
]
.pull-right[
### turns into this...
Blah blah (Shea et al. 2014; Lottridge et al. 2012).
Shea et al. (2014) says blah.
Blah blah (see Shea et al. 2014, 33–35; also Wu 2016, ch. 1).
]
- Add e.g `csl: my-style.csl` in the YAML header to change to other formats
- Browse through and download styles at [zotero.org/styles](https://www.zotero.org/styles)
---
# Citations
For an easy way to insert citations, try the [`citr`](https://github.com/crsh/citr) RStudio add-in.
<img src="https://raw.githubusercontent.com/crsh/citr/master/tools/images/addin_demo.gif" width="75%" />
---
# R Markdown Reference Guide
<https://rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf>
.center[]
---
.center[]
---
class: inverse, center, middle
## What else can we reproduce with R Markdown?
---
# Let's have a tour
<div style="width:100%;height:0;padding-bottom:61%;position:relative;"><iframe src="https://awesome-rmarkdown-2019.netlify.app/imgs/gallery.gif" width="100%" height="100%" style="position:absolute" frameBorder="0"></iframe></div><p>
R Markdown gallery <https://rmarkdown.rstudio.com/gallery.html>
---
# Websites
- Use package `blogdown` <https://bookdown.org/yihui/blogdown/>
- Customize with Hugo <https://themes.gohugo.io/>
- Deploy via GitHub pages or Netlify
---
class: inverse, center, middle
# Live demo
## Build your own website in a few minutes
---
##
.center[]
---
class: inverse, center, middle
## To go further
---
# Books
---
class: title-slide-final, middle
background-size: 55px
background-position: 9% 15%
# Thanks!
### I created these slides with [xaringan](https://github.com/yihui/xaringan) and [R Markdown](https://rmarkdown.rstudio.com/) using the [rutgers css](https://github.com/jvcasillas/ru_xaringan) that I slightly modified.
### Credit: I borrowed slides from [Garrett Grolemund](https://rstudio.com/speakers/garrett-grolemund/) and [Ulrik Lyngs](https://ulriklyngs.com/). I also used the beautiful illustrations shared by [Allison Horst](https://github.com/allisonhorst/stats-illustrations).
| | |
| :--------------------------------------------------------------------------------------------------------- | :-------------------------------- |
| <i class="fas fa-envelope "></i> | **[email protected]** |
| <i class="fas fa-home "></i> | [**https://oliviergimenez.github.io/**](https://oliviergimenez.github.io/) |
| <i class="fab fa-twitter "></i> | [**@oaggimenez**](https://twitter.com/oaggimenez) |
| <i class="fab fa-github "></i> | [**@oliviergimenez**](https://github.com/oliviergimenez)
</textarea>
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