Touchdown your research

# Touchdown your research with <img src="assets/img/rmarkdown.png" style="vertical-align: middle;margin:10px" width="120px"></img>

Steve Vissault, Marie-Hélène Brice,
  David Beauchesne & Kevin Cazelles
]

<div style="color:white;">
.font60[Adapted from [Alison Hill](https://rmd4medicine.netlify.com/slides/01-rmd-anatomy.html#8)]
</div>

---

# Workshop setup

- Make sure you have an updated version of [RStudio](https://rstudio.com/products/rstudio/download/)
- Install the [code version-control system Git](https://git-scm.com/downloads)
- Create a [Github account](https://github.com/join?source=header-home)
- Run the following R command:

```r
  install.packages(c("rmarkdown",
                      "htmlwidgets",
                      "bookdown",
                      "blogdown",
                      "DT",
                      "leaflet",
                      "rbokeh"))
```
- Be prepared to turn into a geek or just learn cool stuff

---

---

## R Markdown universe

R Markdown produces dynamic document in a variety of format.

### Opens new possibilities with R:

* make CV, poster & online presentation
* format scientific paper (`rticles`)
* help to document your research through notebook (`bookdown`)
* build an academic blog or website (`blogdown`)

---

## But what's R Markdown?

- ["An authoring framework for data science."](https://rmarkdown.rstudio.com/lesson-1.html) (✔️)
- [A document format (.Rmd).](https://bookdown.org/yihui/rmarkdown/) (✔️)
- [An R package named rmarkdown.](https://rmarkdown.rstudio.com/docs/) (✔️)
- ["A tool for integrating text, code, and results."](https://r4ds.had.co.nz/communicate-intro.html) (✔️)
- ["A file format for making dynamic documents with R."](https://rmarkdown.rstudio.com/articles_intro.html) (✔️)
- ["A computational document."](http://radar.oreilly.com/2011/07/wolframs-computational-documen.html) (✔️)
- [Wizardry.](https://raw.githubusercontent.com/allisonhorst/stats-illustrations/master/rstats-artwork/rmarkdown_wizards.png) (🧙)

---

# Workshop objective

## Build a website | notebook | presentation with <code style="color:rgb(11, 43, 70)">rmarkdown</code> and deploys it on the web

---
class: inverse, center, middle

# Basic Anatomy

## R Markdown (<i class="ion  ion-social-markdown "></i> + <i class="fab  fa-r-project "></i>)

---

# <i class="fas  fa-gamepad "></i> Exercice

1. Open RStudio
2. File > New File > R Markdown
3. Fill the fields *author* and *title*
4. Set default output format to HTML
5. Look at the source, then 🧶 Knit to HTML.

### Try to identify these parts in the source and the output:

- The metadata
- The text <i class="ion  ion-social-markdown "></i>
- The code <i class="fab  fa-r-project "></i>
- The output

---

# How does R Markdown work?

.pull-right[
- 🤷
- I press knit, a document appears, and I believe that anything happening in between could be actual magic.
- `knitr` executes the code and converts `.Rmd` to `.md`; Pandoc renders the `.md` file to the output format you want.
]

---

![](https://raw.githubusercontent.com/allisonhorst/stats-illustrations/master/rstats-artwork/rmarkdown_wizards.png)

---
class: inverse, center, middle

#  Document metadata

## R Markdown (<i class="ion  ion-social-markdown "></i> + <i class="fab  fa-r-project "></i>)

---

# Metadata and options

Metadata with options are defined in the header of the `.Rmd` document as a set of `key` and `value` (YAML syntax).

.pull-right[
### Two outputs
```r
---
output:
html_document:
    toc: true
  pdf_document:
    toc: false
---
```
]

Options available depend on the output.
See `?html_document `, `?pdf_document`, `?word_document`

???

- You have already notice the keys `author`, `title`, `date`
- What's the purpose of the indentation?

---

# <i class="fas  fa-gamepad "></i> Exercice

### Edit the output options

Use `?html_document` from your R console to:

1. Add a floating table of contents
2. Add a theme
3. Use the "kable" method to print data frames

🧶 Knit to HTML to see the output.

If this was easy, try to embed the Rmd source code to download.

???

### Answer

```r
---
output:
  html_document:
    toc: true
    toc_float: true
    theme: flatly
    df_print: kable
    code_download: true
---

We have done a brief overview of the document options (the shape), we now make an
introduction of the content

```

---
class: inverse, center, middle

#  Document content

## R Markdown (<i class="ion  ion-social-markdown "></i> + <i class="fab  fa-r-project "></i>)

---

---
class: inverse, center, middle

# Text formatting

## Markdown <i class="ion  ion-social-markdown "></i>

---

# Text style

*italic* or _italic_
**bold**
`code`

```r
library(tibble)
data(iris)
glimpse(as_tibble(iris))
```
````

]
.pull-right[
<h1 style="margin:0px;padding:0px">Header 1</h1>
<h2 style="margin:0px;padding:0px">Header 2</h2>
<h3 style="margin:0px;padding:0px">Header 3</h3>
<h4 style="margin:0px;padding:0px">Header 4</h4>
*italic* or _italic_
**bold**
`code`
```r
library(tibble)
data(iris)
glimpse(as_tibble(iris))

```
]

???
Headers help you to structure your Rmd Document

---

# Lists

- Cras convallis purus.
- Nunc faucibus.
- Maecenas ipsum dolor.

Nulla vehicula metus vel tortor
venenatis luctus.
Etiam tempus sit amet ligula
nec pretium. Aenean ultrices
massa sed pulvinar pulvinar.

1. Duis aliquam commodo volutpat.
1. Mauris ultrices.
1. Aliquam eu erat.
```
]

* Cras convallis purus.
- Nunc faucibus.
* Maecenas ipsum dolor.

Nulla vehicula metus vel tortor venenatis luctus.

1. Duis aliquam commodo volutpat.
1. Mauris ultrices.
1. Aliquam eu erat.
]

---

# Images

---

# Links

.pull-left[
```md
[Hulk vs Trump](https://media.giphy.com/media/MkGyW2cOH7uhO/giphy.gif)
![Hulk vs Trump](https://media.giphy.com/media/MkGyW2cOH7uhO/giphy.gif)
```
]

.pull-right[
[Hulk vs Trump](https://media.giphy.com/media/MkGyW2cOH7uhO/giphy.gif)
![Hulk vs Trump](https://media.giphy.com/media/MkGyW2cOH7uhO/giphy.gif)
]

---

# Tables

### Syntax

```md
| Time          | Session | Topic    |
|:--------------|:-------:|---------:|
| _left_        | _center_| _right_  |
| 01:00 - 01:50 | 1       | Anatomy  |
| 01:50 - 02:00 |         | *Break*  |
| 02:00 - 02:45 | 2       | Tables   |
| 02:45 - 03:00 |         | *Break*  |
```

]

### Output

| Time          | Session | Topic    |
|:--------------|:-------:|---------:|
| _left_        | _center_| _right_  |
| 01:00 - 01:50 | 1       | Anatomy  |
| 01:50 - 02:00 |         | *Break*  |
| 02:00 - 02:45 | 2       | Tables   |
| 02:45 - 03:00 |         | *Break*  |

]

- <i class="fas  fa-exclamation-triangle "></i> the `:` specify the alignement.
- Not convenient for long table, we will use instead <i class="fab  fa-r-project "></i> to print the markdown table for us.

---
class: inverse, center, middle

#  Code chunks

## The <i class="fab  fa-r-project "></i>  part

---

# Chunks

````md
This text is written in markdown

```{r}
library(tibble)
data(iris)
head(iris)
```
````

- <i class="fas  fa-exclamation-triangle "></i> `r` between brackets `{}`, why is that?
- Where is the <i class="fab  fa-r-project "></i> code and the <i class="ion  ion-social-markdown "></i> section?

---

# Chunks

### Code

```r
library(tibble)
data(iris)
head(iris)
```

### Print output

```
##   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1          5.1         3.5          1.4         0.2  setosa
## 2          4.9         3.0          1.4         0.2  setosa
## 3          4.7         3.2          1.3         0.2  setosa
## 4          4.6         3.1          1.5         0.2  setosa
## 5          5.0         3.6          1.4         0.2  setosa
## 6          5.4         3.9          1.7         0.4  setosa
```

---

# Chunks
.pull-left[

### Code

```r
library(ggplot2)
data(iris)
ggplot(
      data=iris,
      aes(x = Sepal.Length,
          y = Sepal.Width)
  ) +
geom_point(
  aes(color=Species, shape=Species)
) +
xlab("Sepal Length") +
ylab("Sepal Width") +
ggtitle("Sepal Length-Width")
```
]

![](index_files/figure-html/unnamed-chunk-11-1.png)
]

---

# Chunks

```r
library(leaflet)
leaflet(height=400, width=400) %>%
  addTiles() %>%
  addMarkers(lng=174.768, lat=-36.852,
             popup="The birthplace of R")
```
]

<div id="htmlwidget-d9cef98fe54d70eacf2d" style="width:400px;height:400px;" class="leaflet html-widget"></div>
<script type="application/json" data-for="htmlwidget-d9cef98fe54d70eacf2d">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"calls":[{"method":"addTiles","args":["//{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,null,{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"http://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"http://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]},{"method":"addMarkers","args":[-36.852,174.768,null,null,null,{"interactive":true,"draggable":false,"keyboard":true,"title":"","alt":"","zIndexOffset":0,"opacity":1,"riseOnHover":false,"riseOffset":250},"The birthplace of R",null,null,null,null,{"interactive":false,"permanent":false,"direction":"auto","opacity":1,"offset":[0,0],"textsize":"10px","textOnly":false,"className":"","sticky":true},null]}],"limits":{"lat":[-36.852,-36.852],"lng":[174.768,174.768]}},"evals":[],"jsHooks":[]}</script>
]

---

# Chunks

```r
library(rbokeh)
p <- figure() %>%
  ly_points(Sepal.Length, Sepal.Width,
    data = iris,
    color = Species, glyph = Species,
    hover = list(Sepal.Length, Sepal.Width))
p
```
]

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---

# Inline chunks

### <i class="fas  fa-code "></i> Syntax

We studied `` `r
length(levels(iris$Species))` `` iris species and took
measurements on `` `r
nrow(iris)` `` flowers.

We found that Iris virginica had the longest sepal with a mean of
`` `r
mean(subset(iris,Species=="virginica")$Sepal.Length)`
`` millimeters!

### <i class="fas  fa-file-alt "></i> Output

````md
This text is written in markdown.

We studied 3 iris species and took measurements on 150 flowers.

We found that Iris virginica had the longest sepal with a mean of 6.588 millimeters!
````

---
class: inverse, center, middle

# <i class="fas  fa-rocket "></i> Chunks options

---

# Chunks options

- Multiple options separated by commas
  `{r option1=value, option2=value}`

- Label your code chunk!
<img height="160px" width="160px" src="https://d33wubrfki0l68.cloudfront.net/6fcddff214345601f998805adce94ab0e21d8615/2a098/screenshots/rmarkdown-chunk-nav.png"></img>

]

````md
```{r dispIris, option1=value, option2=value}
library(tibble)
data(iris)
head(iris)
```
````
]

---

# Chunk options

Chunk output can be customised with [numerous options](https://yihui.name/knitr/options/):

```r
str(knitr::opts_chunk$get())
```

```
## List of 53
##  $ eval         : logi TRUE
##  $ echo         : logi TRUE
##  $ results      : chr "markup"
##  $ tidy         : logi FALSE
##  $ tidy.opts    : NULL
##  $ collapse     : logi FALSE
##  $ prompt       : logi FALSE
##  $ comment      : chr "##"
##  $ highlight    : logi TRUE
##  $ strip.white  : logi TRUE
##  $ size         : chr "normalsize"
##  $ background   : chr "#F7F7F7"
##  $ cache        : logi FALSE
##  $ cache.path   : chr "index_cache/html/"
##  $ cache.vars   : NULL
##  $ cache.lazy   : logi TRUE
##  $ dependson    : NULL
##  $ autodep      : logi FALSE
##  $ cache.rebuild: logi FALSE
##  $ fig.keep     : chr "high"
##  $ fig.show     : chr "asis"
##  $ fig.align    : chr "default"
##  $ fig.path     : chr "index_files/figure-html/"
##  $ dev          : chr "png"
##  $ dev.args     : NULL
##  $ dpi          : num 72
##  $ fig.ext      : NULL
##  $ fig.width    : num 7
##  $ fig.height   : num 7
##  $ fig.env      : chr "figure"
##  $ fig.cap      : NULL
##  $ fig.scap     : NULL
##  $ fig.lp       : chr "fig:"
##  $ fig.subcap   : NULL
##  $ fig.pos      : chr ""
##  $ out.width    : NULL
##  $ out.height   : NULL
##  $ out.extra    : NULL
##  $ fig.retina   : num 1
##  $ external     : logi TRUE
##  $ sanitize     : logi FALSE
##  $ interval     : num 1
##  $ aniopts      : chr "controls,loop"
##  $ warning      : logi TRUE
##  $ error        : logi FALSE
##  $ message      : logi TRUE
##  $ render       : NULL
##  $ ref.label    : NULL
##  $ child        : NULL
##  $ engine       : chr "R"
##  $ split        : logi FALSE
##  $ include      : logi TRUE
##  $ purl         : logi TRUE
```

---

# Default options

### <i class="fas  fa-code "></i> Syntax

````md
```{r}
head(iris)
```
````

]

### <i class="fas  fa-file-alt "></i> Output

```r
head(iris)
```

]

---

# Chunk option `echo`

### <i class="fas  fa-code "></i> Syntax

````md
```{r echo = FALSE}
head(iris)
```
````

]

### <i class="fas  fa-file-alt "></i> Output

- Display results but not code.
- Useful to present results to people not interested by the code.
- Use `echo = -1` to hide only the first line of a code chunk.

---

# Chunk option `eval`

.pull-left[
### <i class="fas  fa-code "></i> Syntax
````md
```{r eval = FALSE}
head(iris)
```
````
]

```r
head(iris)
```
]

- Code is not evaluated.
- Useful to show exemple code.
- Use `eval = -1` to evaluate every line of a code chunk except the first.

---

# Chunk option `include`

.pull-left[
### <i class="fas  fa-code "></i> Syntax
````md
```{r include = FALSE}
head(iris)
```
````
]

]

- Code is evaluated but no output (code, results and figures) is displayed.
- Useful in setup options and package installation.

---

# Chunk option `results`

.pull-left[
### <i class="fas  fa-code "></i> Syntax
````md
```{r results = "hold"}
1 + 1
2 + 2
```
````
]

```r
1 + 1
2 + 2
```

```
## [1] 2
## [1] 4
```
]

- Hold all results in a code chunk and display them at the end.

---

# Chunk option `results`

.pull-left[
### <i class="fas  fa-code "></i> Syntax
````md
```{r results = "hide"}
1 + 1
ggplot(data = iris,
       aes(x = Petal.Length,
           y = Petal.Width)) +
  geom_point()
```
````

- Hide results but not plots

]

```r
1 + 1
ggplot(data = iris,
       aes(x = Petal.Length,
           y = Petal.Width)) +
  geom_point()
```

<img src="index_files/figure-html/unnamed-chunk-23-1.png" width="288" style="display: block; margin: auto;" />
]

---

# Chunk options `fig.height` & `fig.width`
.pull-left[
### <i class="fas  fa-code "></i> Syntax
````md
```{r fig.height = 3,
      fig.width = 5,
      echo = FALSE}
ggplot(data = iris,
       aes( x = Sepal.Length,
            y = Sepal.Width,
            color = Species)) +
  geom_point()
```
````
]

.pull-right[
### <i class="fas  fa-file-alt "></i> Output
![](index_files/figure-html/unnamed-chunk-24-1.png)
]

- width and height of the plot in inches
- Note that options are separated by commas

---
# Chunk options

### What output each option suppresses?

Option             | Run code | Show code | Output | Plots | Messages | Warnings
-------------------|:--------:|:---------:|:------:|:-----:|:--------:|:-------:
`eval = FALSE`     |<i class="fas  fa-times "></i>|         |<i class="fas  fa-times "></i>|<i class="fas  fa-times "></i>|<i class="fas  fa-times "></i>|<i class="fas  fa-times "></i>
`include = FALSE`  | |<i class="fas  fa-times "></i>|<i class="fas  fa-times "></i>|<i class="fas  fa-times "></i>|<i class="fas  fa-times "></i>|<i class="fas  fa-times "></i>
`echo = FALSE`     |  |<i class="fas  fa-times "></i>|     |    |      |
`results = "hide"` |        |        |<i class="fas  fa-times "></i>|     |        |
`fig.show = "hide"`|        |       |     | <i class="fas  fa-times "></i>|      |
`message = FALSE`  |          |           |        |       |<i class="fas  fa-times "></i>|
`warning = FALSE`  |          |           |        |       |          |<i class="fas  fa-times "></i>

Table from [R for Data Science](https://r4ds.had.co.nz/r-markdown.html#chunk-options)

---
# Global chunk options

## Setup

You can change the default chunk options for all following chunks in your document.

````md
```{r include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  cache = TRUE,
  comment = "#>",
  fig.width = 6,
  fig.align = "center"
)
```
````

---

# <i class="fas  fa-gamepad "></i> Exercice

## Let's practice !

1. Open a new `.Rmd` document and run `data(diamonds)` within a chunk
2. Add the following text and fill it: `
We have data about XXXX diamonds. Only
XXXX are larger than 2.5 carats.
`

3. Display all diamonds larger than 2.5 carats with the function `DT::datatable()`.
4. Make an histogram of the carats. The figure should have an height and width of 4 inches.
5. `DT::datatable()` doesn't work with PDF or Word document, why?

---

# Wrapping up

✔️ **Document your document**: use YAML to set up meaningful metadata

✔️ **Style your document**: use YAML to add options to your chosen output format

✔️ **Organize your text**: use markdown headers with `#`

✔️ **Organize your code**: use `knitr` chunk labels

✔️ **Style your text**: use markdown **bold**, *italics*, <i class="fas fa-list-ul"></i> bullets, and <i class="fas fa-list-ol"></i> lists

✔️ **Style your output**: use `knitr` chunk options

🧶 early, 🧶 often

---

# Why using it?

<i class="fas  fa-arrow-circle-right "></i> Multiplateform | Portable | Reproducible

<i class="fas  fa-arrow-circle-right "></i> Impress your director with dynamic output | Turn into a geek | Expose your skills on the web

---
class: inverse, center, middle