Science Communication with R

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# Science Communication with R
## Style, R Markdown & Xaringan
### Antoine Bichat
### State of the R - AgroParisTech<br>February 23, 2018

---

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# Code presentation

---
# Syntax

* Use `<-` for assignation and `=` for arguments

* Leave a space

* before `(` (except when it's part of a function call)

* after `)` or `,`

* around `=`, `<-`, `+`, `*`, `==`, etc

```r
x <- rnorm(n = 100000)^2 + rnorm(n = 100000)^2
hist(x[x < 10], col = "grey", xlab = "", ylab = "Count", 
     main = "Chi-squared empirical distribution")
```

---
# Functions names
 
* When possible, use verbs for function names: `add_row()` or instead of `row_adder()`

* A function should do one thing well (it should be called either because it has side-effects or because it returns a value; not both)

* Don't hesitate to split your long function in smaller ones

* Only use `return()` for early returns

* Comment your functions (use the `Ctrl + Maj + C shortcut`)

---
# Pipes

* For long pipes, use one verb per line

* Don't ommit the parenthesis

```r
# Good
summary_SL <-
  iris %>% 
  drop_na() %>% 
  group_by(Species) %>% 
  summarise(Mean_SL = mean(Sepal.Length))

# Bad
summary_SL <- iris %>% drop_na %>% group_by(Species) %>% 
  summarise(Mean_SL=mean(Sepal.Length))

iris %>% 
  drop_na %>% 
  group_by(Species) %>% 
  summarise(Mean_SL=mean(Sepal.Length)) -> summary_SL
```

---
# Useful help

* The Ctrl + Maj + A shortcut rearranges your code

* {styler} package

```r
ugly_code <- "a<-function( x){1+1}           "
styler::style_text(ugly_code)
```

```
## a <- function(x) {
##   1 + 1
## }
```
---
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# R Markdown
<img src="https://www.rstudio.com/wp-content/uploads/2014/04/rmarkdown-200x232.png" width="200" height="232">

---
#R Markdown?

* Markdown is a _lightweight markup language_ with plain text formatting syntax that can be converted to HTML. It is completely independent from R. The extention is typically `.md`.

.footnote[[<i class="fa  fa-stack-overflow "></i> Relationship between R Markdown, Knitr, Pandoc, and Bookdown](https://stackoverflow.com/questions/40563479)]

* R Markdown is an extension of the markdown syntax that enables R code to be executed. The extention is typically `.Rmd`.

* `rmarkdown` is a a library which proceses and converts `.Rmd` files into a number of different formats, including HTML or `.pdf`. The core function is `rmarkdown::render()`.

```r
install.packages("rmarkdown")
```

---
# Create a new `.Rmd`

.pull-left[
.center[
  <img src="CreateRmd1.png" width="400">
]
]

.pull-right[
  <div style = "margin-top: 80px"></div> 
  .center[
    <img src="CreateRmd2.png" width="400">
  ]
]

---
# New `.Rmd`

.center[
  <img src="CreateRmd3.png" width="700">
]

---
# Compile `.Rmd`

Use the `Knit` button to produce a HTML file

.center[
  <img src="CreateRmd4.png" width="300">
]

Shortcut: Ctrl + Maj + K

---
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# Markdown syntax

---
# Titles and text fonts

```
# Big title

## Title

### Small title

_Italic_, *italic*, __bold__, **bold**, and `monospace`
```

# Big title

## Title

### Small title

_Italic_, *italic*, __bold__, **bold**, and `monospace`

---
# Lists and more

.pull-left[
```
1. This is

2. an ordered

3. list
```
1. This is
2. an ordered
3. list
]

.pull-right[
```
 * This is

* a bullet list

* with indent
```
* This is
* a bullet list
  * with indent
]

<br>

```
> You can insert quotes, $\LaTeX$ expressions and horizontal rule:
```

> You can insert quotes, `$\LaTeX$` expressions and horizontal rule:

```
---
```

***

```
$$ \frac{1}{n} \sum_{i=1}^n X_i $$
```

$$ \frac{1}{n} \sum_{i=1}^n X_i $$

---
# Insert links and pictures

```
[My personal page](https://abichat.github.io/)
```

[My personal page](https://abichat.github.io/)

```
![](https://slides.yihui.name/gif/impossible-parking.gif)
```

![](https://slides.yihui.name/gif/impossible-parking.gif)

It also works directly with HTML syntax:

```
<a href="https://abichat.github.io/">My personal page</a>
<img src="https://slides.yihui.name/gif/impossible-parking.gif">
```

---
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# Chunks

---
# Basic chunk

````
```{r}
x <- 4
x
```
````

Output:

```r
x <- 4
x
```

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

---
# Echo

To display the output of a code chunk but not the underlying R code, you specify the `echo=FALSE` option

````
```{r chunkecho, echo=FALSE}
x <- 5
x
```
````

Output:

```
## [1] 5
```

---
# Eval

To display R code without evaluating it, you specify the `eval=FALSE` chunk option

````
```{r chunkeval, eval=FALSE}
x <- 5
```
````

Output:

```r
x <- 10
```

```r
x 
```

```
## [1] 5
```

---
# Fig options

````
```{r chunkfig, fig.align="center", fig.height=4, fig.width=8}
plot(iris$Sepal.Length, iris$Sepal.Width)
```
````

```r
plot(iris$Sepal.Length, iris$Sepal.Width)
```

Finding the good picture size is a trial and error process...

---
# Better way to include picture

````
```{r betterway, fig.align="center", out.width="70%", echo=FALSE}
knitr::include_graphics(
  "https://slides.yihui.name/gif/impossible-parking.gif")
```
````

It allows you to use the chunk options for image size

---
# Name your chunks!

* In RStudio you can navigate named chunks fairly easily

.footnote[[<i class="fa  fa-link "></i> Pets or livestock? Naming your RMarkdown chunks](http://www.masalmon.eu/2017/08/08/chunkpets/)]

* The goal of named chunk is clear (or it should be)

* Easier to debug

* Caching is more efficient with named chunks (otherwise it uses chunk positions)

---
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# Xaringan
<img src="https://camo.githubusercontent.com/f91f64981633838bdedfee54df8595534c3cd9ba/68747470733a2f2f75706c6f61642e77696b696d656469612e6f72672f77696b6970656469612f636f6d6d6f6e732f622f62652f53686172696e67616e5f747269706c652e737667" width="232" height="232">

---
# Xaringan?

Xaringan is a package to create slides with R Markdown

It is developped by Yihui Xie <i class="fa  fa-github "></i> <a href="https://github.com/yihui">@yihui</a>

```r
devtools::install_github('yihui/xaringan')
```

.center[
  <img src="CreateRmd5.png" width="400">
]

---
# How it works?

The syntax is almost the same as R Markdown

Slides are separated by `---`

You can build incremental slides with `--`

<br>

```
---
# How it works?

The syntax is almost the same as R Markdown

Slides are separated by `---`

You can build incremental slides with `--` 
```

---
# Tips

You can change slide configuration (for titles) with `class`

```
---
class: middle, center, inverse
```

<br>

To skip a lign, use the `<br>` HTML tag

<br>

Use `.footnote[Text]` to add a footnote and `.center[Text]` to center text

<br>

.center[I'm centered]

.footnote[I'm a footnote]

---
# Include an interactive map with leaflet

```r
library(leaflet)
leaflet() %>% addTiles() %>% setView(2.34822, 48.83976, zoom = 17)
```

<div id="htmlwidget-5c1da3b1010f92beb673" style="width:100%;height:360px;" class="leaflet html-widget"></div>
<script type="application/json" data-for="htmlwidget-5c1da3b1010f92beb673">{"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,"maxNativeZoom":null,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"continuousWorld":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":null,"unloadInvisibleTiles":null,"updateWhenIdle":null,"detectRetina":false,"reuseTiles":false,"attribution":"© <a href=\"http://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"http://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]}],"setView":[[48.83976,2.34822],17,[]]},"evals":[],"jsHooks":[]}</script>

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# References

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## Style

* The tidyverse style guide http://style.tidyverse.org

## R Markdown

* Official site https://rmarkdown.rstudio.com

* Cheat Sheet https://www.rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf

## Xaringan

* Documentation  https://slides.yihui.name/xaringan

---
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# Thanks for your attention!

#### <i class="fa  fa-github "></i> <a href="https://github.com/abichat" target="_blank">@abichat</a>
<div style = "margin-top: -20px"></div>
#### <i class="fa  fa-link "></i> <a href="https://abichat.github.io" target="_blank">abichat.github.io</a>
<div style = "margin-top: -20px"></div>
####<i class="fa  fa-envelope "></i> <a href="mailto:antoine.bichat@mines-nancy.org?subject=Science%20Communication%20with%20R">antoine.bichat@mines-nancy.org</a>

.footnote[Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan).]