Sharing data and code in R

class: center, middle, inverse, title-slide

# Sharing data and code in R
## Developing skills in R, DEEP, SU
### Andreas Novotny
### 14 November 2018

---

name: intro
class: spaced

## Sharing data, code and analysis
* Packages (data and code)
* Interactive plots

![](interactive.jpg)

---

## What is an R package?

![](package.jpg)
---
## What is an R package?

* A directory containing a specific file structure

* A way of transferring functions, data and code

* An efficient, well documented analysis or method

![](package.jpg)

---

## What is an R package?

* Efficient

* Improvable

* **Reproducible**

![](package.jpg)

---

![](devtools/Picture1.png)

[LINK TO THE CHEAT SHEET](devtools-cheatsheet.pdf)
---

![](devtools/Picture2.png)

---
## Initialize an r package in Rstudio:

1. File - New project
2. New Directory
3. New R package
4. Add name and description
5. OK

## Make connection to github

1. Open git-hub:
2. New repository
3. Follow instructions from git-hub

---
![](devtools/Picture5.png)

---
![](devtools/Picture4.png)
---

![](devtools/Picture3.png)

---
![](devtools/Picture6.png)
---
![](devtools/Picture8.png)

---

![](devtools/Picture7.png)
---

## README.md file

This is what the users will see when the enter Git Hub:

* Short (or long) description of the package.

* How to install the package?

* What are the dependencies of the package?

---
## Make your packege available on GitHub!

* git add *

* git commit -m 'I just wrote a cool package.'

* git push

---

## Install others packages from github

```r
devtools::install_github("repository")
```

---

## Other resources

[R Packages book](http://r-pkgs.had.co.nz)

![](http://r-pkgs.had.co.nz/cover.png)

---

## Interactive plots

![](interactive2.jpg)
---
## Plotly

The function ggplotly converts a ggplot object to an HTML widget

```r
library(tidyverse)
library(plotly)
```
---
## Plotly

```r
plot <- ggplot(iris, aes(x=Sepal.Length, y=Petal.Length)) +
 geom_point(aes(color=Species))
plot
```

<img src="packages_files/figure-html/unnamed-chunk-5-1.png" style="display: block; margin: auto auto auto 0;" />
---
## Plotly

```r
plot <- ggplot(iris, aes(x=Sepal.Length, y=Petal.Length)) +
 geom_point(aes(color=Species))
ggplotly(plot)
```

<div id="htmlwidget-85892aa42c479a7a3f14" style="width:504px;height:504px;" class="plotly html-widget"></div>
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---
## Flexdashboard

[Example flexdash](https://walkerke.shinyapps.io/neighborhood_diversity/)

![](flexdash.jpg)
---
## Resources:

[FlexDashboard](https://rmarkdown.rstudio.com/flexdashboard/)

[Shiny](https://shiny.rstudio.com/)

[Plotly](https://plot.ly/)

---

```r
R.version
```

```
##                _                           
## platform       x86_64-pc-linux-gnu         
## arch           x86_64                      
## os             linux-gnu                   
## system         x86_64, linux-gnu           
## status                                     
## major          3                           
## minor          5.1                         
## year           2018                        
## month          07                          
## day            02                          
## svn rev        74947                       
## language       R                           
## version.string R version 3.5.1 (2018-07-02)
## nickname       Feather Spray
```

---
name: end-slide
class: end-slide

# Thank you