RStudio and R Resources

class: center, middle, title-slide

# RStudio and R Resources
## Happy Scientist Seminar
### Emil Hvitfeldt
### 2019-1-22

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# Motivation

We will talk about what you are able to do in RStudio with R and where to find information and rescources to do it great.

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.pull-left[
![](images/RStudio-Logo.png)
- Data analysis scripts
- Interactive web applications
- Documents
- Reports
- Graphs
- more
]

.pull-right[
- Syntax highlighting
- code completion
- smart indentation
- Integrated R help
- data viewer
- Version control with Git
]

---

.center[![:scale 100%](images/gui-view.png)]

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.center[![:scale 100%](images/gui-source.png)]

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![](images/gui-history.png)

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![](images/gui-console.png)

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![](images/gui-plots.png)

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# Packages

Idea -> Code -> Package -> Share -> Happiness

If you want to do something, chance has it someone have worked on it before

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## CRAN (The Comprehensive R Archive Network)

![](images/cran.png)

.center[https://cran.r-project.org/]

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.center[https://cran.r-project.org/web/packages/available_packages_by_name.html]

![](images/cran-package-alphabet.png)

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.center[https://cran.r-project.org/web/views/]

![](images/cran-task-view.png)

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.center[https://www.bioconductor.org/]

![](images/bioconducter.png)

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.center[https://www.bioconductor.org/packages/release/BiocViews.html#___Software]

![](images/bioconducter-packages.png)

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# R Markdown <img src='https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/rmarkdown.png' align="right" height="139" />

- Compile a single R Markdown document to a report in different formats, such as PDF, HTML, or Word.
- Make slides for presentations (HTML5, LaTeX Beamer, or PowerPoint).
- Build interactive applications based on Shiny.
- Write journal articles.
- Much more.

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# Creating a R Markdown file

.center[![:scale 60%](images/create-document.png)]

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# Creating a R Markdown file

.center[![:scale 50%](images/new-document-document.png)]

---

# Creating a R Markdown file

.center[![:scale 50%](images/new-document-presentation.png)]

---

# Creating a R Markdown file

.center[![:scale 50%](images/new-document-shiny.png)]

---

# Creating a R Markdown file

.center[![:scale 50%](images/new-document-template.png)]

---

.pull-left[
```
---
title: "Amazing Document"
author: "Emil Hvitfeldt"
date: "1/20/2019"
output: html_document
---
```
]

.pull-right[
### YAML (optional)
]

---

.pull-left[
```
---
title: "Amazing Document"
author: "Emil Hvitfeldt"
date: "1/20/2019"
output: html_document
---
```
]

.pull-right[
### YAML: YAML Ain't Markup Language
]

---

.pull-left[
```
---
title: "Amazing Document"
author: "Emil Hvitfeldt"
date: "1/20/2019"
output: html_document
---
```

<br>

**Chunks** of code surrounded by ` ``` `
]

.pull-right[
### YAML (optional)

### The R in R Markdown
]

---
.pull-left[
```
---
title: "Amazing Document"
author: "Emil Hvitfeldt"
date: "1/20/2019"
output: html_document
---
```

<br>

**Chunks** of code surrounded by ` ``` `

<br>

Text with simple text formating.
]

.pull-right[
### YAML (optional)

### The R in R Markdown

<br>

### The Markdown in R Markdown
]

---

.pull-left[
**What we write**
````
---
author: "Emil Hvitfeldt"
date: "1/20/2019"
output: html_document
---

We built a **linear** regression model.

```{r}
fit <- lm(mpg ~ disp, data = mtcars)
b   <- coef(fit)
plot(mpg ~ disp, mtcars)
```

The slope of the regression is `r
round(b[1], digits = 1)` in the output.
````
]
 
--

.pull-right[
**What we get**  
![](images/rmarkdown-html_document.png)
]

---

.pull-left[
**What we write**
````
---
author: "Emil Hvitfeldt"
date: "1/20/2019"
output: pdf_document
---

We built a **linear** regression model.

```{r}
fit <- lm(mpg ~ disp, data = mtcars)
b   <- coef(fit)
plot(mpg ~ disp, mtcars)
```

The slope of the regression is `r
round(b[1], digits = 1)` in the output.
````
]

.pull-right[
**What we get**  
![](images/rmarkdown-pdf_document.png)
]

---

# Build-in Formats

.pull-left[
- github_document
- html_document
- latex_document
- md_document
- odt_document
- pdf_document
- rtf_document
- word_document
]

.pull-right[
- ioslides_presentation
- powerpoint_presentation
- slidy_presentation
- beamer_presentation
]

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# Notable Extensions

- xaringan
--

- flexdashboard
--

- learnr
--

- rticles

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![](images/xaringan-github.png)

<br>

.center[https://github.com/yihui/xaringan]

---

---

![](images/flexdashboard-github.png)

---

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![](images/learnr-github.png)

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![](images/rticles-github.png)

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# Shiny <img src='https://raw.githubusercontent.com/rstudio/hex-stickers/master/PNG/shiny.png' align="right" height="139" />

Combines the computational power of R with the interactivity of the modern web.

Powerful web framework.

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.center[https://gallery.shinyapps.io/050-kmeans-example/]

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.center[https://gallery.shinyapps.io/082-word-cloud/]

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.center[https://gallery.shinyapps.io/086-bus-dashboard/]

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.center[https://apps.garrickadenbuie.com/rstudioconf-2019/]

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.center[http://www.dataseries.org/]

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# Where do I go for more information?

- Cheatsheets
- Books
- rweekly.org
- Forums
- USCbiostats/software-dev

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# Have a question? Google it

![](images/google-logo.gif)

.center[https://www.google.com/]

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![](images/parsnip-google.png)

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.center[https://rseek.org/]

![](images/rseek.png)

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.center[https://rseek.org/]

![](images/parsnip-rseek.png)

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# Cheatsheets

.pull-left[
![](images/cheatsheets-small-1.png)
]

.pull-right[
![](images/cheatsheet-small-2.png)
]

.center[https://www.rstudio.com/resources/cheatsheets/]
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# Books

.center[https://bookdown.org/]

![](images/bookdown-head.png)

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# Books

![](images/bookdown-show.png)

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.center[https://www.rweekly.org/]
 
![](images/rweekly.png)

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![](images/rstudio-community-logo.png)

.center[https://community.rstudio.com/]

<br>

![](images/stackoverflow-logo.png)

.center[https://stackoverflow.com/]

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.center[https://github.com/USCbiostats/software-dev]
 
![](images/usc-dev.png)