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‎0-preamble/index.Rmd

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---
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title: "Preamble"
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subtitle: "SISBID 2016"
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author: "Di Cook ([email protected], @visnut); Heike Hofmann ([email protected], @heike_hh)"
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date: "07/13/2016"
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subtitle: "SISBID 2017 <br> https://github.com/SISBID/Module2"
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author: "Di Cook ([email protected], @visnut) <br> Heike Hofmann ([email protected], @heike_hh)"
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date: "07/12-14/2017"
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output:
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ioslides_presentation:
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transition: default
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widescreen: true
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css:
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styles.css
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xaringan::moon_reader:
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css: ["default", "myremark.css"]
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self_contained: false
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nature:
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highlightStyle: github
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highlightLines: true
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countIncrementalSlides: false
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---
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```{r, echo = FALSE, message = FALSE, warning = FALSE, warning = FALSE}
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warning = FALSE,
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error = FALSE,
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collapse = TRUE,
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comment = "#",
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fig.height = 4,
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fig.width = 8,
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comment = "",
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fig.height = 8,
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fig.width = 12,
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fig.align = "center",
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cache = FALSE
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)
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```
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##
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![](Hello-Di.png)
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##
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---
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![](Hello-Heike.png)
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##
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---
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![](Hello-Brian.png)
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##
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---
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![](Hello-Bryan.png)
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## Getting up and running
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![](Hello-Jeremy.png)
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---
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# Getting up and running
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- R and RStudio
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- Projects
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- RMarkdown
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- Web site
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## R is ...
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---
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# R is ...
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* __Free__ to use
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* __Extensible__
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* Over 8500 user contributed add-on packages currently on CRAN!
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* Most commonly used data science software [kdnuggets](http://www.kdnuggets.com/2017/05/poll-analytics-data-science-machine-learning-software-leaders.html)
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* __Free__ to use, __open source__ so you can see what code is doing to your data
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* __Extensible__: Over 10000 user contributed add-on packages currently on CRAN! Bioconductor has more than 1300 packages, and many researchers provide packages through github.
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* __Powerful__
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* With the right tools, get more work done, faster.
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* __Flexible__
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* Not a question of _can_, but _how_.
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* __Frustrating__
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* Flexibility comes at a cost (easy to shoot yourself in the foot!).
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```{r, eval = FALSE, echo = FALSE}
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# devtools::install_github("metacran/crandb")
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# [1] 8654
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```
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## RStudio is ...
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---
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# RStudio is ...
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[From Julie Lowndes](http://jules32.github.io/resources/RStudio_intro/):
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<blockquote>
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<b>If R were an airplane, RStudio would be the airport</b>, providing many, many supporting services that make it easier for you, the pilot, to take off and go to awesome places. Sure, you can fly an airplane without an airport, but having those runways and supporting infrastructure is a game-changer.
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</blockquote>
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## The RStudio IDE
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1. Source editor: Docking station for multiple files, Useful shortcuts ("Knit"), Highlighting/Tab-completion, Code-checking (R, HTML, JS), Debugging features
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2. Console window: Highlighting/Tab-completion, Search recent commands
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3. Other tabs/panes: Graphics, R documentation, Environment pane, File system navigation/access, Tools for package development, git, etc
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## Files for this workshop
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- [github site](https://github.com/SISBID/Module2) contains all the markdown files, code files, and data for this workshop
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- Clone a copy to your desktop
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---
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# The RStudio IDE
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<div align="center">
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<img src="dir.png" width="300">
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</div>
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- Source editor: Docking station for multiple files, Useful shortcuts ("Knit"), Highlighting/Tab-completion, Code-checking (R, HTML, JS), Debugging features
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- Console window: Highlighting/Tab-completion, Search recent commands
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- Other tabs/panes: Graphics, R documentation, Environment pane, File system navigation/access, Tools for package development, git, etc
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## Projects
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---
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class: inverse middle
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# Your turn: Getting started
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Creating a project helps organise work. For this workshop, I have created a project on my laptop called `SISBID-2016`.
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- __Download a zip archive__ of the workshop files from [github site](https://github.com/SISBID/Module2) contains all the markdown files, code files, and data for this workshop. __Unzip the file__ and __rename__ it `SISBID-2017`
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- __Create a project__ helps organise your work over these next few days called `SISBID-2017`.
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![](projectname.png)
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## Your turn
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Create a project for this workshop, in the directory where you downloaded the files from github. (Be sure that you open this at the start of each session. Generally it is a good idea NOT TO SAVE THE WORKSPACE when you close a project for the day.)
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* File -> New Project -> Existing Directory -> Empty Project
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## Hello R Markdown!
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* File -> New File -> R Markdown -> OK -> Knit HTML
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<div align="center">
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<img src="newFile.png" width="1000">
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</div>
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- __Get started with RMarkdown__, by creating a new R notebook. Knit it.
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- Now __open the file that created these slides__ `0-preamble/index.Rmd`. Navigate to the code chunks at the bottom of the file and run them.
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## What is R Markdown?
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- From the [R Markdown home page](http://rmarkdown.rstudio.com/):
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---
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# What is R Markdown?
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From the [R Markdown home page](http://rmarkdown.rstudio.com/):
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- R Markdown is an authoring format that enables easy creation of dynamic documents, presentations, and reports from R.
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- It combines the core syntax of __markdown__ (an easy-to-write plain text format) __with embedded R code chunks__ that are run so their output can be included in the final document.
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- R Markdown documents are fully reproducible (they can be automatically regenerated whenever underlying R code or data changes).
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## Installing packages
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---
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# Installing packages
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From CRAN
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```{r eval=FALSE}
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install.packages("ggenealogy")
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```
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##
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From bioconductor
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biocLite("ggbio")
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```
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##
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From github repos
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```{r eval=FALSE}
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devtools::install_github("heike/gglogo")
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devtools::install_github("haleyjeppson/ggmosaic")
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```
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## Resources
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---
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# Resources
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- [RStudio IDE cheat sheet](http://www.rstudio.com/wp-content/uploads/2016/01/rstudio-IDE-cheatsheet.pdf)
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- [rmarkdown cheat sheet](http://www.rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf)
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- [Q/A site: http://stackoverflow.com](http://stackoverflow.com)
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- [Dynamic Documents with R and knitr, Yihui Xie](http://yihui.name/knitr/)
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- RStudio IDE [RStudio IDE cheat sheet](https://www.rstudio.com/wp-content/uploads/2016/01/rstudio-IDE-cheatsheet.pdf)
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- RMarkdown [cheat sheet](https://www.rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf), [reference guide](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf)
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- Q/A site: [http://stackoverflow.com](http://stackoverflow.com)
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- Dynamic Documents with R and knitr [Yihui Xie](http://yihui.name/knitr/)
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## Share and share alike
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---
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# Share and share alike
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Materials for this workshop build on slides provided by several people, but primarily Hadley Wickham and Carson Sievert.
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‎0-preamble/index.html

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‎0-preamble/myremark.css

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@import url(https://fonts.googleapis.com/css?family=Actor);
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@import url(https://fonts.googleapis.com/css?family=Droid+Serif);
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@import url(https://fonts.googleapis.com/css?family=Yanone+Kaffeesatz);
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@import url(https://fonts.googleapis.com/css?family=Source+Code+Pro:400,500,600);
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@import url("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css");
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body {
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font-family: 'Actor', sans-serif;
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}
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h1, h2, h3 {
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font-family: 'Yanone Kaffeesatz';
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font-weight: 400;
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margin-bottom: 0;
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color: #1B9E77;
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}
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h1:before {
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color: #D95F02;
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font-family: "FontAwesome";
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margin-right: 10px;
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}
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.remark-slide-content h1 { font-size: 3em; }
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.remark-slide-content h2 { font-size: 1.9em; }
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.remark-slide-content h3 { font-size: 1.5em; }
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.footnote {
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position: absolute;
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bottom: 3em;
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font-style: italic;
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font-size: 70%;
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}
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li { line-height: 1.85em; }
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li p { line-height: 1.25em; }
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li {
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list-style-type: none;
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}
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ul li:before {
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content: "\f080";
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font-family: "FontAwesome";
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margin-right: 10px;
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color: #D95F02;
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}
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ul li li:before {
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content: "\f1fe";
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font-family: "FontAwesome";
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margin-right: 10px;
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}
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.red { color: #D00000; }
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.orange { color: #FFBA08; }
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.blue { color: #3F88C5; }
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.large { font-size: 2em; }
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a, a > code {
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color: #D95F02;
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text-decoration: none;
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}
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code {
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border-radius: 5px;
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}
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.remark-code, .remark-inline-code { font-family: 'Source Code Pro'; font-size: 80%; }
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.remark-code-line-highlighted { background-color: #373832; }
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.pull-left {
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float: left;
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width: 47%;
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}
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.pull-right {
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float: right;
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width: 47%;
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}
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.pull-right ~ p {
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clear: both;
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}
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#slideshow .slide .content code {
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font-size: 0.8em;
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}
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#slideshow .slide .content pre code {
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font-size: 0.9em;
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padding: 15px;
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}
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.inverse {
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background: #464646;
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color: #D8DAEB;
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text-shadow: 0 0 0px #333;
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}
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.inverse h1 {
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color: #1B9E77;
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font-size: 2.5em;
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line-height: 1.2em;
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}
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.inverse h2 {
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color: #1B9E77;
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font-size: 2.5em;
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line-height: 1.2em;
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}
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.inverse h3 {
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color: #D8DAEB;
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font-size: 1.5em;
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line-height: 1.0em;
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}
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.inverse ul li:before {
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content: "\f080";
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font-family: "FontAwesome";
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margin-right: 10px;
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color: #D95F02;
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}
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/* Slide-specific styling */
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#slide-inverse .footnote {
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bottom: 12px;
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left: 20px;
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}
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#slide-how .slides {
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font-size: 0.9em;
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position: absolute;
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top: 151px;
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right: 140px;
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}
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#slide-how .slides h3 {
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margin-top: 0.2em;
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}
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#slide-how .slides .first, #slide-how .slides .second {
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padding: 1px 20px;
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height: 90px;
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width: 120px;
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-moz-box-shadow: 0 0 10px #777;
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-webkit-box-shadow: 0 0 10px #777;
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box-shadow: 0 0 10px #777;
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#slide-how .slides .first {
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background: #fff;
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position: absolute;
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top: 20%;
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left: 20%;
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z-index: 1;
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}
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#slide-how .slides .second {
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position: relative;
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background: #fff;
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z-index: 0;
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}
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/* Two-column layout */
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.left-column {
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color: #777;
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width: 20%;
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height: 92%;
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float: left;
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}
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.left-column h2:last-of-type, .left-column h3:last-child {
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color: #000;
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}
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.right-column {
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width: 75%;
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float: right;
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padding-top: 1em;
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}

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‎0-preamble/styles.css~

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/* Thanks Kevin Ushey -- https://github.com/rstudio/webinars/blob/master/2014-04/styles.css */
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pre.prettyprint {
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width: inherit;
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left: 0px !important;
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padding: 10px !important;
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box-shadow: 1px 1px 5px #9c9c9c !important;
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border-style: solid;
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border-width: 1px;
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border-radius: 5px;
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border-color: #ADADAD;
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}
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pre.prettyprint + pre {
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width: inherit;
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left: 0px !important;
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padding: 10px !important;
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box-shadow: 1px 1px 5px #9c9c9c !important;
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border-style: solid;
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border-width: 1px;
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border-radius: 5px;
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border-color: #ADADAD;
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background-color: #F3F3F3;
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}
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h1, h2, h3, h4, h5, h6 {
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color: #b55 !important;
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line-height: 95%;
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}

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