The R Markdown Ecosystem

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# The R Markdown Ecosystem
## Reproducible Reports, Papers, Books, Websites, and Presentations
### <a href="https://yihui.org">Yihui Xie</a>, <a href="https://www.rstudio.com">RStudio Inc</a>
### 2017/03/02 @ Kansas State University

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# About myself

- Native Chinese (1st language: Chinese; 2nd? 3rd?)

- Statistician by training (Iowa State University)

- Software engineer for a living (working remotely for RStudio)

- Authored and co-authored a few R packages (knitr, animation, rmarkdown, shiny, bookdown, blogdown, and so on)

- Enjoys programming more than data analysis (no, I'm not a data scientist)

```r
    x11()
    library(animation)
    ani.options(nmax = 213, interval = 0.03)
    quincunx(balls = 200, col.balls = rainbow(200))

library(fun)
    x11(type = "Xlib")
    mine_sweeper()
    ```

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# Outline

- R Markdown

- Regular documents

- Journal papers

- Presentations

- Books

- Websites

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# R Markdown

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# Dynamic Documents

---
    title: "A Simple Regression"
    author: "Yihui Xie"
    output:
      html_document:
        toc: true
    ---

# Model

We built a linear regression model.

```{r}
    fit <- lm(dist ~ speed, data = cars)
    b   <- coef(fit)
    plot(fit)
    ```

# Results

The slope of the regression is `r b[1]`.

???

In fact, I have used this minimal example for a few years, and one day I suddenly realized I made a mistake here: the slope should be `b[2]` instead of `b[1]`. Although it is a little ironic, it is also a good example of why you should generate reports from source code instead of pasting a fixed number. If it is just a fixed number, say, 3.87, it will be difficult to realize that you copied a wrong coefficient.

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# Reproducible research

- Keyword: automation (i.e. produce results via code instead of manual operations)

- You will be stumbled over and over again by things that cannot be automated (e.g. the source data may be updated)

.center[<img src="gif/stumble-baby.gif" width=400 />]

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# Reproducible research is hard

- The Duke Saga: http://www.economist.com/node/21528593

- If you have 40 minutes, I strongly recommend this video by Keith Baggerly: https://youtu.be/7gYIs7uYbMo

- Not easy for large projects

.center[<img src="gif/pass-chase.gif" width=400 />]

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# A regular R Markdown document

- The rmarkdown package http://rmarkdown.rstudio.com &approx; [knitr](https://yihui.org/knitr) + [Pandoc](http://pandoc.org)

- Markdown syntax (YAML metadata, section headings, math expressions, figures, tables, ...)

- One document, different output formats

- Customization

- Demos

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# Sounds simple?

.center[![](gif/get-into-the-car.gif)]

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# More advanced applications of R Markdown

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# Journal papers

- The rticles package https://github.com/rstudio/rticles

- Basic idea: translate R Markdown to LaTeX via the template of the journal

- Files -> New File -> R Markdown -> From Template

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# Presentations

- Built-in presentation formats (ioslides, Slidy, beamer)

- My current favorite format: xaringan https://github.com/yihui/xaringan

- HTML5 slides (in web browser)

- Much more customizable than built-in formats (e.g. easily align elements, set background images, change CSS, create template slides, and so on)

- Useful keyboard shortcuts (fullscreen, mirror, presenter mode, ...)

???

Sharingan, from the Japanese anime Naruto

![Sharingan](https://upload.wikimedia.org/wikipedia/commons/b/be/Sharingan_triple.svg)

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# Books

- The bookdown package (on [CRAN](https://cran.rstudio.com/package=bookdown) and [Github](https://github.com/rstudio/bookdown)); Showcase https://bookdown.org

- Why?

- books should have been much easier to write (technically)

- cheaper to buy (on the order of $10)

- richer to read (dynamic content -- imagine you can fit a linear regression
    right inside the book)

- quicker to iterate (not waiting for eight years for a second edition)

- and authored by a small number of people but have attracted a large number of contributors (on the order of 100) instead of only relying on the feedback of three anonymous reviewers

- How? A series of Rmd files, each being a chapter

- Extended the Markdown syntax (number and reference figures / tables / equations / theorems / ...)

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# Websites

- The blogdown package https://github.com/rstudio/blogdown

- Based on R Markdown and Hugo

- Set up a website in one minute! (`blogdown::new_site()` under an empty directory)

- Structure of the website

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# Contact info

- Yihui Xie

- https://yihui.org

- Twitter [@xieyihui](https://twitter.com/xieyihui) Github [@yihui](https://github.com/yihui)

- RStudio

- https://www.rstudio.com

- Twitter [@rstudio](https://twitter.com/rstudio) Github [@rstudio](https://github.com/rstudio)