So far you've seen R Markdown used to produce HTML documents. This chapter gives a brief overview of some of the many other types of output you can produce with R Markdown. There are two ways to set the output of a document:
RStudio's knit button renders a file to the first format listed in its `output` field. You can render to additional formats by clicking the dropdown menu beside the knit button.
Each output format is associated with an R function. You can either write `foo` or `pkg::foo`. If you omit, `pkg` the default is assumed to be rmarkdown. It's important to know the name of the function that makes the output because that's where you get help. For example, to figure out what parameters you can set with `html_document`, look at `?rmarkdown:html_document()`
To override the default parameter values, you need to use an expanded `output` field. For example, if you wanted to render an `html_document` with a floating table of contents, you'd use:
The previous chapter focussed on the default `html_document` output. There are number of basic variations on that theme, generating different types of documents:
Remember, when generating a document to share with decision makers, you can turn off the default display of code by setting global options in the setup chunk:
A notebook, `html_notebook`, is a variation on a `html_document`. The rendered outputs are very similar, but the purpose is different. A `html_document` is focussed on communicating with decisions makers, while a notebook is focussed on collaborating with other data scientists. These different purposes lead to using the HTML output in different ways. Both HTML outputs will contain the fully rendered output, but the notebook also contains the full source code. That means you can use the `.nb.html` generated by the notebook in two ways:
Emailing `.nb.html` files is a simple way to share analyses with your colleagues. But things will get painful as soon as they want to make changes. If this starts to happen, it's a good time to learn Git and GitHub. Learning Git and GitHub is definitely painful at first, but the collaboration payoff is huge. As mentioned earlier, Git and GitHub are outside the scope of the book, but there's one tip that's useful if you're already using them: use both `html_notebook` and `github_document` outputs:
`html_notebook` gives you a local preview, and a file that you can share via email. `github_document` creates a minimal md file that you can check into git. You can easily see how the results of your analysis (not just the code) change over time, and GitHub will render it for you nicely online.
You can also use R Markdown to produce presentations. You get less visual control than with a tool like Keynote or PowerPoint, but automatically inserting the results of your R code into a presentation can save a huge amount of time. Presentations work by dividing your content into slides, with a new slide beginning at each first (`#`) or second (`##`) level header. You can also insert a horizontal rule (`***`) to create a new slide without a header.
Dashboards are a useful way to communicate large amounts of information visually and quickly. Flexdashboard makes it particularly easy to create dashboards using R Markdown and a convention for how the headers affect the layout:
Flexdashboard also provides simple tools for creating sidebars, tabsets, value boxes, and gauges. To learn more about flexdashboard visit <http://rmarkdown.rstudio.com/flexdashboard/>.
HTML is an interactive format, and you can take advantage of that interactivity with __htmlwidgets__, R functions that produce interactive HTML visualisations. For example, take the __leaflet__ map below. If you're viewing this page on the web, you can drag the map around, zoom in and out, etc. You obviously can't do that on a book, so rmarkdown automatically inserts a static screenshot for you.
The great thing about htmlwidgets is that you don't need to know anything about HTML or JavaScript to use them. All the details are wrapped inside the package, so you don't need to worry about it.
htmlwidgets provide __client-side__ interactivity --- all the interactivity happens in the browser, independently of R. On one hand, that's great because you can distribute the HTML file without any connection to R. However, that fundamentally limits what you can do to things that have been implemented in HTML and JavaScript. An alternative approach is to use __shiny__, a package that allows you to create interactivity using R code, not JavaScript.
I can't show you a live shiny app here because shiny interactions occur on the __server-side__. This means you can write interactive apps without knowing JavaScript, but it means that you need a server to run it on. This introduces a logistical issue: Shiny apps need a Shiny server to be run online. When you run shiny apps on your own computer, shiny automatically sets up a shiny server for you, but you need a public facing shiny server if you want to publish this sort of interactivity online. That's the fundamental trade-off of shiny: you can do anything in a shiny document that you can do in R, but it that requires someone to be running R.
Execute `rmarkdown::render_site()` to build `_site`, a directory of files ready to deploy as a standalone static website, or if you use an RStudio Project for your website directory. RStudio will add a Build tab to the IDE that you can use to build and preview your site.
Read more at <http://rmarkdown.rstudio.com/rmarkdown_websites.html>.
* The __prettydoc__ package, <https://github.com/yixuan/prettydoc/>,
provides lightweight document formats with a range of attractive
themes.
* The __rticles__ package, <https://github.com/rstudio/rticles>, compiles a
selection of formats tailored for specific scientific journals.
See <http://rmarkdown.rstudio.com/formats.html> for a list of even more formats. You can also create your own by following the instructions at <http://rmarkdown.rstudio.com/developer_custom_formats.html>.
