As your can see in, there was quite a debate on what metadata format to include. In conclusion, it is very useful, but tends to be very. Raw markdown content without the front matter. Useful with remarkjs.com.ReadingTime the estimated time, in minutes, it takes to read the content.Resources resources such as images and CSS that are associated with this page.Ref returns the permalink for a given reference (e.g.,.Ref 'sample.md').Ref does not handle in-page fragments correctly. Stack Overflow The World’s Largest Online Community for Developers. A simple, in-browser, markdown-driven slideshow tool. - More information about remarkjs(The logos and images are the properties of their respective authors (for instance, ENS.
What is Markdown?
Markdown is basically a syntax (a markup language) that conveys how text should be displayed. In practice, it allows you to use plain text for a document with bits of other things thrown in, but which will ultimately be converted to any number of other languages, especially HMTL, for eventual display in the format you desire.
The basic markdown syntax hasn’t even really been developed for many years, but there are now dozens of flavors, of which R Markdown is one. Most Markdown syntax is preserved and works identically no matter what flavor you use. However, the different flavors will have different options or slightly different implementations of certain things. The main point is knowing one flavor means you know some Markdown, and thus would easily work with others.
Remarkjs Plugins
Documents
To start using R Markdown, simply go to File/New File/R Markdown...
As you can see right away, you have your choice of several types of formats, some of which will be of interest to you as you get more used to using R Markdown.
Documents are what you’ll probably use primarily, especially since they can be used in place of normal R scripts. You have the choice of HTML, PDF and MS Word. The main thing you’ll want to do is make your choice early, because it is not really possible to have the document look like you’d want in all formats simultaneously. As these are the focus of this document, more detail is forthcoming.
Standard HTML
As mentioned, the default, and likely most commonly used document for R Markdown is the standard, single-page HTML document. It is highly flexible, and works well for short or longer works. Some of the other different formats are variations of it. You will probably want to get comfortable with it before moving on to other types of formats, but it will serve you well even as you advance your R Markdown skills.
R Notebooks
Many are using R Notebooks as their primary scripting tool, and these are definitely something to consider for your own approach. While there are some drawbacks in efficiency, many like the feel of them. In my experience, they lack the smooth approach of Jupyter Notebooks, and they really aren’t as suited to publishable work as the standard R Markdown document (at least I’ve had issues). Having your output inline also means you may be looking at stale results that don’t reflect previous data changes, and it’s easy for a few lines of code to become what would be equivalent to several printed pages of output. Again though, they might be useful for some purposes.
Radix
One of the newer formats for R Markdown is the Radix template. It is specifically suited toward scientific publishing, and very visually appealing. Along with some subtle alternative default settings relative to the standard html document, it has asides (marginal presentation), hover-over citations and footnotes, easy incorporation of metadata (e.g. license, author contribution), and other useful things that are, or should be, common to a scientific publication. You can even create a website with it (as I have)!
Bookdown
Remarkjs Github
You’re reading the output of a Bookdown template now. You might not think you will have that much to say, but if you are using a standard html document and it tends to get notably long, you might prefer the bookdown format to the constant scrolling. You could even use it for a slide-like presentation, but with a lot more flexibility. Many R publications, and more all the time, are being published via bookdown rather than traditional print (or both). See bookdown.org and my own website for more examples.
Presentations
You can do slide-style presentations with R Markdown, with three options shown, though two are bizarrely absent. Two shown are HTML based, and you should not even consider Beamer/pdf (i.e. (LaTeX)). Slides are not for printing, and in fact, really don’t work for text in general. They should be very visual if they are to be effective. The two notable formats not shown are revealjs5 and the kind you can create by going to File/New File/R Presentation, which is also revealjs but a different format. I do not recommend the latter. In addition, many seem to be really high on xaringan, which is based on remarkjs, but I am not sure what it offers over the others.
Creating a presentation is easy enough, and the following shows an example.
You should really question whether you need slides. They are a unnecessarily restrictive format, do not work well with text, and often don’t work well with interactive visualizations. Furthermore, their development doesn’t appear to be as much of a priority for the RStudio crowd relative to other formats (rightly so in my opinion). And finally, there is nothing substantive they offer that can’t be done with a standard HTML doc or its variants.
Shiny Apps
Shiny is an inherently interactive format geared toward the creation of websites and applications. While there are far more apt programming languages than R for creating a website/app, at least Shiny allows you to stay completely within the R environment, and that means you don’t have to be expert in those other languages.
You can run shiny apps on your machine well enough, though usually the point is to make something other people can interact with. This means you’ll need some place to house your work, and shinyapps.io allows for some free hosting and other options. As long as you have a web server people will be able to access your work. Other formats in this area to be aware of are websites and flexdashboard.
Templates
Templates are available for any number of things, and one can find plenty among specific packages. Once a package with a particular template is installed, you’ll then have it as an option here. All these typically do is provide a R Markdown file similar to when you open a document, with a couple specific options, and demonstration of them if applicable. It’s not much, but at least you won’t have to mess with some of it.
After you get the hang of R Markdown, you should strongly consider making your own template. It’s actually pretty easy, and then you’ll always have the option.
How to start
The best way to get started with R Markdown is to see a document you like, copy the relevant parts for your own document, and get to it! It really is the best way in my opinion. Many people host their files on GitHub, so you can just download it directly from there. The author of bookdown, a particular format for R Markdown, actually suggests people simply clone his repository for his book that teaches bookdown, and go from there. That’s how I started using bookdown, which became my favored format for longer documents, and even presentations. Now bookdown is available as a template as well.
Remarkjs To Pdf
Again though, just see what others are doing, and then tailor it to your own needs.
We have introduced a few HTML5 presentation formats in Chapter 4. The xaringan package (Xie 2021e) is an R Markdown extension based on the JavaScript library remark.js (https://remarkjs.com) to generate HTML5 presentations of a different style. See Figure 7.1 for two sample slides.
Remarkjs Examples
FIGURE 7.1: Two sample slides created from the xaringan package.
The name “xaringan” came from Sharingan (http://naruto.wikia.com/wiki/Sharingan) in the Japanese manga and anime “Naruto.” The word was deliberately chosen to be difficult to pronounce for most people (unless you have watched the anime), because its author (me) loved the style very much, and was concerned that it would become too popular.8 The concern was somewhat naive, because the style is actually very customizable, and users started to contribute more themes to the package later.
The xaringan package is based on the JavaScript library remark.js (https://remarkjs.com); remark.js only supports Markdown, and xaringan added the support for R Markdown as well as other utilities to make it easier to build and preview slides.
Remarks For Students Report Cards
You can learn more about the background stories and the usage of the xaringan package from the documentation at http://slides.yihui.name/xaringan/, which is actually a set of slides generated from xaringan. You may also read a potentially biased blog post of mine to know why I preferred xaringan / remark.js for HTML5 presentations: https://yihui.name/en/2017/08/why-xaringan-remark-js/.