R Markdown Output to HTML Web Page Word Slides Shiny Dashboards Wordpress Git Hub PDF Kindle Ebook. Markdown to wordpress. Chapter 18 Test drive R Markdown. We will author an R Markdown document and render it to HTML. We discuss how to keep the intermediate Markdown file, the figures, and what to commit to Git and push to GitHub. If GitHub is the primary venue, we render directly to GitHub-flavored markdown and never create HTML.
- If the HTML generated by the chunk includes spaces, pandoc can be fooled into thinking the text is markdown rather than HTML. Using results=“asis” to display HTML markup: Regression Tables There are many packages that can create near-publication-quality regression tables.
- An R Markdown (.Rmd) file is a record of your research. It contains the code that a scientist needs to reproduce your work along with the narration that a reader needs to understand your work. Dynamic Documents You can choose to export the finished report as a html, pdf, MS Word, ODT, RTF, or markdown document; or as a html or pdf based slide show.
In the previous tutorials we’ve learned about the
R Markdown format and how to create a report using
R Markdown in
RStudio. In this tutorial, we will render or
R Markdown document to a web friendly,
html format using the
knitr can be used to convert
R Markdown files to many different formats including:
.md) and more.
At the end of this lesson, you will:
- Be able to produce (
htmlfile from an
- Know how to modify chuck options to change what is rendered and not rendered on the output
What You Need
You will need the most current version of
R and, preferably,
RStudio loaded on your computer to complete this tutorial. You will also need an
R Markdown document that contains a
YAML header, code chunks and markdown segments.
Install R Packages
What is Knitr?
knitr is the
R package that we use to convert an
R Markdown document into another, more user friendly format like
knitr package allows us to:
- Publish & share preliminary results with collaborators.
- Create professional reports that document our workflow and results directly from our code, reducing the risk of accidental copy and paste or transcription errors.
- Document our workflow to facilitate reproducibility.
- Efficiently change code outputs (figures, files) given changes in the data, methods, etc.
knitr package was designed to be a transparent engine for dynamic report generation with
R – Yihui Xi – knitr package creator
When To Knit: Knitting is a useful exercise throughout your scientific workflow. It allows you to see what your outputs look like and also to test that your code runs without errors. The time required to knit depends on the length and complexity of the script and the size of your data.
How to Knit
To knit in
RStudio, click the Knit pull down button. You want to use the Knit HTML option for this lesson.
When you click the Knit HTML button, a window will open in your console titled R Markdown. This pane shows the knitting progress. The output (
html in this case) file will automatically be saved in the current working directory. If there is an error in the code, an error message will appear with a line number in the R Console to help you diagnose the problem.
Markdown Embed Html
Data tip: You can run
knitr from the command prompt using:
View the Output
When knitting is complete, the
html file produced will automatically open.
Notice that information from the
YAML header (title, author, date) is printed at the top of the HTML document. Then the
html shows the text, code, and results of the code that you included in the
Add the code below to your
.Rmd document. Then
.Rmd file to
Where is the File?
In the steps above, we downloaded a file. However, where did that file go on your computer? Let’s find it before we go any further.
boulder-precip.csv file there?
Leading up to the UseR! 2016 conference, I had been looking forward to attending Yihui Xie’s tutorial on R Markdown - there were a few things I had wanted to ask him on how to make custom formats using
Then, a funny thing happened. A few days before the conference started, I got an email from Yihui, sent also to Karl Broman. Yihui’s visa had been delayed, so he could not attend the conference: could one or both of us deliver his tutorial material?
Given everything Yihui has done for the community, the only possible answer was “yes”. So Karl and I divvied up his slides and each up us did our own deep-dive into our material. As it happened, I was to deliver the material that dealt with my questions - so this was a first-rate opportunity to get it figured out!
In days before the tutorial, with help from Yihui, I got most of it worked out, and in the days and weeks to follow, we sorted out the rest. This page is a distillation of what I had been wanting to figure out.
As I write the rest of this out, I remember fondly the four (somewhat panicked) days of getting everything sorted out with Karl and Yihui. A word of thanks here to Karl for putting together the framework that let us bring tutorial in for a landing. Also, thanks to Yihui for thinking of me as someome not completely unsuitable to fill in. And a huge thanks to the participants in the tutorial for their patience.
RStudio has a great series of articles:
Get the tutorial slides, etc.
This is a great place to get started on the concepts I try to demonstrate here.
First, it important to note that this is based on the dev version of R Markdown - pending the next CRAN release.
Rmd File To Pdf
To follow along here, you will need to install a package, user2016docdemo, that has a series of functions that return custom formats.
Examining the format
It will be a lot easier to figure out how customize things if we understand (a little bit) what is going on. Even though R Markdown is capable of so much more, for the purposes of this discussion we will assume that you are interested only in producing an html file.
rmarkdown::render() function has two jobs: (1) to knit the R Markdown file into a Markdown file, (2) to use pandoc to turn the Markdown file into an html file. In order to do this,
render() needs a set of instructions - this set of instructions is a format, and it is stored as a list.
The purpose of the
rmarkdown::html_document() function is to help you to generate this list. Using Kent Russell’s listviewer package, let’s look at the default format returned by
For our purposes, we are most-interested in the first parts of the list, entitled “knitr” and “pandoc”. You may wish to click around to see what’s what.
The job of any R Markdown format function, including your custom format functions, is to return the format list.
These should look familiar, as they are these are parameters that you use to put in a yaml header at the start of an R Markdown document. For example:
rmarkdown::render() is run (either from the knit button, or from the command line), it passes along the yaml information “under”
html_document: to the
rmarkdown::html_document() function. It bears repeating that the best way to figure out how to construct your yaml header is to look at the help page for
As you design your custom formats, keep in mind that you will be able to pass arguments to your format function using the yaml header.
The biggest biggest mental-block (as least for me) to making an easily deployable custom-format is building a package. The reason this is necessary is that when we hit the knit button in RStudio, the
render() function runs in a new R session - this is for a very good reason. The only way I know to get the
render() function the “list of instructions” is to provide a package function that returns it.
Luckily, Hadley has made it a whole lot easier for all of us to develop packages. I’d highly recommend his book on building packages, available online: http://r-pkgs.had.co.nz/.
Here’s a minimal list of steps.
- open an empty project
devtools::use_mit_license()(if that’s your thing)
use_github()(assumes you have a github.com account)
- write and save some custom functions (rest of this section)
- hit the build button to install locally
- commit and push to GitHub every so often
Simplest possible (do nothing)
The simplest possible custom format is a a function that simply passes everything on to
rmarkdown::html_document(). Here’s the source code for the simplest-possible custom-format function, one that simply passes everything along to
When we look at the list of instructions returned by the default, we see that it is (hopefully) no different than before.
At some point, I’d like to put some screenshots here of a sample page - or maybe just link to the results.
Change some defaults
One simple thing that you can do is to change some of the defaults of the
Similary, we can look at what the function returns:
It is not immedately apparent that there is a difference between the output of
html_doc_1(). Being both stubborn and not-so-bright, I spent way too much time tracking down where we can find the difference. Here it is: the format list has some elements that are functions; functions have environments. Therein lies the difference. Let’s look at the environment of one of the functions returned as a part of
We see our information in the
code_folding has a value of
theme has a value of
It is probably more useful to demonstrate what this does, rather than show the details of environments, so put a link here eventually.
Make your own theme
Here’s where we can have some fun. If the standard themes are not what you need (or want), you can create your own bootstrap theme at http://bootstrap-live-customizer.com/.
This is a re