Rmd and HTML

Much of your work for this class will be accomplished by editing .Rmd files.

When you knit an Rmd file, you are translating it into another format: typically HTML or PDF or Word.

Once you have done this, you will have two files relating to your work, for instance:

1. Assignment-1.Rmd — the Rmd file you edited
2. Assignment-1.html — a file suitable for display over the web

Which one do you hand in?

Both

• The Rmd is easier to handle and can be revised or have comments or corrections added.
• The HTML is easier to read and shows the results of your computations, such as graphics.

Systems for submitting files

There are many different kinds of systems for submitting files for grading. Three examples are:

1. Uploading files to course support systems like Moodle.
2. Publishing your files to a web service, e.g. RPubs.
3. Using a file management system like git/GitHub.

Your instructor will select the system you are to use.

git/GitHub

Once you’ve learned the basic operation of this system — cloning repositories, pulling, pushing, etc. — then submitting an assignment is easy.

For both the Rmd and HTML versions of your assignment (and any related files such as data):

1. “Stage” both the Rmd and HTML files (and any others, if needed).
2. “Commit” the staged files. Use a message like “Assignment 1”.
3. “Pull” from the remote repository (just to make sure that you’ve captured any changes made there).
4. “Push” to the remote repository.

Moodle or RPubs

It’s difficult to upload two files with these systems, so the strategy is to submit the HTML file, but embed the Rmd file within the HTML file.

The DataComputing package provides a way to do this easily. Include the following chunk in your document:

 ```{r results = "asis"}
 DataComputing::includeSourceDocuments()
 ```

You can follow the link to see the Rmd file that generated these slides. When the file is compiled to HTML, the above command will embed the Rmd file within the HTML and provide a link to it, like this.

⇒ Submitting-files.Rmd

Clicking on the link will (in most browsers) extract the Rmd file and install it in your Downloads directory.

Embedding other files, too

You can embed multiple files in a document, which you may find convenient for CSV files, etc.

When embedding a file other than the source Rmd file, give as an argument to includeSourceDocuments() the quoted character string containing the path and filename for your Rmd file.

You can construct the character string easily by using file.choose() in the console, and copying the result as the argument to the includeSourceDocuments() function.

Author: Daniel T. Kaplan