R Markdown basics

Create a new notebook using File > New File > R Notebook. Read the instructions. Practice running the chunks. Verify that you can modify the code, re-run it, and see modified output.

2. Create a new R Markdown document with File > New File > R Markdown …. Knit it by clicking the appropriate button. Knit it by using the appropriate keyboard short cut. Verify that you can modify the input and see the output update.

Recall that the keyboard shortcut to knit a file is Cmd/Ctrl + Alt + K.

3. Compare and contrast the R notebook and R markdown files you created above. How are the outputs similar? How are they different? How are the inputs similar? How are they different? What happens if you copy the YAML header from one to the other?

R notebook files show the output of code chunks inside the editor, while hiding the console, when they are edited in RStudio. This contrasts with R markdown files, which show their output inside the console, and do not show output inside the editor. This makes R notebook documents appealing for interactive exploration. In this R markdown file, the plot is displayed in the “Plot” tab, while the output of summary() is displayed in the tab.

However, when this same file is converted to a R notebook, the plot and summary() output are displayed in the “Editor” below the chunk of code which created them.

Both R notebooks and R markdown files and can be knit to produce HTML output. R markdown files can be knit to a variety of formats including HTML, PDF, and DOCX. However, R notebooks can only be knit to HTML files, which are given the extension .nb.html. However, unlike R markdown files knit to HTML, the HTML output of an R notebook includes copy of the original .Rmd source. If a .nb.html file is opened in RStudio, the source of the .Rmd file can be extracted and edited. In contrast, there is no way to recover the original source of an R markdown file from its output, except through the parts that are displayed in the output itself.

R markdown files and R notebooks differ in the value of output in their YAML headers. The YAML header for the R notebook will have the line,

---
ouptut: html_notebook
---

For example, this is a R notebook,

---
title: "Diamond sizes"
date: 2016-08-25
output: html_notebook
---

Text of the document.

The YAML header for the R markdown file will have the line,

ouptut: html_document
For example, this is a R markdown file.

---
title: "Diamond sizes"
date: 2016-08-25
output: html_document
---

Text of the document.

Copying the YAML header from an R notebook to a R markdown file changes it to an R notebook, and vice-versa. More specifically, an .Rmd file can be changed to R markdown file or R notebook by changing the value of the output key in the header.

The RStudio IDE and the rmarkdown package both use the YAML header of an .Rmd file to determine the document-type of the file.

For more information on R markdown notebooks see the following sources:

• R Markdown: The Definitive Guide section, Chapter Notebook
• Difference between R MarkDown and R NoteBook StackOverflow thread.

4. Create one new R Markdown document for each of the three built-in formats: HTML, PDF and Word. Knit each of the three documents. How does the output differ? How does the input differ? (You may need to install LaTeX in order to build the PDF output — RStudio will prompt you if this is necessary.)

They produce different outputs, both in the final documents and intermediate files (notably the type of plots produced). The only difference in the inputs is the value of output in the YAML header. The following .Rmd would be knit to HTML.

---
title: "Diamond sizes"
date: 2016-08-25
output: html_document
---

Text of the document.

If the value of the output key is changed to word_document, knitting the file will create a Word document (DOCX).

---
title: "Diamond sizes"
date: 2016-08-25
output: word_document
---

Text of the document.

Similarly, if the value of the output key is changed to pdf_document, knitting the file will create a PDF.

---
title: "Diamond sizes"
date: 2016-08-25
output: pdf_document
---

Text of the document.

If you click on the Knit menu button and then on one of Knit to HTML, Knit to PDF, or Knit to Word, you will see that the value of the output key will change to html_document, pdf_document, or word_document, respectively.

You will see that the value of output will look a little different than the previous examples. It will add a new line with a value like, pdf_document: default.

---
title: "Diamond sizes"
date: 2016-08-25
output:
  pdf_document: default
---

Text of the document.

This format is more general, allows the document have multiple output formats as well as configuration settings that allow more fine-grained control over the look of the output format. The lecture R Markdown Formats discusses output formats for R markdown files in more detail.