5 Notebook Workflow

5.1 Create a New Notebook

R Markdown Codebook

5.1.1 YAML header

YAML: YAML Ain’t Markup Language

YAML is a human-readable data-serialization language. It is commonly used for configuration files and in applications where data is being stored or transmitted Wikipedia: YAML

A YAML header contains YAML arguments, such as “title”, “author”, and “output”, demarcated by three dashes (—--) to start and end.

Example: YAML

5.1.3 Plain Text

Simply add text below the YAML header. To start a new paragraph, you will need to end your plain text line with two (2) spaces.

5.1.4 Markup for Formatting

Bold: surround text with double astrics (**)

Italics: surround text with single astric (*)

5.1.5 Code Chunks

Top line: ```{r}

Bottom line: ```

Example: Code chunk

5.2 Interact within a Notebook

5.2.1 Run Code Chunks

Press the “Run” button to run a chunk

Key strokes:

Run highlighted section or a single bit of code:

  • Windows: Ctrl + Enter

  • Mac: Cmnd + Enter

Run an entire code chunk:

  • Windows: Ctrl + Shift + Enter

  • Mac: Cmnd + Shift + Enter

5.2.2 Keyboard Shortcuts

Example: shortcuts

5.2.3 Chunk Options

Add specification after the r inside the {r} at the start of the code chunk:

Examples: Chunk options

5.3 Knit a Notebook

5.3.1 Storing all associated files

If you are using any files, such as datasets or images, they need to be stored in the same folder location as the R Notebook (.Rmd file).

This folder location must be the Working Directory for the R Studio session. If you opened your .Rmd notebook file by double-clicking on its name, then this should be the case.

5.3.2 Setting the working directory

To ensure that R Studio knows where to find the files, you can manually set the Working Directory through the menu:

  • Click Session
  • Select Set Working Directory by hovering your mouse over it
  • Click on To Source File Location

You can double check that you were successful by

  • Click on the Files tab in the many-tab panel
  • Click on the button with the gear that says More
  • Click Go To Working Directory

At this point you should see all the files that reside in the folder location where the open .Rmd files is also saved.

5.3.3 Press Knit