Notebooks

Download This Notebook

You can download an R Notebook version of this lesson to follow along with here.

About R Notebooks

This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.

We will talk more about R Markdown on Day 2, and all the wonderful things you can do using it to create documents, but today we are going to focus on using R Markdown Notebooks to create reproducible code.

Briefly, R Markdown is a simple way to create documents with formatting by using specific symbols and characters. Programs capable of reading R Markdown can render a nicely formatted document. This is similar to the way that HTML files are text documents with specific tags, which are read by specific programs (web browsers, etc.) that apply those tags to the text, interpret the formatting, apply it to the document, and display it. R Markdown files (and R Notebooks) have the base file extension *.Rmd. An R Notebook will have the line output: html_notebook in the header.

R Notebooks have a few extra features over regular R Markdown documents:

• When you execute code in a Notebook, it is done line by line, so it can be easier to check execution for errors. In a regular R Markdown document, code is executed all at once.

• You can Preview your notebook using the Preview button - this displays a rendered HTML copy of the contents of the editor, but does not actually run any code. This makes it a bit faster to check your output.

• When you save your notebook, it creates a special *.nb.html file, which is actually a package of the HTML rendering (of the page, with the code sections as separate image files in their own directory) and the Markdown file. This can be shared with others and opened like a regular fine from within RStudio.

Text Formatting

To create a new R Markdown Notebook in RStudio, select File -> New File -> R Notebook.

You can enter text into a Notebook as you normally would into any other text document and use Markdown conventions to format it.

Enter text between the double asterisks below to format it as bold: ** **

Enter text between the underscores below to format it as italic: _ _

Click Preview when you are finished to view your changes.

Take advantage of this to document your code and data to keep it readable, understandable, and reproducible!

Embedding Code Chunks

You can embed R code into Notebooks by using chunks, set off above and below by three reverse ticks: ```

Try executing this chunk by clicking the Run button (small green arrow) within the chunk or by placing your cursor inside it and pressing Cmd+Shift+Enter.

a <- 17
b <- 34
a + b

## [1] 51

The designation {r} tells the Notebook that this is executable R code.

Here’s another example - run it the same way:

plot(cars)

The ‘cars’ dataset is an example dataset built into R, and the ‘plot’ command is a basic R command to create a default plot of simple data. We’ll talk more about plotting using ggplot later on in this workshop.

Note the addition of cars_plot in the {r} designation - this is the name of the code chunk. This can be used to navigate your Notebook using the menu in the lower left of the document window. It is also used when you are calling an external R script into a Notebook, and we’ll see an example of that in the next example. You can also add sections to your document using headings designated by ### - you’ll learn more about that tomorrow.

Add a new chunk in the space below by clicking the Insert Chunk button on the toolbar or by pressing Cmd+Option+I.

1. Name your chunk ‘math_trick_nb_example’.
2. Perform the following operations:
3. Assign your shoe size to a variable.
4. Multiply this variable by 5.
5. Add 50.
6. Multiply by 20.
7. Add 1017 (1018 if you have already had your birthday this year)
8. Subtract the year you were born.
9. Display the answer.

shoe_size <- 9
shoe_size_mod <- (((shoe_size * 5) + 50) * 20) + 1018 - 1979
shoe_size_mod

## [1] 939

If you wanted to call this script in multiple Notebooks, you could save it as an R code file:

1. Click File -> New File -> R Script.
2. Copy and paste your code into the new file.
3. Add the line ## ---- math_trick at the top of your file.
4. Save your file as math_trick.R.
5. In your R Notebook, load the script using an {r setup} using the knitr::read_chunk() function as such:

knitr::read_chunk("math_trick.R")

Note that nothing will display.

6. You can now call this R script using {r math_trick} in an otherwise empty code chunk as such:

shoe_size <- 10
shoe_size_mod <- (((shoe_size * 5) + 50) * 20) + 1018 - 1979
shoe_size_mod

## [1] 1039

Save and Preview

After you save the notebook, an HTML file containing the code and output will be saved alongside it when you click the Preview button (or press Cmd+Shift+K) to preview the HTML file.