x <- 1 # Assign 1 to x
2 * x # Multiply x by 2[1] 21 Getting started with R
Motivating scenario: You have heard about R and RStudio, and maybe used them, but want a foundation so you can know what is going on as you do more and more with it.
Learning goals: By the end of this chapter you should be able to
- Explain why we are using R and RStudio.
- Use vectors, do math, ask logical questions, and assign variables in R.
- Use R functions, and “get” them.
- Install R packages.
- Load data into R, view it, and find the types of variables in each column.
- Know your way about RStudio.
- Describe and visualize data,
- Test null hypotheses,
- Develop complex models, and
- Share our workflow to allow for our work to be reproduced, reevaluated, questioned, and improved.
1.1 What is R? What is RStudio?
R is a computer program built for data analysis. As opposed to GUIs, like Excel, or click-based stats programs, R is focused on writing and sharing scripts. This allows analyses to be shared and replicated, ensuring that data manipulation occurs in a script, thus preserving the integrity of the original data, while providing tremendous flexibility. R has become the computer language of choice for most statistical work because it’s free, allows for reproducible analyses, makes great figures, and has many “packages” that support the integration of novel statistical approaches. In a recent paper, we used R to analyze hundreds of Clarkia genomes and learn about the (Figure 1.1 from Sianta et al. (2024)). RStudio is an Integrated Development Environment (IDE)—a nice setup to interact with R and make it easier to use.
More precisely, R is a programming language that runs computations, while RStudio is an integrated development environment (IDE) that provides an interface by adding many convenient features and tools. So just as the way of having access to a speedometer, rearview mirrors, and a navigation system makes driving much easier, using RStudio’s interface makes using R much easier as well.
1.2 The Shortest Introduction to R
Before opening RStudio, let’s get familiar with two simple ways to get started using R – (1) Using R as a calculator, and (2) Storing information by assigning values to variables.
R can perform simple (or complex) calculations. For example, entering 1 + 1 returns 2, and entering 2^3 (two raised to the power of three) returns 8. Try it yourself by running the code below, and then experiment with other simple calculations.
Math in R: See posit's recipe for using R as a calculator for more detail.
Commenting code The hash, #, tells R to stop reading your code. This allows you to “comment” your code – keeping notes to yourself and other readers about what the code is doing. Commenting your code is very valuable and you should do it often!Commenting code The hash, #, tells R to stop reading your code. This allows you to “comment” your code – keeping notes to yourself and other readers about what the code is doing. Commenting your code is very valuable and you should do it often!
Storing values in variables allows for efficient (and less error-prone) analyses, while paving the way to more complex calculations. In R, we assign values to variables using the assignment operator, <-. For example, to store the value 1 in a variable named x, type x <- 1. Now, 2 * x will return 2.
But R must “know” something before it can “remember” it. The code below aims to set y equal to five and see what y plus one is (it should be six). However, it returns an error. Run the code to see the error message, then fix it!
Now try assigning different numbers to x and y, or even using them together in a calculation, such as x + y. This simple concept of assigning values will become a key tool as we move into statistical analysis.
1.3 Let’s get started with R
The following sections introduce the very basics of R including:
- Functions and vectors in R.
- Loading packages and data into R.
- Data types in R.
- An orientation to RStudio.
Then we summarize the chapter, present practice questions, a glossary, a review of R functions and R packages introduced, and provide links to additional resources.