Introduction to R and RStudio

Overview

Teaching: 20 min
Exercises: 5 min

Questions

• How to find your way around RStudio?

• How to interact with R?

Objectives

• Describe the purpose and use of each pane in the RStudio IDE

• Locate buttons and options in the RStudio IDE

• Define a variable

• Assign data to a variable

• Use mathematical and comparison operators

• Call functions

• Manage packages

Motivation

Science is a multi-step process: once you’ve designed an experiment and collected data, the real fun begins! This lesson will teach you how to start this process using R and RStudio. We will begin with raw data, perform exploratory analyses, and learn how to plot results graphically. This example starts with a dataset from gapminder.org containing population information for many countries through time. Can you read the data into R? Can you plot the population for Senegal? Can you calculate the average income for countries on the continent of Asia? By the end of these lessons you will be able to do things like plot the populations for all of these countries in under a minute!

Before Starting The Workshop

Participants who have completed the workshop setup are ready to complete this lesson.

Please ensure you have the latest version of R and RStudio installed on your machine. This is important, as some packages used in the workshop may not install correctly (or at all) if R is not up to date.

• Download and install the latest version of R here
• Download and install RStudio here

Introduction to RStudio

Throughout this lesson, we’re going to teach you some of the fundamentals of the R language as well as some best practices for organizing code for scientific projects that will make your life easier.

We’ll be using RStudio: a free, open source R integrated development environment (IDE). It provides a built in editor, works on all platforms (including on servers) and provides many advantages such as integration with version control and project management.

Basic layout

When you first open RStudio, you will be greeted by three panels:

• The interactive R console (entire left)
• Environment/History (tabbed in upper right)
• Files/Plots/Packages/Help/Viewer (tabbed in lower right)

Once you open files, such as R scripts, an editor panel will also open in the top left.

Workflow within RStudio

There are two main ways one can work within RStudio.

1. Test and play within the interactive R console then copy code into a .R file to run later.
   • This works well when doing small tests and initially starting off.
   • It quickly becomes laborious
2. Start writing in an .R file and use RStudio’s shortcut keys for the Run command to push the current line, selected lines or modified lines to the interactive R console.
   • This is a great way to start; all your code is saved for later
   • You will be able to run the file you create from within RStudio or using R’s source() function.

Tip: Running segments of your code

RStudio offers you great flexibility in running code from within the editor window. There are buttons, menu choices, and keyboard shortcuts. To run the current line, you can

1. click on the Run button above the editor panel, or
2. select “Run Lines” from the “Code” menu, or
3. hit Ctrl+Enter in Windows, Ctrl+Return in Linux, or ⌘+Return on OS X. (This shortcut can also be seen by hovering the mouse over the button). To run a block of code, select it and then Run. If you have modified a line of code within a block of code you have just run, there is no need to reselect the section and Run, you can use the next button along, Re-run the previous region. This will run the previous code block including the modifications you have made.

Introduction to R

Much of your time in R will be spent in the R interactive console. This is where you will run all of your code, and can be a useful environment to try out ideas before adding them to an R script file. This console in RStudio is the same as the one you would get if you typed in R in your command-line environment.

The first thing you will see in the R interactive session is a bunch of information, followed by a “>” and a blinking cursor. In many ways this is similar to the shell environment you learned about during the shell lessons: it operates on the same idea of a “Read, evaluate, print loop”: you type in commands, R tries to execute them, and then returns a result.

Using R as a calculator

The simplest thing you could do with R is do arithmetic:

1 + 100

[1] 101

And R will print out the answer, with a preceding “[1]”. Don’t worry about this for now, we’ll explain that later. For now think of it as indicating output.

Like bash, if you type in an incomplete command, R will wait for you to complete it:

> 1 +

+

Any time you hit return and the R session shows a “+” instead of a “>”, it means it’s waiting for you to complete the command. If you want to cancel a command you can simply hit “Esc” and RStudio will give you back the “>” prompt.

Tip: Cancelling commands

If you’re using R from the command line instead of from within RStudio, you need to use Ctrl+C instead of Esc to cancel the command. This applies to Mac users as well!

Cancelling a command isn’t only useful for killing incomplete commands: you can also use it to tell R to stop running code (for example if it’s taking much longer than you expect), or to get rid of the code you’re currently writing.

When using R as a calculator, the order of operations is the same as you would have learned back in school.

From highest to lowest precedence:

• Parentheses: (, )
• Exponents: ^ or **
• Divide: /
• Multiply: *
• Add: +
• Subtract: -

3 + 5 * 2

[1] 13

Use parentheses to group operations in order to force the order of evaluation if it differs from the default, or to make clear what you intend.

(3 + 5) * 2

[1] 16

This can get unwieldy when not needed, but clarifies your intentions. Remember that others may later read your code.

(3 + (5 * (2 ^ 2))) # hard to read
3 + 5 * 2 ^ 2       # clear, if you remember the rules
3 + 5 * (2 ^ 2)     # if you forget some rules, this might help

The text after each line of code is called a “comment”. Anything that follows after the hash (or octothorpe) symbol # is ignored by R when it executes code.

Really small or large numbers get a scientific notation:

2/10000

[1] 2e-04

Which is shorthand for “multiplied by 10^XX”. So 2e-4 is shorthand for 2 * 10^(-4).

You can write numbers in scientific notation too:

5e3  # Note the lack of minus here

[1] 5000

Don’t worry about trying to remember every function in R. You can look them up on Google, or if you can remember the start of the function’s name, use the tab completion in RStudio.

This is one advantage that RStudio has over R on its own, it has auto-completion abilities that allow you to more easily look up functions, their arguments, and the values that they take.

Typing a ? before the name of a command will open the help page for that command. As well as providing a detailed description of the command and how it works, scrolling to the bottom of the help page will usually show a collection of code examples which illustrate command usage. We’ll go through an example later.

Comparing things

We can also do comparison in R:

1 == 1  # equality (note two equals signs, read as "is equal to")

[1] TRUE

1 != 2  # inequality (read as "is not equal to")

[1] TRUE

1 < 2  # less than

[1] TRUE

1 <= 1  # less than or equal to

[1] TRUE

1 > 0  # greater than

[1] TRUE

1 >= -9 # greater than or equal to

[1] TRUE

Tip: Comparing Numbers

A word of warning about comparing numbers: you should never use == to compare two numbers unless they are integers (a data type which can specifically represent only whole numbers).

Computers may only represent decimal numbers with a certain degree of precision, so two numbers which look the same when printed out by R, may actually have different underlying representations and therefore be different by a small margin of error (called Machine numeric tolerance).

Instead you should use the all.equal function.

Further reading: http://floating-point-gui.de/

Variables and assignment

We can store values in variables using the assignment operator <-, like this:

x <- 1/40

Notice that assignment does not print a value. Instead, we stored it for later in something called a variable. x now contains the value 0.025:

x

[1] 0.025

More precisely, the stored value is a decimal approximation of this fraction called a floating point number.

Look for the Environment tab in one of the panes of RStudio, and you will see that x and its value have appeared. Our variable x can be used in place of a number in any calculation that expects a number:

log(x)

[1] -3.688879

Notice also that variables can be reassigned:

x <- 100

x used to contain the value 0.025 and and now it has the value 100.

Assignment values can contain the variable being assigned to:

x <- x + 1 #notice how RStudio updates its description of x on the top right tab
y <- x * 2

The right hand side of the assignment can be any valid R expression. The right hand side is fully evaluated before the assignment occurs.

Challenge 1

What will be the value of each variable after each statement in the following program?

mass <- 47.5
age <- 122
mass <- mass * 2.3
age <- age - 20

Solution to challenge 1

mass <- 47.5

This will give a value of 47.5 for the variable mass

age <- 122

This will give a value of 122 for the variable age

mass <- mass * 2.3

This will multiply the existing value of 47.5 by 2.3 to give a new value of 109.25 to the variable mass.

age <- age - 20

This will subtract 20 from the existing value of 122 to give a new value of 102 to the variable age.

Challenge 2

Run the code from the previous challenge, and write a command to compare mass to age. Is mass larger than age?

Solution to challenge 2

One way of answering this question in R is to use the > to set up the following:

mass > age

[1] TRUE

This should yield a boolean value of TRUE since 109.25 is greater than 102.

Variable names can contain letters, numbers, underscores and periods. They cannot start with a number nor contain spaces at all. Different people use different conventions for long variable names, these include

• periods.between.words
• underscores_between_words
• camelCaseToSeparateWords

What you use is up to you, but be consistent.

It is also possible to use the = operator for assignment:

x = 1/40

But this is much less common among R users. The most important thing is to be consistent with the operator you use. There are occasionally places where it is less confusing to use <- than =, and it is the most common symbol used in the community. So the recommendation is to use <-.

Challenge 3

Which of the following are valid R variable names?

min_height
max.height
_age
.mass
MaxLength
min-length
2widths
celsius2kelvin

Solution to challenge 3

The following can be used as R variables:

min_height
max.height
MaxLength
celsius2kelvin

The following creates a hidden variable:

.mass

We won’t be discussing hidden variables in this lesson. We recommend not using a period at the beginning of variable names unless you intend your variables to be hidden.

The following will not be able to be used to create a variable

_age
min-length
2widths

Key Points

• Use RStudio to write and run R programs.

• R has the usual arithmetic operators.

• Use <- to assign values to variables.