13/08/2019 Chapter 2 Getting Started with R and RStudio | Introduction to Data Science

Chapter 2 Getting Started with R and

RStudio

2.1 Why R?

R is not a programming language like C or Java. It was not created by software engineers for
software development. Instead, it was developed by statisticians as an interactive environment
for data analysis. You can read the full history here. The interactivity is an indispensable
feature in data science because, as you will soon learn, the ability to quickly explore data is a
necessity for success in this field. However, like in other programming languages, you can
save your work as scripts that can be easily executed at any moment. These scripts serve as
a record of the analysis you performed, a key feature that facilitates reproducible work. If you
are an expert programmer, you should not expect R to follow the conventions you are used to
since you will be disappointed. If you are patient, you will come to appreciate the unequal
power of R when it comes to data analysis and, specifically, data visualization.

Other attractive features of R are:

1. R is free and open source.

2. It runs on all major platforms: Windows, Mac Os, UNIX/Linux.
3. Scripts and data objects can be shared seamlessly across platforms.
4. There is a large, growing, and active community of R users and, as a result, there are
numerous resources for learning and asking questions.
5. It is easy for others to contribute add-ons which enables developers to share software
implementations of new data science methodologies. This gives R users early access to
the latest methods and to tools which are developed for a wide variety of disciplines,
including ecology, molecular biology, social sciences and geography, just to name a few
examples.

2.2 The R console

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Interactive data analysis usually occurs on the R console that executes commands as you
type them. There are several ways to gain access to an R console. One way is to simply start
R on your computer. The console looks something like this:

As a quick example, try using the console to calculate a 15% tip on a meal that cost $19.71:

0.15 * 19.71
#> [1] 2.96

Note that in this book, grey boxes are used to show R code typed into the R console.
The symbol #> is used to denote what the R console outputs.

2.3 Scripts

One of the great advantages of R over point-and-click analysis software is that you can save
your work as scripts. You can edit and save these scripts using a text editor. The material in
this book was developed using the interactive integrated development environment (IDE)
RStudio. RStudio includes an editor with many R specific features, a console to execute your
code, and other useful panes, including one to show figures.

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Most web-based R consoles also provide a pane to edit scripts, but not all permit you to save
the scripts for later use.

All the R scripts used to generate this book can be found on GitHub.

2.4 RStudio

RStudio will be our launching pad for data science projects. It not only provides an editor for
us to create and edit our scripts but also provides many other useful tools. In this section, we
go over some of the basics.

2.4.1 The panes

When you start RStudio for the first time, you will see three panes. The left pane shows the R
console. On the right, the top pane includes tabs such as Environment and History, while the
bottom pane shows five tabs: File, Plots, Packages, Help and Viewer (these tabs may change
in new versions). You can click on each tab to move across the different features.

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To start a new script, you can click on File, the New File, then R Script.

This starts a new pane on the left and it is here where you can start writing your script.

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2.4.2 Key bindings

Many tasks we perform with the mouse can be achieved with a combination of key strokes
instead. These keyboard versions for performing tasks are referred to as key bindings. For
example, we just showed how to use the mouse to start a new script, but you can also use a
key binding: Ctrl+Shift+N on Windows and command+shift+N on the Mac.

Although in this tutorial we often show how to use the mouse, we highly recommend that
you memorize key bindings for the operations you use most. RStudio provides a useful
cheat sheet with the most widely used commands. You can get it from RStudio directly:

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and it looks like this:

You might want to keep this handy so you can look up key-bindings when you find yourself
performing repetitive point-and-clicking.

2.4.3 Running commands while editing scripts

There are many editors specifically made for coding. These are useful because color and
indentation are automatically added to make code more readable. RStudio is one of these
editors, and it was specifically developed for R. One of the main advantages provided by
RStudio over other editors is that we can test our code easily as we edit our scripts. Below we
show an example.

Let’s start by opening a new script as we did before. A next step is to give the script a name.
We can do this through the editor by saving the current new unnamed script. To do this, click
on the save icon or using the key binding Ctrl-S on Windows and command-S on the Mac.

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When you ask for the document to be saved for the first time, RStudio will prompt you for a
name. A good convention is to use a descriptive name, with lower case letters, no spaces,
only hyphens to separate words, and then followed by the suffix .R. We will call this script my-
first-script.R.

Now we are ready to start editing our first script. The first lines of code in an R script are
dedicated to loading the libraries we will use. Another useful RStudio feature is that once we
type library() it starts auto-completing with libraries that we have installed. Note what
happens when we type library(ti) :

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Another feature you may have noticed is that when you type library( the second
parenthesis is automatically added. This will help you avoid one of the most common errors in
coding: forgetting to close a parenthesis.

Now we can continue to write code. As an example, we will make a graph showing murder
totals versus population totals by state. Once you are done writing the code needed to make
this plot, you can try it out by executing the code. To do this, click on the Run button on the
upper right side of the editing pane. You can also use the key binding: Ctrl+Shift+Enter on
Windows or command+shift+return on the Mac.

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Once you run the code, you will see it appear in the R console and, in this case, the generated
plot appears in the plots console. Note that the plot console has a useful interface that permits
you to click back and forward across different plots, zoom in to the plot, or save the plots as
files.

To run one line at a time instead of the entire script, you can use Control-Enter on Windows
and Command-Return on the Mac.

2.4.4 Changing global options

You can change the look and functionality of RStudio quite a bit.

To change the global options you click on Tools then Global Options….

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As an example, we show how to change the appearance of the editor. To do this click on
Appearance and then notice the Editor theme options.

You can click on these and see examples of how your editor will look.

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I personally like the Cobalt option. This makes your editor look like this:

As a second example, we show how to make a change that we highly recommend. This is to
change the Save workspace to .RData on exit to Never and uncheck the Restore .RData into
workspace at start. By default, when you exit R saves all the objects you have created into a
file called .RData. This is done so that when you restart the session in the same folder, it will
load these objects. We find that this causes confusion especially when we share code with
colleagues and assume they have this .RData file. To change these options, make your
General settings look like this:

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2.5 Installing R packages

The functionality provided by a fresh install of R is only a small fraction of what is possible. In
fact, we refer to what you get after your first install as base R. The extra functionality comes
from add-ons available from developers. There are currently hundreds of these available from
CRAN and many others shared via other repositories such as GitHub. However, because not
everybody needs all available functionality, R instead makes different components available
via packages. R makes it very easy to install packages from within R. For example, to install
the dslabs package, which we use to share datasets and code related to this book, you would
type:

install.packages("dslabs")

In RStudio, you can navigate to the Tools tab and select install packages. We can then load
the package into our R sessions using the library function:

library(dslabs)

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As you go through this book, you will see that we load packages without installing them. This
is because once you install a package, it remains installed and only needs to be loaded with
library . The package remains loaded until we quit the R session. If you try to load a
package and get an error, it probably means you need to install it first.

We can install more than one package at once by feeding a character vector to this function:

install.packages(c("tidyverse", "dslabs"))

You can also install packages using RStudio in the following way:

One advantage of using RStudio is that it auto-completes package names once you start
typing, which is helpful when you do not remember the exact spelling of the package:

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Once you select your package, we recommend selecting all the defaults:

Note that installing tidyverse actually installs several packages. This commonly occurs when
a package has dependencies, or uses functions from other packages. When you load a
package using library , you also load its dependencies.

Once packages are installed, you can load them into R and you do not need to install them
again, unless you install a fresh version of R. Remember packages are installed in R not
RStudio.

It is helpful to keep a list of all the packages you need for your work in a script because if you
need to perform a fresh install of R, you can re-install all your packages by simply running a
script.

You can see all the packages you have installed using the following function:

installed.packages()

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