INTRODUCTION TO R

A FIRST COURSE IN R
 Introduction to R 2

Contents

Goals 4
What You Will Need 4

What is R? 5

Getting Started 6
Installation 6
Layout 7
Console 7
Script Editor & Related Programming Functionality 7
Output 8
Menus 8

Working with the Language 9

Basics 9
Coding Practices 10
Functions 10
Conditionals, Control Flow, Operators 10
Loops & Alternative Approaches 11
Conditional Statements 11

Importing & Working with Data 12

Creation of Data 12
Importing Data 13
Working with the Data 14
Indexing 14
Data Sets & Subsets 15
Merging and Reshaping 16
Miscellaneous 17
3 A First Course

Initial Data Analysis & Graphics 17

Initial Data Analysis: Numeric 18
Initial Data Analysis: Graphics 20

The Basic Modeling Approach 20

Visualization of Information 23
Examples 23
Enhancing Standard Graphs 23
Beyond base R plots 25
Getting Interactive 26

Getting Help 26
Basics 26
A Plan of Attack for Diving In 27
Some Issues 28

Summary 28
Why R? 29
Who is R for? 29
R as a solution 29

Resources 30
General Web Assistance 30
Manuals 30
Graphics 30
Development Sites 30
Commercial Versions 30
Miscellaneous 30
 Introduction to R 4

Goals
The goal of this tutorial and associated short course is fairly straight-
forward - I wish to introduce the program well enough for one to un-
derstand some basics and feel comfortable trying things on their own.
In this light the focus will be on some typical applications (colored by
a social science perspective) with simple examples, and furthermore
to identify the ways people can obtain additional assistance on their
own in order to eventually become self-sufficient. It is hoped that those
taking it will obtain a good sense of how R is organized, what it has to
offer above and beyond the package they might already be using, and
have a good idea how to use it once they leave the course.

What You Will Need

You will need R and it helps to have something like Rstudio to do your
programming. Some exposure to statistical science is assumed but
only the minimum that would warrant your interest in R in the first
place. Programming experience is useful but no specific experience is
assumed.
5 A First Course

What is R?
R is a dialect of the S language1 (’Gnu-S’) and in that sense it has a 1
S was developed primarily by John
long past but a shorter history. R’s specific development is now pushing Chambers at Bell Labs in the 70s.

near 20 years2 . From the horse’s mouth: 2

R was initially written by Robert
Gentleman and Ross Ihaka 1993, and
“R is a language and environment for statistical computing and graphics" version 1.0.0 came out in 2000.
and from the manual, "The term environment is intended to characterize
it as a fully planned and coherent system, rather than an incremental
accretion of very specific and inflexible tools, as is frequently the case
with other data analysis software."

This will be the first thing to get used to- R is not used in a manner
like many such as SPSS, Stata, etc. It is a programming environment
within which statistical analysis and visualization is conducted, not
merely a place to run canned routines that come with whatever you
have purchased. This is not intended as a knock on other statistical
software, many of which accomplish their goals quite well. Rather, the
point is that it may require a different mindset in order to get used to it
depending on the kind of exposure you’ve had to other programs.
The initial install of R and accompanying packages provides a fully
functioning statistical environment in which one may conduct any
number of typical and advanced analyses. You could already do most
of what you would find in the other programs, but also have the flex-
ibility to do much more. However, there are over 73933 user con- 3
As of the date of this document, which
tributed packages that provide a vast amount of enhanced functioning. includes CRAN, GitHub, and Bioconduc-
tor.
If you come across a particular analysis, it is unlikely there wouldn’t al-
ready be an R package devoted to it. Unfortunately, there is not much
sense to be made of a list of all those packages just by looking at them,
and I don’t recommend that you install all of them. The CRAN Task
views provides lists of primary packages in an organized fashion by
subject matter, and is a good place to start exploring.
R is a true object-oriented programming language, much like oth-
ers such as C++, Python etc. Objects are manipulated by functions,
creating new objects which may then have more functions that can be
applied to them. Objects can be just about anything: a single value,
variable, datasets, lists of several types of objects etc. The object’s
class (e.g. numeric, factor, data frame, matrix etc.) determines how a
generic function (like summary and plot) will treat the object. It may For example the summary function
be a little confusing at first, and it will take time to get used to, but in can work on single variables, whole
data sets, or specific models. The plot
the end R can be much more efficient than other statistical packages function can be used for e.g. a simple
for many applications. scatterplot, or have specific capabilities
depending on what type of object is
Typically there are often several ways to do the same thing depend- supplied to it.
ing on the objects and functions being used and the same function may
do different things for different classes of objects. One can see below
 Introduction to R 6

how to create an object and three different ways to produce the same
variable. This code creates an object called UScapt
that is just the string "D.C.". After that
UScapt = 'D.C.' is demonstrated three different ways in
UScapt which to produce an object myvar∗ that
is the series of numbers from 1 to 3.
## [1] "D.C."

myvar1 = c(1, 2, 3)
myvar2 = 1:3
myvar3 = seq(from=1, to=3, by=1)
myvar1

## [1] 1 2 3

myvar2

## [1] 1 2 3

myvar3

## [1] 1 2 3

Getting Started
Installation

Getting R up and running is very easy. Just head to the website4 and 4
One can just do a web search R and it
once done basking in the 1997 nostalgia of the front page, click the may be the first return.

download link, choose a mirror5 , select your operating system, choose 5

It doesn’t matter where really, though
’base’, and voila, you are now able to download this wonderful sta- download speeds will be different.

tistical package. The installation process after that is painless- R does

not ’infect’ your machine like a lot of other software does; you can
even just delete the folder to uninstall it. Note also that it is free as in
speech and beer6 and as such you actually own your copy, no inter- 6
Freedom!
net connection is required or extra software that has to run to tell the
parent company you aren’t a thief. It is not a trial or crippled version.
It should be noted again that this base installation is fully function-
ing and out of the box it does more than standard statistical packages,
but you’ll want more packages for additional functionality, and I sug-
gest adding them as needed7 . When you upgrade R8 you’ll be down- 7
install.packages(c("Rpack1","Rpack2"))
8
loading and installing the program as before, after which you can copy Always upgrade to the latest available.
A new version is available every few
your packages from the old installation library folder over to the new months. Don’t forget to update your
folder, and then update the packages from within the new installation packages. As one who uses R regu-
larly, I do every start up. If you use it
once you start it up. You can alter the Rprofile.site in your R/etc folder
infrequently, just get into the habit of
file to update everytime you start R, as well as set other options. It’s updating every time you use it.
just a text file so you can open it with something like Notepad and just
insert update.packages(ask=F) on a new line. Otherwise you will
7 A First Course

have to update manually or via Rstudio’s gui.

The workspace is your current R working environment and includes
any and every user-defined object (vectors, matrices, functions, data
frames, lists, even plots). In a given session one may save all objects
created together in a single .Rdata file, but note that this is not a data
set like with other packages. When you load an .Rdata file you will
have everything you worked on during the session it was saved in, and
readily available with no need to rerun scripts. All objects from single
values to lists of matrices, analysis results, graphical objects etc. is at
the ready to be called upon as needed.

Layout

I’ll spend a little time here talking about the basic R installation, but
there is typically little need on your own to not work with an IDE
of your choice to make programming easier. The layout for R when
first started shows only the console but in fact you’ll often have three
windows open9 . The console is where everything takes place, the script 9
You have the choice of whether you
file for extended programming, and a graphics device. As I will note want a single document interface (SDI),
which has separate windows to deal
shortly though, an IDE such as Rstudio is a far more efficient means with, or multi-document interface
of using R. Even there though, you will have the basic components of (MDI), where all windows open within
one single window (think of the Stata
console, script editor, and graphics device just as you do in base R. layout).

Console
The console is not too friendly to the R beginner (or anyone for that
matter) and best reserved for examining the output of code that has
been submitted to it.
One can use it as a command
line interface (similar to Stata’s
with single line input), but it’s
far too unforgiving and inflexible
to spend much time there. I still
use it for easy one-liners like the
hist() or summary() functions,
but otherwise do not do your programming there.

Script Editor & Related Programming Functionality

Rather than use the console, one can write their program in the script
editor that comes with R10 . This is just a plain text editor not unlike 10
File/New Script... Ctrl+R will send
Notepad, but far easier than just using the console. While it gets the the current line or or selection to the
console.
job done I suggest something with script highlighting and other fea-
tures, and in that vein I would suggest Rstudio, an interactive develop-
 Introduction to R 8

ment environment built specifically for R. It is highly functional, and

quite simply it will make R a great deal easier to work with. You get
syntax highlighting, project management, better data views, and a host
of other useful features. See the pic at the right.
One might also check out Revolution Analytics. Although this tool is
geared toward the high-performance computing environment, it also
provides a host of nifty features and is free to the academic community.

Output
Unlike some programs (e.g. SPSS), there is no designated output
file/system with R. One can look at it such that everything created
within the environment is "output". All created objects are able to be
examined, manipulated, exported etc., graphics can be saved as one of
many typical file extensions e.g. jpeg, bmp etc. Results of any analysis
may be stored as an object, which may then be saved within the .Rdata
file mentioned previously, or perhaps as a text file to be imported into
another program (see e.g. sink). There are even ways to have the re-
sults put into a document and updated as the code changes11 . Thus 11
For example, this handout was created
rather than have a separate output file full of tables, graphics etc., without ever leaving Rstudio.

which often get notably large and much of which is disregarded after
a time, one has a single file that provides the ability to call up any- load("myworkspace.Rdata")

thing one has ever done in a session very easily, to go along with other
possibilities for capturing the output from analysis.

Menus
Let’s just get something out of the way now. The R development team
has no interest in providing a menu system of the sort you see with
SPSS, Stata and others. They’ve had plenty of opportunity and if they
wanted to they would have by now. For those that like menus, you’d be
out of luck, except that the power of open source comes to the rescue.
There are a few packages here and there that come with a menu
system specifically designed for the package, but for a general all-
purpose one akin to what you see in those other packages, you might
want to consider R-commander from John Fox (at right). This is a true
menu system, has a notable variety of analyses, and has additional
functionality via Rcmdr-specific add-ons and other customization. I
think many coming to R from other statistical packages will find it
useful for quickly importing data, obtaining descriptive statistics and
plots, and familiarizing oneself with the language, but you’ll know you
are getting a very good feel for R as you rely on it less and less12 . 12
After installing the package you load
Note also that there are proprietary ways to provide a menu system the library just like any other and it will
bring up the gui.
along with R. S-plus is just like the other programs with menus and
spreadsheet, and most of the R language works in that environment.
9 A First Course

SPSS, SAS and others have add-ons that allow one to perform R from
within those programs. In short, if you like menus for at least some
things, you have options.

Working with the Language

Basics

The language of R can prove to be quite a change for some, even if

they have quite a bit of programming experience in other statistical
packages. It is more like Python or other general purpos languages
than it is like SPSS or SAS syntax. This is an advantage however, as it
makes for a far more flexible approach to statistical programming.
Recall that the big idea within the R environment is to create objects
of certain types and pass them to functions for further processing. When looking through texts or websites
Most of the time you will be doing just that- creating an object by regarding R or even these notes, you
will notice objects assigned with either
means of some function, applying a function to the object to create yet ’<-’ or ’=’. This used to be of some con-
another object, and so forth. As an example, you may create a data cern, and you are more than welcome to
browse R-help archives for more infor-
object through use of the data.frame function, use subset on the data mation. For some users it is a pragmatic
object to use only a portion of the data for analysis, use summary on issue (one takes fewer keystrokes and
the subsetted data object for summary statistics etc. Doing things in it is commonly used for assignment in
other languages), but others find that <-
this manner allows you to go back to any object and change something makes code easier to read (a subjective
up and process it further. The following graphic provides an overview assessment) and it technically can be
used more flexibly, not to mention it
of how one can think about dealing with objects in R if they are not allows them to be snobby toward those
overly familiar with programming. who use the = sign. Type ?’<-’ at the
console (with quotes) to find out some
basic info. There is a bit of a difference
Packages Collection of functions, datasets, help files etc. but it is typically not an issue except
perhaps in writing some functions in
Function 1
Function 2
particular ways. Normal usage should
Function ...
not result in any mishap. I will flop be-
tween both styles so that you are used to
Manipulate objects Input to the function
Have arguments Functions Input Argument Parameters that the value returned by a seeing it either way. Beginner’s should
Return a value function depends on
Tied to objects via Can be supplied objects as well as other values maybe start with <- until they decide for
methods
themselves.
Me
tho
d
Typing ls() or objects() with the empty
parentheses will list all objects you’ve
Assigned to object Value Assignment Object Objects are representations (functions, variables)
Used as argument that can be manipulated in some fashion, and created.
belong to some class

Example. You import a dataset using the read.csv function, and this returns a value which is a data frame. However, unless
you assign the value to an object, you’d have to repeat the read.csv process everytime you wanted to use the dataset.
Assigning it to an object, one can now supply it to a function, which can then use elements of that data as values to other
arguments.

read.csv function file argument

assigned object mydata <- read.csv(file = ”C:/data.csv”) file address as value

lm function formula and data arguments

assigned object myreg <- lm(formula = myY ~ myX, data = mydata)

formula value data object as value

 Introduction to R 10

Coding Practices

As it is a true programming language, there are ways to program in

general that can be helpful in making code easier to read and inter-
pret. Some coding practices specific to R have been suggested, such as
Google’s R style guide and this one from Hadley Wickham. While some
of those suggestions are very useful, one should not assume they are
commandments from on high13 , nor have any studies been conducted 13
Quite frankly, a couple of the sugges-
on what would make the best R code. Furthermore, heavy commenting tions would make coding less legible to
me.
does a lot more for making code legible than any of the little details of-
fered in those links. I tell people to assume they will finish the project
only to pick it up again a year later, and that their code needs to be
clear and obvious to that future version of them.

Functions

Writing your own user-defined function can enhance or make more

efficient the work you do, though it won’t always be easy. It’s a very
good idea to search for what you are attempting first as a relevant
package may already be available14 , and as the code is open source, 14
No sense reinventing the wheel,
you can take existing functions and change them to meet your needs though if you’re like me this won’t stop
you from trying.
very easily. But if you can’t find it already available or you need a
function specific to your data needs, R’s programming language will
surely allow you to do the trick and often very efficiently.
The following provides an example for a simple function to produce
the mean of an input x. This code creates a function that takes
some input vector x, returns an error
mymean = function(x) { and message if x is not of the numeric
if (!is.numeric(x)) { class (the ! means ’not’, so when the
stop("STOP! Does not compute.") is.numeric function applied to x returns
} ’ F A L S E ’ the error will be returned),
return(sum(x)/length(x)) and returns the mean of whatever x
} is otherwise. I could have also put
var1 = 1:5 if(is.numeric(x)==FALSE).
mymean(var1)

## [1] 3

mymean("thisisnotanumber")

## Error: STOP! Does not compute.

Conditionals, Control Flow, Operators

In general, conditionals (if... then), flow control (for, while), and oper-
ators (!=, >=) work much the same as they do in other programming
languages, though some specific functions are available to aid in these
matters, and some that may not be found in other stat packages.
11 A First Course

Loops & Alternative Approaches

Looping can allow iteration over indices of vectors, matrices, lists etc.
and generally is a good way to efficiently do repetitive procedures.
The following example will illustrate how one can do it so they can see
parallels with other statistical programs’ syntax, and then provide an
alternative and better way to go about it. The code to the left first creates a 10
column matrix temp from 100 random
temp = matrix(rnorm(100), ncol = 10) draws of a N (0, 1) distribution. Next we
means = vector("numeric", 10) create an empty vector that will be filled
with column means. Then for each value
for (i in 1:ncol(temp)) { i of 1 through the number of columns in
means[i] = mean(temp[, i]) temp, we calculate the mean of column
} i of the temp matrix, and place it in the
means vector at index i. Typing means
means afterward produced the result seen,
though since I didn’t set the seed you
## [1] -0.20605 0.03044 -0.39658 -0.51270 -0.40480 -0.13326 0.06791 will get a different random sample.
## [8] -0.56291 0.28177 0.41740

The above works but is only shown for demonstration purposes, and
mostly to demonstrate that you are typically better served using other
approaches, as when it comes to iterative processes there are usually
more efficient means of coding so in R than using explicit loops. For
example it would have been more easy to simply type:

means <- apply(temp, 2, mean)

Or even more efficiently:

means <- colMeans(temp)

Note these are not (usually) simply using a particular function that
internally does the same loop we just demonstrated, but performing a
vectorized operation, i.e. operating on whole vectors rather than indi-
vidual parts of a sequence, and do not have to iterate some processes
(e.g. particular function calls) as one does with an explicit loop. Some
functions may even be calling compiled C code which can result in
even greater speed gains. One can start by looking up the apply and
related functions tapply, lapply, sapply etc.15 Using such functions 15
I should probably point out that these
can often make for clearer code and may be faster in many situations. apply functions do not always work
in a way many would think logical.
There is the plyr package available for
an approach that is oftentimes more
Conditional Statements straightforward. The next iteration, dplyr
is in the works.
As an example, the ifelse function compares the elements of two
objects according to some Boolean statement. It can return scalar or
vector values for a true condition, and a different set of values for a
false condition. In the following code, x is compared to y and if less,
one gets cake, and for any other result, death.
 Introduction to R 12

x <- c(1, 3, 5)
y <- c(6, 4, 2)
z <- ifelse(x < y, "Cake", "Death")
z

## [1] "Cake" "Cake" "Death"

You also have the usual flow control functions available such as the
standard if, while, for etc.

Importing & Working with Data

Creation of Data

To start with a discussion of dealing with data in the R environment it

might be most instructive to simply create some.
One can easily generate data in a variety of ways. The following
creates objects that are a simple random sample, random draws from a
binomial distribution, and random draws from the normal distribution.

x = sample(c('Heads', 'Tails', 'Edge', 'Blows Up'),

5, replace=T, prob=c(.45, .45, .05, .05))
x2 = rbinom(5, 1, .5)
x3 = rnorm(50, mean=50, sd=10)

Here is an example simulating data from a correlation matrix using

the MASS library. Code comments are provided in light gray here16 . 16
As in other packages, anything after
the comment indicator will be ignored.
cormat = matrix(c(1, 0.5, 0.5, 1), nrow = 2) R uses the pound sign for comments.
# type cormat at the command prompt if you want to look at it after creation

library(MASS) # for the mvrnorm function

# Setting empirical = F in the following will produce data that will
# randomly deviate from the assumed correlation matrix. empirical = T will
# reproduce the original correlation matrix exactly.

xydata = mvrnorm(40, mu = c(0, 0), Sigma = cormat, empirical = T)

head(xydata) #take a look at it

## [,1] [,2]
## [1,] -0.3896 0.1247
## [2,] -0.1636 -1.1703
## [3,] -0.9783 -2.5762
## [4,] -0.1991 0.8355
## [5,] -0.4534 0.7477
## [6,] 1.8228 1.6047

cor(xydata)

## [,1] [,2]
## [1,] 1.0 0.5
## [2,] 0.5 1.0
13 A First Course

The following uses more advanced techniques to create a data set of

the kind you’d normally come across. It uses several functions to create
a dataset with the variables subject, gender, time and y. Afterwords, the
lattice package is used to create different dot plots. Look at each object
as it is created to help understand what’s being done on each line and
use ?functionname to find out more about each function used.
Male Female

# Create data set with factor variables of time, subject and gender 70

mydata <- expand.grid(time = factor(1:4), subject = factor(1:10))

60
# In the next line, R will recycle the result to match the
# length of the data.frame upon attachment.
mydata$gender <- factor(rep(0:1, each=4), labels=c('Male', 'Female'))

DV
50

mydata$y <- as.numeric(mydata$time) + # basic effect

rep(rnorm(10, 50, 10), e=4) + # individual effect
40
rnorm(nrow(mydata), 0, 1) # observation level noise

30

library(lattice) 1 2 3 4 1 2 3 4

dotplot(y~time, data=mydata,xlab='Time', ylab='DV') #example plot Time

# Other plot variations

dotplot(y ~ time, data=mydata, groups=gender, xlab='Time', ylab='DV',
key = simpleKey(levels(mydata$gender)))
dotplot(y ~ time|gender, data=mydata, groups=subject, xlab='Time', ylab='DV',
pch=19, cex=1)

Importing Data

Reading in data from a variety of sources can be a fairly straightfor-

ward task, though difficulties can arise for any number of reasons. The
following assumes a clean data source.
To read your basic text file, two functions are likely to be used most-
read.table and read.csv for tab-delimited comma-separated value
data sets respectively. For files that come from other statistical pack-
ages one will want the foreign package, especially useful for Stata and
SPSS via read.dta and read.spss respectively. For Excel17 things tend 17
I would generally avoid Excel for
to get a bit tricky due to its database properties, but you can use Rcmdr data management if you can. In my
experience with clients there are far
menus very easily or read.xls in the gdata package, although gdata more issues with Excel data because of
requires Perl installation. You can always just save the data as a *.csv the various ’features’ and other things
that end up greatly adding to time spent
file from there anyway. cleaning data.
Examples follow18 . Note the slashes (as in Unix)- if you want to use 18
Save the last, these are just syntax
backslash as is commonly seen in Windows you must double them up examples and not actually to be run.

as \\.

## not run; visual example only

# mydata <- read.table('c:/trainsacrossthesea.txt', header = TRUE, sep=',', row.names='id')

# library(foreign)
 Introduction to R 14

# statadat <- read.dta('c:/rangelife.dta', convert.factors = TRUE)

# spssdat <- read.spss('c:/ourwaytofall.sav', to.data.frame = TRUE)

# example read from web source

mydata <- read.table("http://csr.nd.edu/assets/22641/testwebdata.txt", header = T,
sep = "")

To save the data you can typically use ’write’ instead of ’read’ while
specifying a file location and other options (e.g. write.csv(objectname,
filelocation) ) .

Working with the Data

Indexing
R19 has a lot of data sets at the ready and more come with almost 19
R manual
every package for demonstration purposes. As an example we’ll use
the state data set which is initially a matrix class object20 . To provide 20
Matrix and data.frame are functions

some more flexibility we will want to convert it to a data frame. The for creating matrices and data frames
as well the name of their respective
state level data regards population, income, illiteracy, life expectancy, object classes. One should check out the
murder rate, high school graduation rate, the number of days in which data.table package for additional data set
functionality.
the temperature goes below freezing, and area21 . Note also there are 21
Type ?state.x77 at the console for
other variable objects as separate vectors which we might also make additional detail.
use of, e.g. state.region.
To begin:

state2 <- data.frame(state.x77)

str(state2) #object structure

## 'data.frame': 50 obs. of 8 variables:

## $ Population: num 3615 365 2212 2110 21198 ...
## $ Income : num 3624 6315 4530 3378 5114 ...
## $ Illiteracy: num 2.1 1.5 1.8 1.9 1.1 0.7 1.1 0.9 1.3 2 ...
## $ Life.Exp : num 69 69.3 70.5 70.7 71.7 ...
## $ Murder : num 15.1 11.3 7.8 10.1 10.3 6.8 3.1 6.2 10.7 13.9 ...
## $ HS.Grad : num 41.3 66.7 58.1 39.9 62.6 63.9 56 54.6 52.6 40.6 ...
## $ Frost : num 20 152 15 65 20 166 139 103 11 60 ...
## $ Area : num 50708 566432 113417 51945 156361 ...

Next we want to examine specific parts of the data such as the first
10 rows or 3rd column, as well as examine its overall structure to de-
termine what kinds of variables we are dealing with. To get at different
parts of typical data frame, type brackets after the data set name and
specify the row number left of the comma and column number to its
right.
head(state2, 10) #first 10 rows

## Population Income Illiteracy Life.Exp Murder HS.Grad Frost

## Alabama 3615 3624 2.1 69.05 15.1 41.3 20
## Alaska 365 6315 1.5 69.31 11.3 66.7 152
15 A First Course

## Arizona 2212 4530 1.8 70.55 7.8 58.1 15

## Arkansas 2110 3378 1.9 70.66 10.1 39.9 65
## California 21198 5114 1.1 71.71 10.3 62.6 20
## Colorado 2541 4884 0.7 72.06 6.8 63.9 166
## Connecticut 3100 5348 1.1 72.48 3.1 56.0 139
## Delaware 579 4809 0.9 70.06 6.2 54.6 103
## Florida 8277 4815 1.3 70.66 10.7 52.6 11
## Georgia 4931 4091 2.0 68.54 13.9 40.6 60
## Area
## Alabama 50708
## Alaska 566432
## Arizona 113417
## Arkansas 51945
## California 156361
## Colorado 103766
## Connecticut 4862
## Delaware 1982
## Florida 54090
## Georgia 58073

# tail(state2, 10) #last 10 rows (not shown)

state2[,3] #third column

## [1] 2.1 1.5 1.8 1.9 1.1 0.7 1.1 0.9 1.3 2.0 1.9 0.6 0.9 0.7 0.5 0.6 1.6
## [18] 2.8 0.7 0.9 1.1 0.9 0.6 2.4 0.8 0.6 0.6 0.5 0.7 1.1 2.2 1.4 1.8 0.8
## [35] 0.8 1.1 0.6 1.0 1.3 2.3 0.5 1.7 2.2 0.6 0.6 1.4 0.6 1.4 0.7 0.6

state2[14,] #14th row

## Population Income Illiteracy Life.Exp Murder HS.Grad Frost Area

## Indiana 5313 4458 0.7 70.88 7.1 52.9 122 36097

state2[3,6] #3rd row, 6th column

## [1] 58.1

state2[,'Frost'] #variable by name

## [1] 20 152 15 65 20 166 139 103 11 60 0 126 127 122 140 114 95
## [18] 12 161 101 103 125 160 50 108 155 139 188 174 115 120 82 80 186
## [35] 124 82 44 126 127 65 172 70 35 137 168 85 32 100 149 173

Note that one can also examine and edit the data with the fix func-
tion (or clicking the data object in Rstudio), though if you want to do
this sort of thing a lot I suggest popping over to a statistics package
that takes the spreadsheet approach seriously. However using code for
data manipulation is far more efficient.

Data Sets & Subsets

Often we want to examine specific parts of the data set, and depending
on the situation a variety of techniques might be available to help us
do so. To begin with, one particular function, subset , is expressly
devised for this purpose. The basic approach is identify what you want
to subset, e.g. a data frame object, and what rule to follow.
# note that state.region is a separate R object of the same length as the
# number of rows in our state data frame
mysubset = subset(state2, state.region == "South")

However, like most situations there are viable alternative approaches,

for example:
 Introduction to R 16

mysubset = state2[state.region == "South", ]

Often you might want to subset a collection of variables and there

are two typical ways of going about it, either referring to the number
or the name like we did previously. Both lines following accomplish the
same thing, though the former will probably be a bit troublesome in
cases where we have perhaps hundreds of variables.
mysubset = state2[, c(1:2, 7:8)]
mysubset = state2[, c("Population", "Income", "Frost", "Area")]

# get any States starting with 'I' and ending with 'a' using regular
# expressions
mysubset = state2[grep("^I.*a$", rownames(state2)), ]

One may also drop variables in a likewise fashion for numerically

identified variables by placing a minus sign before the column entry
or sequence (or before the c if combining entries). If your goal is to do
something in particular across subsets of a data set, then I again call
your attention to the apply functions.

Merging and Reshaping

Once you get the hang of knowing how to find the rows and columns
of interest, merging different pieces of data can be relatively straight-
forward. While it may be obvious to some that doing so requires data
sets that have at least something exactly the same about them, this
appears to be the biggest hindrance to many data issues we at the CSR
come across, often because people don’t take the care to do the neces-
sary checks on data integrity from the outset. A simple issue of a v1 in
one data set with 100 variables and v.1 that represents the same vari-
able in the other data set will cause problems in merging, and the same
goes for ID variables that don’t use the same alphanumeric approach.
As an example of how to merge, the following code will first create
a demonstration dataset, and then show various ways in which one can
attach rows and columns.
# Merging and Reshaping
mydat <- data.frame(id = factor(1:12), group = factor(rep(1:2, e = 3)))
x = rnorm(12)
y = sample(70:100, 12)
x2 = rnorm(12)

# add columns
mydat$grade = y #add y via extract operator
df <- data.frame(id = mydat$id, y)
mydat2 <- merge(mydat, df, by = "id", sort = F) #using merge
mydat3 <- cbind(mydat, x) #using cbind

# add rows
df <- data.frame(id = factor(13:24), group = factor(rep(1:2, e = 3)), grade = sample(y))
17 A First Course

mydat2 <- rbind(mydat, df)

Sometimes you will have to reshape data (e.g. with repeated mea-
surements) from ’long’ with multiple observations per unit to wide,
where each row would represent a case, and vice versa. This is typi-
cally very nuanced depending on the data set, so you’ll probably have
to play with things a bit to get your data just the way you want. Along
with the reshape function one should look into the melt and related
functions from the reshape2 package. The following uses y from the
merge example, but first creates the original data in long format,
makes it wide, then reverts to long form.

mydata <- data.frame(id = factor(rep(1:6, e = 2)), time = factor(rep(1:2, 6)),

y)
mydataWide <- reshape(mydata, v.names = "y", direction = "wide")
mydataLong <- reshape(mydataWide, direction = "long")

Miscellaneous
FA C T O R S
I want to mention specifically how to deal with factors (categori-
cal variables) as it may not be straightforward to the uninitiated. In
general they are similar to what you deal with in other packages, and
while we typically would prefer numeric values with associated labels,
they don’t have to be labeled. The following shows two ways in which
to create a factor representing gender.

gender <- gl(2, k = 20, labels = c("male", "female"))

gender <- factor(rep(c("Male", "Female"), each = 20))

At times you may only have the variable as a numeric class, but the
R function you want to use will require a factor. To create a factor on
the fly use the as.factor function on the variable name22 . 22
As an example, the lrm function in
AT TA C H I N G the rms package will realize that the
numeric variable for the outcome for the
Attaching data via the attach function can be useful at times, es- ordinal regression is to be treated as a
pecially to the new user, as it allows one to call variables by name as categorical, but the polr function in the
MASS library would need something like
though they were an object in the current working environment. How- as.factor(y) ~ x1 + x2.
ever this should be used sparingly as one tends to use several versions
of a data set, and attaching a recent dataset will mask variables in the
previous. As it is very common to use multiple data sets to accomplish
one’s goal, in the long run it’s generally just easier to type e.g. my-
data$myvar than attaching the data and calling myvar. Look also at the
with function.
 Introduction to R 18

Initial Data Analysis & Graphics

Many applied researchers seem to ignore the importance of what goes
by the name of Exploratory Data Analysis, Initial Examination of Data,
Initial Data Analysis (IDA)23 , Descriptive Statistics etc. However, if 23
I prefer this terminology as it empha-
you’re doing things correctly, you’ll likely be spending a lot of time here sizes it as an essential part of the overall
analytic process.
(and your analysis should go much more smoothly because of the time
spent in this initial stage), and it is with IDA that one gets a feel for the
data they’re dealing with, finds problems, and develops solutions so
that the main analysis goes smoothly.

Initial Data Analysis: Numeric

Obtaining basic numeric information about specific variables or whole

data sets can be done with various functions from the base package
or enhanced with other packages. I like to use the describe function
from the psych package for numeric variables.
mean(state2$Life.Exp)

## [1] 70.88

sd(state2$Life.Exp)

## [1] 1.342

summary(state2$Population)

## Min. 1st Qu. Median Mean 3rd Qu. Max.

## 365 1080 2840 4250 4970 21200

table(state.region) #region is a separate vector

## state.region
## Northeast South North Central West
## 9 16 12 13

library(psych)
describe(state2)

## varsn mean sd median trimmed mad min

## Population 1
50 4246.42 4464.49 2838.50 3384.28 2890.33 365.00
## Income 2
50 4435.80 614.47 4519.00 4430.07 581.18 3098.00
## Illiteracy 3
50 1.17 0.61 0.95 1.10 0.52 0.50
## Life.Exp 4
50 70.88 1.34 70.67 70.92 1.54 67.96
## Murder 5
50 7.38 3.69 6.85 7.30 5.19 1.40
## HS.Grad 6
50 53.11 8.08 53.25 53.34 8.60 37.80
## Frost 7
50 104.46 51.98 114.50 106.80 53.37 0.00
## Area 8
50 70735.88 85327.30 54277.00 56575.72 35144.29 1049.00
## max range skew kurtosis se
## Population 21198.0 20833.00 1.92 3.75 631.37
## Income 6315.0 3217.00 0.20 0.24 86.90
## Illiteracy 2.8 2.30 0.82 -0.47 0.09
## Life.Exp 73.6 5.64 -0.15 -0.67 0.19
## Murder 15.1 13.70 0.13 -1.21 0.52
## HS.Grad 67.3 29.50 -0.32 -0.88 1.14
## Frost 188.0 188.00 -0.37 -0.94 7.35
## Area 566432.0 565383.00 4.10 20.39 12067.10
19 A First Course

Often we’ll want information across groups. The following all ac-
complish the same thing, but note the describe function is specific to
the psych library. It is worth noting how R is dealing
with region as illustrative of the power
# tapply(state2$Frost, state.region, describe) #not shown of object-oriented programming. The
Region variable and the state2 data
# by(state2$Frost, state.region,describe) #not shown set are the same length, and for the
describeBy(state2$Frost, state.region) purposes of carrying out the function,
R is able to index the data by means of
## group: Northeast the region vector. An error will result
## vars n mean sd median trimmed mad min max range skew kurtosis se if you substitute state.region with
## 1 1 9 132.8 30.89 127 132.8 35.58 82 174 92 -0.1 -1.46 10.3 state.region[-1], which will drop the first
## -------------------------------------------------------- entry. One can instantly create objects
## group: South and use them in conjunction with other
## vars n mean sd median trimmed mad min max range skew kurtosis objects quite seamlessly. They don’t have
## 1 1 16 64.62 31.31 67.5 65.71 33.36 11 103 92 -0.46 -1.22 to be in the data.frame object.
## se
## 1 7.83
## --------------------------------------------------------
## group: North Central
## vars n mean sd median trimmed mad min max range skew kurtosis se
## 1 1 12 138.8 23.89 133 137.2 20.02 108 186 78 0.58 -1 6.9
## --------------------------------------------------------
## group: West
## vars n mean sd median trimmed mad min max range skew kurtosis
## 1 1 13 102.2 68.88 126 103.6 69.68 0 188 188 -0.29 -1.77
## se
## 1 19.1

Once we examine univariate information we’ll likely be interested in

bivariate and multivariate examination. As a starting point try the cor
function.

cor(state2)

## Population Income Illiteracy Life.Exp Murder HS.Grad

## Population 1.00000 0.2082 0.10762 -0.06805 0.3436 -0.09849
## Income 0.20823 1.0000 -0.43708 0.34026 -0.2301 0.61993
## Illiteracy 0.10762 -0.4371 1.00000 -0.58848 0.7030 -0.65719
## Life.Exp -0.06805 0.3403 -0.58848 1.00000 -0.7808 0.58222
## Murder 0.34364 -0.2301 0.70298 -0.78085 1.0000 -0.48797
## HS.Grad -0.09849 0.6199 -0.65719 0.58222 -0.4880 1.00000
## Frost -0.33215 0.2263 -0.67195 0.26207 -0.5389 0.36678
## Area 0.02254 0.3633 0.07726 -0.10733 0.2284 0.33354
## Frost Area
## Population -0.33215 0.02254
## Income 0.22628 0.36332
## Illiteracy -0.67195 0.07726
## Life.Exp 0.26207 -0.10733
## Murder -0.53888 0.22839
## HS.Grad 0.36678 0.33354
## Frost 1.00000 0.05923
## Area 0.05923 1.00000
 Introduction to R 20

Initial Data Analysis: Graphics

As an introduction to graphical analysis, to which will return in more

detail later, here are some basic plots to start with. However when
using these standard plots from the base package, realize there are a
great many options available to tweak almost any aspect of the graph
both via the function and through other parameters that generally
available to plotting functions. See the help for plot and par. Histogram of state2$Illiteracy

25
hist(state2$Illiteracy)

20
barplot(table(state.region), col = c("lightblue", "mistyrose", "papayawhip",

15
Frequency
"lavender"))

10
plot(state2$Illiteracy ~ state2$Population)
stripchart(state2$Illiteracy ~ state.region, data = state2, col = rainbow(4),

5
method = "jitter")

0
0.5 1.0 1.5 2.0 2.5 3.0
state2$Illiteracy

15
The Basic Modeling Approach

10
5
R’s format for analysis of models may have a bit of a different feel than

0
other statistical packages, but it does not require much to get used to.
Northeast South North Central West

At a minimum you will need a formula specification and identification ●

of the data set to which the variables of interest belong.

2.5
●
●
● ●
●

Typical statistics packages fit a model and output the results in some
2.0
●

state2$Illiteracy
● ●
● ●
●
●

fashion after the syntax is run. R produces ’model objects’ that store
1.5
●
● ● ●
● ●

all the relevant information. Where other packages sometimes require

●● ● ● ●
1.0

●
● ● ● ●
● ● ●
●● ● ● ●

several steps in order to obtain and subsequently process results, R

●
●●●●● ● ●●
0.5

●
● ●

0 5000 10000 15000 20000

state2$Population

makes this very easy and is far more efficient. Some commonly used
model functions include lm24 for linear models, glm for generalized ●
West

●
● ● ● ● ● ●
● ● ●

linear models, and a host of functions from general purpose packages

North Central

● ● ●
● ● ●
● ●

such as MASS, rms, and Zelig.

The following demonstrates creation of a single predictor model and
South

● ● ● ●
● ● ● ● ●
● ● ● ● ●
● ●

using summary to obtain standard table output. There isn’t anything

Northeast

● ● ● ● ● ●
●
●

here you haven’t seen in other package model summaries, but those 0.5 1.0 1.5
state2$Illiteracy
2.0 2.5

new to statistical analysis may find it confusing upon first glance if 24

I would also recommend ols and
they’ve only seen it presented in one other package. other functions from the rms package
for enhanced approaches to standard
mod1 = lm(Life.Exp ~ Income, data = state2) models.
summary(mod1)
Just as an aside, one could use the semi-
## colon here to put both steps on a single
## Call: line, and in logical 1-2 steps like this you
## lm(formula = Life.Exp ~ Income, data = state2) will sometimes come across it in others’
## code. However, unlike some programs,
## Residuals: the semi-colon is never needed to end
## Min 1Q Median 3Q Max a line in the R environment, and in
## -2.9655 -0.7638 -0.0343 0.9288 2.3295 general you probably want to avoid it.
##
21 A First Course

## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 6.76e+01 1.33e+00 50.91 <2e-16 ***
## Income 7.43e-04 2.97e-04 2.51 0.016 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.28 on 48 degrees of freedom
## Multiple R-squared: 0.116,Adjusted R-squared: 0.0974
## F-statistic: 6.28 on 1 and 48 DF, p-value: 0.0156

mod2 = update(mod1, ~. + Frost + HS.Grad)

summary(mod2)

##
## Call:
## lm(formula = Life.Exp ~ Income + Frost + HS.Grad, data = state2)
##
## Residuals:
## Min 1Q Median 3Q Max
## -3.0878 -0.6604 -0.0043 0.6791 2.1029
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 6.59e+01 1.25e+00 52.82 < 2e-16 ***
## Income -7.32e-05 3.33e-04 -0.22 0.82703
## Frost 1.45e-03 3.32e-03 0.44 0.66495
## HS.Grad 9.68e-02 2.65e-02 3.65 0.00067 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.12 on 46 degrees of freedom
## Multiple R-squared: 0.342,Adjusted R-squared: 0.299
## F-statistic: 7.98 on 3 and 46 DF, p-value: 0.000217

mod3 = update(mod2, ~. - Frost)

summary(mod3)

##
## Call:
## lm(formula = Life.Exp ~ Income + HS.Grad, data = state2)
##
## Residuals:
## Min 1Q Median 3Q Max
## -3.0082 -0.6866 -0.0644 0.6186 2.2306
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 6.59e+01 1.24e+00 53.34 < 2e-16 ***
## Income -7.34e-05 3.30e-04 -0.22 0.82501
## HS.Grad 1.00e-01 2.51e-02 3.99 0.00023 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.11 on 47 degrees of freedom
## Multiple R-squared: 0.34,Adjusted R-squared: 0.312
## F-statistic: 12.1 on 2 and 47 DF, p-value: 5.81e-05
 Introduction to R 22

anova(mod1, mod2)

## Analysis of Variance Table

##
## Model 1: Life.Exp ~ Income
## Model 2: Life.Exp ~ Income + Frost + HS.Grad
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 48 78.1
## 2 46 58.1 2 20 7.93 0.0011 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

anova(mod3, mod2)

## Analysis of Variance Table

##
## Model 1: Life.Exp ~ Income + HS.Grad
## Model 2: Life.Exp ~ Income + Frost + HS.Grad
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 47 58.3
## 2 46 58.1 1 0.24 0.19 0.66

After creation of the initial model object, summary is called upon to

get the output. The model is then updated and the code is telling the
update function to keep all previous explanatory variables (~.) and
add Population and HS.Grad. The third model includes an update of
the second, again telling it to initially keep all other previous predictors
but to drop Population. The anova function can be used for model
comparison, and works beyond lm objects.
One of the powerful aspects of modeling in R is that the model ob-
jects have many things of use within them that allow for immediate
further analysis and exploration. For example, one can use the func-
tion coef to extract coefficients directly, one can also extract residuals
and fitted values. In addition, the basic plot and other functions are
often applicable to both base R and analysis objects from other pack-
ages, though various package will offer unique versions of output and
graphs.
mod1$coef

## (Intercept) Income
## 6.758e+01 7.433e-04

coef(mod1)

## (Intercept) Income
## 6.758e+01 7.433e-04

# mod1$res #not run

confint(mod1)

## 2.5 % 97.5 %
## (Intercept) 6.491e+01 70.25058
## Income 1.472e-04 0.00134

plot(mod1) #not shown

23 A First Course

As your needs vary you will likely move to packages beyond the
base offerings, and this will require you to get used to the specifics
of each. For example, some may not require a summary function to
produce the basic output, others require matrix rather than formula
input, plots will produce different graphs or perhaps no default plot is
available etc. Depending on the analysis of choice there may be quite a
few options, and as you use a new package you should investigate the
help file thoroughly before getting too carried away. 1
gear ●
0.8
am ● ●
# Example poisson, additive and mixed model. 0.6
drat ● ●

glm(Y ~ X, data = d, family = poisson) mpg

0.4

gam(Y ~ s(X)) vs 0.2

●
lmer(Y ~ X + (1 | group), data = d) qsec 0

wt −0.2

disp
−0.4

cyl
−0.6

hp
−0.8

carb
−1

Visualization of Information
Examples

To start with visualization in R, you might peruse some of the graphs in 10000

the margin to see what’s possible, sometimes remarkably easily even. 8000

Creating graphs in R allows you fine detail control over all aspects 6000
cut

Fair

of the graph and you have the ability to create extremely impressive
Good

count
Very Good

Premium

4000 Ideal

images that are publication ready.

2000

The typical statistical plots are available, but most have enhanced
0

versions in other packages. One can use generic functions such as plot 55 60
depth
65 70

followed by lines, points, legend, text(), and others to add further

information or changes. The generic plot function is also able to be
used after many analyses, such that using it on a model object will bring
up plot(s) specific to the analysis. In other cases, there are functions
for specific types of graphs such as the ones we did earlier. To get an
idea of the control you have over your plots look at the help file for
plot and par.

Enhancing Standard Graphs

carat cut color clarity depth table price x y z
0%

10%

Earlier we created some standard graphs, but they typically aren’t 20%

what we want, especially if we want to present them to others either

30%

40%

formally or informally. However it’s best not to rush things so what

50%

60%

we’ll do here is start with the usual and tweak as we go along. To 70%

80%

begin with we will take some random data and plot the histogram and 90%

100%
Fair D I1

a boxplot (the latter is not shown).

E SI2
Good SI1
row bins: F
100 VS2
Very Good G
VS1
H VVS2
objects: Premium
I VVS1
53940 Ideal J IF
 Introduction to R 24

x <- rnorm(100)
hist(x)
boxplot(x)

Such graphs are as basic as they come and not too helpful except
as an initial pass. For the following we’ll use the Cars93 data from the
MASS package. Load up the MASS library if you haven’t already.
Political Trust Media Trust
hist(Cars93$MPG.highway, col = "lightblue1", main = "Distance per Gallon 1993",
Andorra
xlab = "Highway MPG", breaks = "FD") Argentina
Australia
Brazil
Bulgaria
Burkina Faso
Canada
Chile

Which will produce the following: Cyprus

Ethiopia
Finland
France
Georgia
Germany
Ghana
India
Indonesia
Distance per Gallon 1993 Italy
Japan
Jordan
Mali
Mexico
Moldova
Morocco
Netherlands
Norway
Peru
Poland
15

Romania
Rwanda
Serbia
Slovenia
S Africa
S Korea
Spain
Sweden
Switzerland
Frequency

Taiwan
10

Thailand
Trinidad and Tobago
Ukraine
UK
Uruguay
USA
Vietnam
Zambia
5

Education
Life Satisfaction
Right Affiliation
Postmaterialism
Interpersonal Trust
Political Interest
Newspapers
TV Radio
Internet

Education
Life Satisfaction
Right Affiliation
Postmaterialism
Interpersonal Trust
Political Interest
Newspapers
TV Radio
Internet
0

20 25 30 35 40 45 50
●●
●

Highway MPG ● ●
●
●●

150
●● ●●
● ●
●
● ●●
●
●● ●
● ●● ●
● ●●
● ●
●
●● ●●●●
● ●● ● ● ● ●
● ● ●●

Follow−up time (months)

● ●●
●● ● ● ●●
●●●
● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●
● ●●● ● ●
● ●● ● ●● ● ●

100
● ● ● ● ●● ●

However we can tweak it a little bit, as well as add an additional

● ● ●
● ● ● ● ● ● ● ● ●● ● ●
● ●● ● ●●
● ● ●●● ● ●
●
● ●● ● ●●●
● ● ● ● ● ●● ● ● ● ● ●
● ● ● ● ●● ●
● ●● ● ●
● ●●
● ● ●
● ●
● ●●●●
●●● ●

plot to the overall graph. The par function is used here to set the num-
●
● ●
● ● ● ●●
● ●● ● ● ●●
● ●
●● ●

50
● ●
● ● ● ●● ●
●●
●●●
●
● ● ●●●● ●
● ●
● ● ●●● ● ●
● ●● ● ●
● ● ●●

ber of rows and columns within the actual graphics device so that more
● ●● ● ●● ●
●●●
● ● ●● ● ● ● ● ● ●
● ● ●● ● ●
● ● ●●● ● ●●
●● ● ● ●
● ● ● ● ● ● ●●
●●●
●
0

than one plot at a time may be displayed, at which point it is reset for Censored Metastasis

displaying one plot at a time in full view.

polygon() segments() symbols()

boxplots

par(mfrow = c(1, 2)) thermometers

hist(Cars93$MPG.highway, col = "lightblue1", prob = T, breaks = "FD") stars

arrows() curve(), abline(), points(), lines()

rectangles
● ● ● ●
● ●
● ●

# add density lines

● ●
● ●
● ●

● ●

● ●

● ●
squares
● ●

lines(density(Cars93$MPG.highway), col = "lightblue4") ●

●

●
●

● ●

● ● circles
● ●

● ●
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● ● ● ●

# add boxplot as second graphic

boxplot(MPG.highway ~ Origin, col = "burlywood3", data = Cars93) 1 Left Text ● ● ●● 1 Right Text

par(mfrow = c(1, 1)) 2 Left Text ● ●● ● 2 Right Text

3 Left Text ● ●● ● 3 Right Text

4 Left Text ● ● ● ● 4 Right Text

Which will produce the following graphic: 5 Left Text ● ● ●● 5 Right Text

6 Left Text ● ● ● ● 6 Right Text

7 Left Text ● ● ● ● 7 Right Text

8 Left Text ● ● ● ● 8 Right Text

9 Left Text ● ● ● ● 9 Right Text

10 Left Text ● ● ● ● 10 Right Text

−3 −1.5 0 1.5 3

● A ● B ● C ● D ● E

228
223 2381 611
233 162126
218
213 31
208
203 36
41
198
193 46
51
188
183
56
61
178 66
173 71
168 76
1 6 11 16 21 26 163 81
223 228 233 238 158 86
213 218 31 36
203 208 41 46 153 91
193 198 51 56 148 96
188
178
183 61 66 143 101
173 71 138 106
168 76 133 111
163 81 128 116
158 86
153 91 123 121
148 96 118 126
143 101
138 106 113 131
133 111 108 136
128 116
103 141
123 121
118 126 98 146
113 131 93 151
108 136 88 156
103 141
83 161
98 146
93 151 78 166

88 156 73 171
83 161 68 176
78 166 63 181
73 171
58 186
68 176
53 191
63 181
58 186
48 196

53 191 43 201

48 196 38 206

43 201 33 211
38 206 28 216
33
28
211
216
23
Openness
Neuroticism 221

23
18
Openness Neuroticism 221
226
18
13
8
226

231

236
13 231

8 236 3 2
3 2 239 7
239 7 234 12
234 12 229 17
229 17 224 22
224 22 219 27
219 27
214 32
214 32
209 37
209 37
204 42
204 42
199 47
199 47
194 52 194 52
189 57 189 57
184 62 184 62
179 67 179 67
174 72 174 72
169 77 169 77
164 82
164 82
159 87
154 Agreeableness Extraversion 92
159

Agreeableness
87

149 97
154

149
Extraversion 92
97
144 102
139 107 144 102

134 112 139 107

129 117 134 112

124 122 129 117
119 127 124 122
114 132
119 127
109 137
114 132
104 142
109 137
99 147
104 142
94 152
89 157 99 147

84 Conscientiousness 162 94 152

79 167 89 157
74
69 177
172
84 Conscientiousness 162

79 167
64 182
74 172
59 187
54 192 69 177

49 197 64 182
44 202 59 187
39 207 54 192
34 212
49 197
29 217
24 222 44 202
19 227 39 207
14 232 34 212
9 237 29 217
4 5
240 10 24 222
235 15 19 227
230 20 14 232
225 25 9 237
220 30
215 35 4 5
210 40 240 10
205 45
200 50 235 15
195 55 230 20
190 60
70 65
185 225 25
180
175 170
80 75 220 30
165 160
90 85 215 35
145 140 135 130 125 120 115 110 105 100 95
155 150 210 40
205 45
200 50
195 55
190 60
185
180 7065
175
170 8075
165
160 9085
155
150
145 100
105 95
140
135
130 110
115
120
125
25 A First Course

Histogram of Cars93$MPG.highway

50
0.10

45
0.08

40
0.06
Density

35
0.04

30
0.02

25
0.00

20

20 25 30 35 40 45 50 USA non−USA
Cars93$MPG.highway

It is worth noting that some typically used plots come with extras
by default. For example, the scatterplot function in the car library
automatically provides a smoothed loess line and marginal boxplots,
providing very useful information with ease.

library(car)
scatterplot(prestige ~ income | type, data = Prestige)
scatterplot(vocabulary ~ education, jitter = list(x = 1, y = 1), data = Vocab,
col = c("green", "red", "gray80"), pch = 19)

type
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5000 10000 15000 20000 25000 education

income ● ● ● ● ● ● ● ● ●

Beyond base R plots

R allows one to take things beyond its statistical environment relatively

easily also. For example, one can use other languages and programs
within R (e.g. Bugs, Python, Mplus), packages allow one to make use
of the Google visualization API, writing out to other formats viable for
network visualization in other packages, animation and so forth25 . As 25
Note that R has similar sorts of capa-
bilities as is, such as interactive plots
far as pure statistical packages go, most are only getting to some of the
(shiny), animation (animate) etc.
capabilities R has long had, while R continues to advance along with
what modern analysis requires to meet its full potential26 . 26
Current directions include interactive
One more thought regarding graphics and presentation in general- web graphics, d3 etc.

the goal is to provide as much information as possible in as clear a

manner as possible. If your graph is only showing single variable out-
comes or is filled with chart junk, you’re just wasting space and likely
 Introduction to R 26

the audience’s time. For guidance on graphs, data visualization etc.,

check out websites such as NY Times (they have stats folk in their
graphics department)27 , Flowing Data, and Infosthetics, folks like Ed- 27
See this link to see how R was inte-
ward Tufte and William Cleveland for some traditional sources, and grated with other approaches to produce
one of their interactive graphics.
within R you can familiarize yourself with lattice and ggplot2 packages
for static plotting capabilities that can take your standard plots further.

Getting Interactive

A lot of work is currently being done on to produce interactive graphics

via R. In particular, many packages attempt to harness the power of
d3 and other javascript libraries in order to make interesting visual-
izations. Check out ggvis, rCharts, for starters, then look at the Shiny
Gallery to catch a glimpse of what’s possible.

Getting Help
Basics

Now that you have some idea of what R can do for you and are ready
to try it on your own, it is imperative that you find out how you can
continue to work with it. It likely won’t take but a minute or two be-
fore you start hitting snags, and truth be told, you’ll probably spend a
lot of time looking up how to do things even after you get very familiar
with it. However that’s not a sign of R’s difficulty so much as its capa-
bility. As you get used to the sorts of things you already are familiar
with, you’ll come across more and more alternatives and enhance-
ments, and you will actually be getting a lot more done in the same
amount of time in the end.
As a start in becoming self-sufficient, get used to using the help files.
As mentioned previously, typing ? or ?? followed by the function name,
e.g. ?hist ??scatterplot, will bring up the help file in the former case, or
do a search for whatever term you’ve inserted28 . Typing help.start() at 28
Same as help and findit in Stata
the console will bring up manuals etc. Note that while there are help
files for every function, not all have the same amount of information.
Some functions/packages come with vignettes, links to reference arti-
cles etc. Others give only the bare minimum of information needed to
use the function. Some examples are exactly what you need, some will
spend 3/4 of many lines of code simply constructing the data set to be
used for the example that’s actually of interest, others might be a single
line or two that do little to illuminate the possibilities. Such is the way
of things when you have thousands of people contributing their efforts,
27 A First Course

but do note that all help files contain the same type of information as
they are required to.
A very useful thing to help you find the information you need is
via the Rseek search engine browser addon; example results are pic-
tured at right. It will return a specialized Google search (just fyi, there
happen to be lots of webpages with the letter R in them, and given
Google’s search tendencies of late any help is useful), introductions,
associated Task Views, R-help list results etc. You might spend some
time getting acquainted with the R-help list or even subscribing to it,
but with this search engine it’s not necessary29 . 29
Furthermore, the help list has gotten
Increasingly of late, many of those who are well-known on the R- out of hand for every day perusal, often
going over 100 messages for a single
help lists, along with many other folks from all walks of life, are now daily digest with most of them quoting
seen more on StackExchange/Cross-Validated. You’ll also find fewer previous messages which were quoting
previous messages and so on. Basically
folks complaining about reading the posting guide (or lack thereof). the thing as a whole is a mess to look
at, so you’re better off searching it via
Rseek.
A Plan of Attack for Diving In

The following are some guidelines that should help someone make for
a quicker transition toward using R regularly.

Use a script editor with syntax highlighting etc., rather than the
console30 . 30
At this point there’s no real reason not
to use Rstudio.
Get used to installing packages and importing data into R, and use
Rstudio menus to help with this initially if need be.
Start with ?functionname to see how to implement any particu-
lar function first. This will get you more acquainted with the help
files and in the habit of trying the examples. Saves time in the long
run.31 31
Type example(functionname) at the
console for any function you want to see
Take simple functions or commands you use in other packages such in action.
as for mean, sd, summary, and simple graphs and reproduce them
in R with no frills. Spend some time at the Quick-R website to help
with this.
Once comfortable with some basics, do a bare bones simple mod-
eling approach that includes: importing data you are familiar with,
describing it, creating a plot, running an analysis, interpreting re-
sults. I suggest a simple analysis and data set.
Redo the things you’ve learned thus far, adding options (e.g. extra
arguments, more complexity) along the way.
There are many users and places for support on the web. Use Rseek
and regular web searching to find the names of useful functions,
peruse the Resources section at the end of this document. There is a
ton of information on R freely available.
 Introduction to R 28

Alternatively, you can find some things R does that you like and/or
does better than your main statistical package, and simply pull out R
as you need it. That is how I initially did things myself, though I wish
I hadn’t. Some R is better than none to be sure, but it didn’t make
it any easier to work within the environment in general, nor does it
give a good sense of the capabilities of the program, as you may just
come to think that it’s merely a more complicated way of doing things
slightly better, instead of a much better way to do statistical analysis in
general. But again, for some that may be the most practical approach
to start.

Some Issues

Be prepared to have to spend some time, perhaps a lot of time, within

R before getting used to it. For most it is more difficult to learn com-
pared to other statistical programs, though this depends in part on
one’s prior experiences with other programs or programming lan-
guages. As mentioned previously, the actual help in help files can vary
quite a bit, often assume the knowledge one might in fact be looking
for and it may simply provide syntax. In the actual implementation
and as with other stat programs, cryptic error messages can leave one
guessing whether there is a data, code or estimation problem. Some
may find it to be slower than other programming languages like C,
but for typical use in applied social science research this will typically
not be an issue. R can at times be relatively slow with huge data sets
(hundreds of thousands) or even smaller with inefficient code, but not
for typical ’large’ sizes. Furthermore there are packages and specialized
versions (Revolution Analytics) that can help optimize processing of
large amounts data and packages such as parallel, snow and others,
one can utilize the cpus on their own machine or over a cluster for
increased processing speeds. 32 . 32
With big data problems your desk or
So yes, R can be a pain in the rear at times, but despite occasional laptop can’t handle, see what the CRC
here on campus can do for you. Also, I
issues one may come across there are many avenues for assistance that have used the multiprocessor packages
are extremely helpful, and various solutions available when you do hit in R for both single machines and
clusters, so can provide direct assistance.
a snag. The reference section provides a list of places to find additional
help on your own.
29 A First Course

Summary
Why R?

R is the premier statistical package going right now. R is free, and

being open-source, rapidly updated, debugged, and advanced. You
are free to use it in any way you wish to accomplish what you want to
statistically. What more could you ask for really?

Who is R for?

R is for anyone that wants to engage in thoughtful statistical analysis

of scientific problems. It will take effort, possibly quite a bit, but you
wouldn’t be interested in the first place if you were short on that.

R as a solution

R can do what you want, and you are not forced into limitations by de-
sign in the way you are with other packages which have no flexibility.
The question is not if R can do this or that analysis, but instead, how.
 Introduction to R 30

Resources
These are resources to keep you on your R journey now that you know
a little bit about it.

General Web Assistance

Main R website The place to start.
R Documentation Search for packages and packages grouped by discipline/subject.
Cross-Validated General stats help site where people post lots of R questions.
Stack Overflow General programming help site where people post lots of R questions.
UCLA Statistical Computing group A great resource for general stats packages.
Statistics with Interactive R Learning Learn stats and R together.
Quick-R website Particularly geared toward SAS and SPSS users.
R For SAS AND SPSS USERS Actually a good way to learn all three (plus S).

Manuals
List at the R website These are accessible via the help menu.
An Introduction to R The main R manual.
Simple R Dated but still useful to someone starting out.
Reference Card Print out and keep handy when starting out with R.

Graphics
ggplot2 library website Hadley Wickham’s helpful website and package.
Paul Murrel’s website A core R developer.

Development Sites
Github Many R developers host code there.
R-forge development site Pacakges in development and unreleased packages.
Rforge development site How fun! A different ’r’ ’forge’ site.

Commercial Versions

Revolution Analytics 33 33
I guess it says something when the
S-Plus creator of SPSS jumps ship for R. I don’t
know what it says though.

Miscellaneous
Rstudio Don’t do R without it.
R blogs For those that like their R with too many links and stories about cats.
Crantastic Note new packages and updates.