SAS for Epidemiologists Applications and Methods

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Charles DiMaggio

SAS for Epidemiologists

Applications and Methods

123
Charles DiMaggio, PhD
Departments of Anesthesiology
and Epidemiology
College of Physicians and Surgeons
Mailman School of Public Health
Columbia University
New York, USA

ISBN 978-1-4614-4853-2 ISBN 978-1-4614-4854-9 (eBook)

DOI 10.1007/978-1-4614-4854-9
Springer New York Heidelberg Dordrecht London
Library of Congress Control Number: 2012947994

© Springer Science+Business Media New York 2013

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For Liz, Katie, and CJ. Thank you for being
there when I come home from epidemiology.
Foreword

Advances in information technology have transformed the field of epidemiology

in profound ways. Data, which had been the most valuable commodity of the
empirical sciences, are increasingly available and accessible. The quantity of data
rises exponentially on a daily basis. The forms and sources of data are also
multiplying. These changes are driving epidemiology into the era of “big data
science” and converting more and more epidemiologists into data analysts. As a
result, practical skills to manage large and complex data sets and make sound
use of them are of increasing importance to future epidemiologists. This book
by Dr. Charles DiMaggio is a valuable addition to the toolbox for epidemiology
students, public health professionals, and researchers in the health-care industry.
This book distinguishes itself from other applied SAS texts in three notable
aspects. First, it is extremely reader-friendly. Dr. DiMaggio has taught the intro-
ductory SAS course at Columbia to hundreds of students for over a decade. This
book is based primarily on his lectures and is written in a conversational style. The
materials are presented in a way that is easy to understand and interesting to learn.
In addition to the technical know-how, each chapter contains some “clinical pearls”
– insight and wisdom that are unavailable in other applied SAS books. In fact, the
reader may feel more like being engaged in a conversation with Dr. DiMaggio than
studying a monotonic, mind-numbing how-to manual. Second, this book focuses on
the fundamentals. In the first five chapters, Dr. DiMaggio explains in painstaking
detail the most basic functions of data input, management, and exploration. These
chapters are followed by intermediate statistical analyses of epidemiologic data,
both categorical and continuous. Going through these chapters will not make
the reader an expert SAS programmer, but it will provide the reader with the
necessary skills to perform analytical responsibilities required for a master’s level
epidemiologist. Finally, this book is filled with illuminating examples from actual
epidemiology research projects. It is written for aspiring epidemiologists by an
experienced epidemiologist. These examples are used not only for procedural
demonstrations but also for explanations of important epidemiological concepts
such as confounding, disease odds ratio, and exposure odds ratio.

vii
viii Foreword

As one of the most sophisticated statistical packages, SAS is so kaleidoscopic

that first-time users often find it intimidating. Public health students will find
this comprehensive text especially helpful for overcoming their initial fears and
confusion. It can serve as a textbook for introductory courses on SAS applications
as well as a self-study reference for epidemiologists and other health professionals.

New York, NY, USA Guohua Li

Columbia University M. Finster
Preface

The path to this book began, as these things so often do, when I was asked to teach
a course. In this case, a semester-long class for master’s students on epidemiologic
analyses using SAS. Over a few years of preparing for and teaching the material I
confronted a combination of practical and conceptual considerations that led me to
believe that perhaps there was room for another book about SAS.
On a practical level, working with a program like SAS is a skill I consider
necessary for all graduating master’s epidemiologists. To be honest, the necessity
that the program actually be SAS is based on a circular argument. Many employers
of epidemiologists use SAS because their current analysts use SAS, and newly
minted analysts will compel additional future analysts to use SAS. This reliance
on SAS of potential employers of master’s-level epidemiology students may change
in the future, but my sense is that it will not be anytime soon. While the practical
motivation to learn SAS is somewhat self-fulfilling, it does not detract from the
capabilities that made SAS an important skill in the first place. And, does it make
the choice of SAS any less necessary. As I sit and write this, a quick search on the
New York Times jobs link returns 15 epidemiology jobs in the New York City area.
A search for SAS returns 457 hits. When I do this search on the first day of class,
with generally the same results, there is invariably an increased interest among the
students in spending a few hours a week learning SAS.
The kinds of SAS-related work that master’s-level epidemiologists are called
upon to undertake do not exceed some fairly straightforward categorical and
continuous data analyses. There was, though, no book that addressed this material
in a similarly straightforward fashion. The feedback I’ve received from the past
students is that the procedures covered in this material account for a good majority
of their daily activity and that knowing how to do those things helps set the stage
for learning more advanced material.
On a conceptual level, the role of statistical software in epidemiologic practice is
in a state of flux, and the kinds of data and analyses epidemiologists are being called
upon to work with are evolving into what might be called the era of “big data” and
the rise of “computational epidemiology.” SAS is tailor-made to deal with the kinds
of huge data sets that are becoming routine in epidemiology. That there has been

ix
x Preface

an explosion in the availability of administrative and routinely collected health data,

free and open-source data, social media data, and other online data is clear. That
the data are amenable to reliable or valid analyses is less clear. The basics, about
missing and incorrect values, about confounding, about bias, about study design,
are if anything even more important. The data can inform, but we may have to teach
them to speak clearly, and in a language that is epidemiologically valid.
Fortunately, SAS is more than up to the task. It has a facility for dealing with
extremely large data sets that I have found unsurpassed in other statistical programs.
SAS allows epidemiologists to pay special attention to the necessary (though not
glamorous) initial steps of reading in, preparing, and cleaning large amounts of data,
when early errors or missteps will be amplified throughout the analysis, sometimes
in ways that are difficult to trace to their origins. For this reason, fully the first third
of this book addresses using SAS to read in and manipulate data to get them into a
form that makes epidemiologic sense.
The one aspect of preparing and teaching this material that I did not expect was
that it was actually fun. I’m certain this says more about me than it does about the
material. But perhaps a kind of geeky enjoyment of some of the practical aspects of
epidemiologic methods, like learning how to use SAS, is a sign that you’ve chosen
the right profession. I tried to capture some of what I found interesting and enjoyable
by using examples and materials that have practical relevance to epidemiologic
practice.
I have come to appreciate that public health practice requires a long-term view,
and that you may not always (or even frequently) see the effects of your work. The
effects of teaching public health are even farther removed from immediacy. Despite
the practical aspects underlying this book, the ultimate motivation is as ephemeral
as public health practice itself. In the end, I hope to contribute in some small way
to the efforts of someone I haven’t met, to improving the health, happiness, and
well-being of someone who may not even be born yet.

New York, NY, USA Charles DiMaggio

Acknowledgments

I was fortunate enough to learn (and hopefully pass on to you) these concepts and
procedures from a small but uniformly excellent set of books and the scientists who
wrote them [1–12]. I try to cite areas where they were particularly illustrative, but I
borrowed from them shamelessly throughout.
I am especially indebted to the SAS Institute for allowing me to draw on their
training manuals, course notes, and data sets. If you want a thorough grounding in
SAS, I strongly recommend you take one of their outstanding training classes. I also
appreciate the willingness of the New York State Department of Health to allow
me to use a version of their Statewide Planning and Research Cooperative System
(SPARCS) data that figure so prominently in these pages.
Finally, many thanks to my colleagues in the departments of anesthesiology and
epidemiology at Columbia University in New York, for their support and feedback,
and to my stellar teaching assistants, Joanne Brady, and George Loo, who know
SAS so much better than I do, and who helped breathe life into this material.

xi
Contents

1 Introduction .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 1
1.1 About SAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 1
1.1.1 Alternatives to SAS. . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 2
1.1.2 Why SAS, Then? . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 3
1.2 About This Book . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 3
1.2.1 Goals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 4
1.2.2 How to Use the Book .. . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 4

Part I Working with Data in SAS

2 The SAS Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 9

2.1 The SAS Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 9
2.2 The Program Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 9
2.3 SAS Statements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 11
2.4 Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 11
2.5 Quick Demonstration of an SAS Program . . . . . .. . . . . . . . . . . . . . . . . . . . 12
2.6 Two Types of SAS Programs . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 13
2.7 Two Kinds of SAS Data.. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 15
2.8 Two Parts to a SAS Data Set . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 15
2.9 Some Simple SAS Utilities . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 16
2.10 Getting Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 16
Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 17
3 Working with SAS Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 19
3.1 SAS Data Libraries .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 19
3.2 Two Special SAS Libraries . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 20
3.3 Three Ways to Browse SAS Data Libraries .. . . .. . . . . . . . . . . . . . . . . . . . 21
3.4 Inputting Data into SAS . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 21
3.5 Reading in Data from the Editor Window.. . . . . .. . . . . . . . . . . . . . . . . . . . 23
3.6 Two Basic INPUT Statements . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 24
3.6.1 Space-Delimited and Column Input . . .. . . . . . . . . . . . . . . . . . . . 25

xiii
xiv Contents

3.7 Reading in Data from External Files . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 26

3.7.1 The INFILE Statement . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 26
3.7.2 Formatted INPUT of External Data Sets . . . . . . . . . . . . . . . . . . 28
3.7.3 Informats .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 29
3.8 Behind the Scenes of a Data Step . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 30
3.8.1 Deciphering Error Statements. . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 31
3.8.2 Error Messages . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 32
3.8.3 A Few Other Common Errors .. . . . . . . . .. . . . . . . . . . . . . . . . . . . . 35
3.9 Notes on Manipulating Data (or How to Tame
an Annoying Data Set) . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 36
3.9.1 Illogically Arrayed Data.. . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 37
3.10 Data Input Miscellany .. . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 38
3.11 Importing Excel Spreadsheets . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 38
Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 39
4 Preliminary Procedures .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 41
4.1 PROC PRINT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 41
4.2 PROC SORT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 42
4.3 Enhancing Output: Titles and Footnotes . . . . . . . .. . . . . . . . . . . . . . . . . . . . 44
4.4 LABELS .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 46
4.5 PROC FORMAT and FORMAT .. . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 47
4.6 ODS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 52
Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 54
5 Manipulating Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 57
5.1 The SET Statement .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 57
5.2 Using SET to Define and Create New Variables .. . . . . . . . . . . . . . . . . . . 58
5.2.1 Operations.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 58
5.2.2 Functions .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 59
5.2.3 Example: Deaths Following the Terrorist
Attacks of September 11, 2001 . . . . . . . .. . . . . . . . . . . . . . . . . . . . 60
5.3 Adding (Concatenating) Data Sets . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 62
5.3.1 Concatenating the September 11 Data Set . . . . . . . . . . . . . . . . 63
5.4 Merging Data Sets Using MERGE – BY . . . . . . .. . . . . . . . . . . . . . . . . . . . 63
5.4.1 SORT Before You MERGE . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 64
5.4.2 Merging the 9/11 Data Set . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 65
5.5 Conditional Expressions Using IF-THEN-ELSE .. . . . . . . . . . . . . . . . . . 67
5.6 Conditional Expressions Using a Restricting IF Statement . . . . . . . . 72
5.6.1 Restricting Variables Read into a New Data Set . . . . . . . . . . 73
5.7 Conditional Expressions with SAS Dates . . . . . . .. . . . . . . . . . . . . . . . . . . . 73
5.7.1 Using Dates to Subset the 9/11 Data. . .. . . . . . . . . . . . . . . . . . . . 73
Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 76
Contents xv

Part II Descriptive and Categorical Analysis

6 Descriptive Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 79
6.1 PROC MEANS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 79
6.2 PROC FREQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 80
6.3 PROC TABULATE. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 81
6.3.1 Using TABULATE for Surveillance Data . . . . . . . . . . . . . . . . . 84
Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 86
7 Histograms and Plots.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 91
7.1 Introduction .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 91
7.2 PROC GCHART for Histograms .. . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 91
7.3 PROC GPLOT to Plot Continuous Data . . . . . . . .. . . . . . . . . . . . . . . . . . . . 93
Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 97
8 Categorical Data Analysis I . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 99
8.1 Introduction to Categorical Outcomes . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 99
8.2 Associations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 100
8.3 Examining Frequency Tables . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 101
8.4 Reordering Categorical Variables . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 103
8.5 Tests of Statistical Significance for Categorical Variables . . . . . . . . . 105
8.5.1 Chi-Square . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 105
8.5.2 Exact Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 108
8.5.3 The Mantel–Haenszel Chi-Square . . . . .. . . . . . . . . . . . . . . . . . . . 112
8.5.4 The Spearman Correlation Coefficient . . . . . . . . . . . . . . . . . . . . 113
8.6 Significance vs. Strength .. . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 114
Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 116
9 Categorical Data Analysis II . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 119
9.1 Probabilities and Odds . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 119
9.2 The Odds Ratio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 120
9.2.1 Why Epidemiologists Need the Odds Ratio . . . . . . . . . . . . . . . 120
9.2.2 The Disease Odds Ratio . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 121
9.2.3 The Exposure Odds Ratio . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 123
9.3 Preterm Labor and Birth Weight Example 1 . . . .. . . . . . . . . . . . . . . . . . . . 124
9.4 Confounding .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 126
9.4.1 Identifying and Controlling Confounding .. . . . . . . . . . . . . . . . 126
9.5 Controlling for Confounding . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 128
9.5.1 Controlling Confounding in Study Design . . . . . . . . . . . . . . . . 128
9.5.2 Analytic Approaches to Confounding .. . . . . . . . . . . . . . . . . . . . 128
9.6 Preterm Labor and Birth Weight Example 2 . . . .. . . . . . . . . . . . . . . . . . . . 129
9.7 Adjusted Odds Ratios . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 129
9.7.1 Cochran–Mantel–Haenszel Statistic . . .. . . . . . . . . . . . . . . . . . . . 131
9.7.2 The Mantel–Haenszel Odds Ratio . . . . .. . . . . . . . . . . . . . . . . . . . 131
9.8 Summarizing Exploratory Contingency Table Analyses . . . . . . . . . . . 135
Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 135