Regression with Linear Predictors

501 Pages·2010·3.09 MB·English

by  Per Kragh Andersen

Statistics for Biology and Health
Series Editors:
M. Gail
K. Krickeberg
J. Samet
A. Tsiatis
W. Wong
For other titles published in this series, go to
http://www.springer.com/series/2848
Per Kragh Andersen • Lene Theil Skovgaard
Regression with Linear
Predictors
With 171 illustrations by Therese Graversen
1 C
Per Kragh Andersen Lene Theil Skovgaard
University of Copenhagen University of Copenhagen
Dept. Biostatistics Dept. Biostatistics
Øster Farimagsgade 5 Øster Farimagsgade 5
DK-1014 Copenhagen K DK-1014 Copenhagen K
Denmark Denmark
[email protected] [email protected]
Series Editors
M. Gail A. Tsiatis
National Cancer Institute Department of Statistics
Bethesda, MD 20892, USA North Carolina State University
Raleigh, NC 27695, USA
K. Krickeberg
Le Chatelet W. Wong
F-63270 Manglieu, France Department of Statistics
Stanford University
J. Samet Stanford, CA 94305-4065, USA
Department of Preventive Medicine
Keck School of Medicine
University of Southern California
1441 Eastlake Ave. Room 4436, MC 9175
Los Angeles, CA 90089
ISSN 1431-8776
ISBN 978-1-4419-7169-2 e-ISBN 978-1-4419-7170-8
DOI 10.1007/978-1-4419-7170-8
Springer New York Dordrecht Heidelberg London
Library of Congress Control Number: 2010931468
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V
Preface
This is a book about regression analysis, that is, the situation in statistics
where the distribution of a response (or outcome) variable is related to ex-
planatory variables (or covariates). This is an extremely common situation in
theapplicationofstatisticalmethodsinmanyfields,andlinearregression,lo-
gistic regression, and Cox proportional hazards regression are frequently used
for quantitative, binary, and survival time outcome variables, respectively.
Several books on these topics have appeared and for that reason one may
well ask why we embark on writing still another book on regression. We have
two main reasons for doing this:
1. First,wewanttohighlightsimilaritiesamonglinear,logistic,proportional
hazards,andotherregressionmodelsthatincludealinearpredictor.These
modelsareoftentreatedentirelyseparatelyintextsinspiteofthefactthat
alloperationsonthemodelsdealingwiththelinearpredictorareprecisely
the same, including handling of categorical and quantitative covariates,
testing for linearity and studying interactions.
2. Second, we want to emphasize that, for any type of outcome variable,
multiple regression models are composed of simple building blocks that
areaddedtogetherinthelinearpredictor:thatis,t-tests,one-wayanalyses
of variance and simple linear regressions for quantitative outcomes, 2×2,
2×(k+1)tables andsimplelogistic regressionsfor binaryoutcomes, and
2-and(k+1)-samplelogranktestsandsimpleCoxregressionsforsurvival
data.Thishastwoconsequences.Allthesesimpleandwellknownmethods
can be considered as special cases of the regression models. On the other
hand, the effect of a single explanatory variable in a multiple regression
model can be interpreted in a way similar to that obtained in the simple
analysis, however, now valid only for the other explanatory variables in
the model “held fixed”. Note the important point that addition of simple
terms in the linear predictor will imply an assumption of no interaction;
that is, the effect of an explanatory variable is the same for all values of
otherexplanatoryvariablesinthemodel.Thisisanassumptionthatoften
needs careful consideration as part of the analysis.
In Chapter 1 the basic ideas are set up and the examples to be used
throughout the book are introduced. Chapter 2 presents a review of back-
ground material on probability distributions and the principles of statistical
inference. In Chapter 3 the simple building blocks for categorical explana-
tory variables are introduced for the three main types of outcome variables.
Chapter 4 deals with one quantitative explanatory variable, first when a lin-
ear effect can be assumed and, next, certain models with a nonlinear effect of
the covariate (still described by a linear predictor, however) are introduced.
A very common example of such a nonlinear effect is a polynomial.
VI
Havingpresentedthebuildingblocks,Chapter5discussesmultipleregres-
sion models (i.e., models with several explanatory variables). We focus on
models with two covariates and introduce the concepts of confounding and
interaction (“effect modification”). In Chapter 6 we discuss model building
strategies,inparticularselectionofexplanatoryvariablesforansweringaspe-
cific research question and illustrate the strategies by thorough analyses of
three specific examples.
WhereasChapters3through6primarilydealwithexamplesoflinearmod-
elsforquantitativeoutcomes,logisticmodelsforbinarydata,andCoxmodels
for lifetimes, Chapter 7 presents a number of other regression models with a
linear predictor. These include the logistic models for ordinal and multino-
mial data, Poisson-type models for counts as well as alternative models for
quantitative, binary, and lifetime data. Chapter 8 briefly mentions a number
of extended models all involving a linear predictor. These include multivari-
ate models with more than one response variable per individual, for example
repeated measurements and other types of correlated outcomes, and models
with covariate measurement errors. The multivariate models include random
effect models and marginal models. The treatment of these topics is by no
means meant to be exhaustive but to serve mainly as a warning that mod-
els more complicated than the ones treated earlier in this book occur quite
frequently and will produce erroneous conclusions if not analyzed properly.
Thebookisconcludedwithfourappendicessummarizingnotation,theuseof
logarithms, some recommendations, and simple programming, respectively.
It is important to notice that some sections of the book are more difficult
to read than others, simply because of the varying level of complexity for the
different methods we wish to cover.
Thebookisbasedonourpersonalexperienceasteachers,consultants,and
researchersinbiostatistics formorethanthreedecadesandalldataexamples
are based on this.
Our intended readers are primarily researchers from scientific areas where
statistics is being applied to analyze numerical data, for example, fields such
as medicine, public health, dentistry, agriculture, and so on. For that rea-
son we do not expect readers to have a strong background in mathematics.
We limit the amount of mathematical formulas used, and we avoid the use
of Greek letters in formulas altogether. We do, however, expect readers to
have some familiarity with basic statistical terms but, to set a common level,
Chapter 2 gives an overview of the necessary concepts. Although we have
mainlywrittenthebookforappliedscientistsitisourhopethatreaderswith
a more mathematical background who wish to enter the field of biostatistics
willalsobenefitfromstudyingthebook.Weintendtoprovideabookthatcan
both serve as a reference source and a course textbook. For the last purpose,
chapters conclude with a series of exercises all dealing with data analysis.
The mainstream of our text presents aspects of the methods that are
important for building regression models, yet we have in some places found
it natural to add brief discussions of related concepts that are less important
VII
for regression analysis. Such digressions are marked in the text as Digression
and also include some historical and more technical remarks.
An applied statistical text such as the present book, obviously includes a
large number of practical examples, and computational aspects are crucial.
We have chosen not to base the presentation of examples in the book on
a single piece of software. Instead, the book is accompanied by Web pages
documenting examples by including computer code for the computations in
R and SAS. It is our intention to supplement the Web pages with code in
STATA as well but we have chosen not to include SPSS code because it is our
impressionthatmostusersofthisprogramusethemenuinterfaceratherthan
writing program code. In addition, a brief appendix (Appendix D) includes
very simple and “raw” commands for fitting the basic types of regression
models in R, SAS, and STATA.
It has been our ambition that the Web pages should be user-friendly with
facilitiesformakinganentrybasedonbothbookchaptersandonthedifferent
examples. The pages can be found at
www.biostat.ku.dk/~linearpredictors
We would like to thank our medical colleagues who have granted us per-
mission to use their data as illustrations. We also wish to thank colleagues at
theDepartmentofBiostatistics,UniversityofCopenhagen,Denmark,forcre-
atingafriendlyandproductiveworkingenvironment. Inparticular,wethank
ØrnulfBorgan,BendixCarstensen,SaskialeCessie,ThomasGerds,NielsKei-
ding, Kajsa Kvist, Maja Olsbjerg Larsen, Henrik Ravn and Willi Sauerbrei
for comments, advice, assistance or encouragement. Part of the manuscript
was written during a week-long workshop in Oberwolfach, Germany, and we
wish to thank Mathematisches Forschungsinstitut, Oberwolfach, for hospital-
ity during that week.
Last, but definitely not least, our most sincere thanks go to Therese Gra-
versen. Not only did she design the accompanying Web pages and produce
all the graphics in the manuscript but she also gave valuable and thoughtful
comments to both contents and lay-out. Without her skillful input this book
would never have become what it is now.
Copenhagen,June2010 PerKraghAndersen,LeneTheilSkovgaard
Contents
1 Introduction............................................... 1
1.1 Introductory examples and types of outcome................ 3
1.1.1 Introductory examples ............................. 3
1.1.2 Types of outcome ................................. 7
1.2 Covariates.............................................. 9
1.2.1 Categorical covariates.............................. 9
1.2.2 Quantitative covariates............................. 11
1.3 Link functions .......................................... 13
1.4 Building a regression model............................... 22
1.4.1 The linear predictor and the link function ............ 24
1.4.2 Regression models and their interpretation ........... 28
1.5 Further examples........................................ 30
1.6 The scope of this book and how to read it .................. 37
2 Statistical models.......................................... 43
2.1 Random variables and probability ......................... 44
2.1.1 The Bernoulli distribution .......................... 47
2.1.2 The Binomial distribution .......................... 48
2.1.3 The Poisson distribution ........................... 50
2.1.4 The Normal distribution ........................... 51
2.1.5 Other common distributions ........................ 55
2.1.6 Conditional probability ............................ 56
2.2 Descriptive statistics..................................... 57
2.2.1 Binary outcome ................................... 57
2.2.2 Quantitative outcome.............................. 59
2.2.3 Survival time outcome ............................. 63
2.3 Statistical inference...................................... 64
2.3.1 Estimation ....................................... 65
2.3.2 Model checking ................................... 73
2.3.3 Hypothesis testing................................. 79
2.3.4 The likelihood function............................. 84
X Contents
2.4 Exercises ............................................... 92
3 One categorical covariate .................................. 95
3.1 Binary covariate......................................... 96
3.1.1 Quantitative outcome: t-tests ....................... 97
3.1.2 Binary outcome: (2×2)-tables and the chi-square test ..110
3.1.3 Survival time outcome: the 2-sample logrank test......123
3.2 Categorical covariate with more than two levels .............137
3.2.1 Quantitative outcome: One-way analysis of variance ...142
3.2.2 Binary outcome: The 2×(k+1)-table ...............157
3.2.3 Survival time outcome: The (k+1)-sample logrank test 161
3.3 Exercises ...............................................166
4 One quantitative covariate.................................173
4.1 Linear effect ............................................175
4.1.1 Quantitative outcome: Simple linear regression ........176
4.1.2 Binary outcome: Simple logistic regression............194
4.1.3 Survival time outcome: Simple Cox regression.........201
4.2 Nonlinear effect .........................................210
4.2.1 Dividing the covariate range into intervals ............214
4.2.2 Polynomials ......................................221
4.2.3 Other nonlinear models with a linear predictor ........223
4.3 Exercises ...............................................228
5 Multiple regression, the linear predictor ...................231
5.1 Two covariates: Models without interaction .................234
5.1.1 Two categorical covariates..........................234
5.1.2 One categorical and one quantitative covariate ........245
5.1.3 Two quantitative covariates.........................254
5.2 Two covariates: Models with interaction....................263
5.2.1 Two categorical covariates..........................264
5.2.2 One categorical and one quantitative covariate ........273
5.2.3 Two quantitative covariates.........................278
5.2.4 Saving degrees-of-freedom ..........................285
5.3 Several covariates........................................287
5.3.1 Models without higher-order interactions .............287
5.3.2 Models with higher-order interactions ................289
5.4 Matched studies.........................................294
5.5 Exercises ...............................................300
6 Model building: From purpose to conclusion...............303
6.1 General principles for model selection ......................304
6.1.1 Identification of covariates..........................305
6.1.2 Model diagrams ...................................308
6.1.3 Initial model building ..............................311
Contents XI
6.1.4 Strategy of analysis................................314
6.1.5 Model checks and diagnostics .......................317
6.1.6 Collinearity.......................................318
6.1.7 Interactions.......................................319
6.2 Examples...............................................320
6.2.1 The vitamin D example ............................321
6.2.2 The surgery example...............................331
6.2.3 The PBC-3 trial...................................342
6.3 Sample size determination ................................354
6.4 Exercises ...............................................365
7 Alternative outcome types and link functions..............367
7.1 Multinomial outcome ....................................367
7.1.1 Ordinal outcome ..................................368
7.1.2 Nominal outcome..................................383
7.2 Count outcome..........................................387
7.3 Quantitative outcome ....................................394
7.4 Binary outcome .........................................403
7.4.1 Alternatives to the logit link ........................404
7.4.2 Case-control studies ...............................409
7.5 Survival time outcome ...................................416
7.5.1 Multiplicative hazard models .......................416
7.5.2 Additive hazard models ............................422
7.5.3 Accelerated failure time models .....................427
7.6 Exercises ...............................................429
8 Further topics .............................................431
8.1 Multivariate outcome ....................................431
8.1.1 Random effects models.............................433
8.1.2 Marginal models ..................................438
8.1.3 Longitudinal and life history data ...................440
8.2 Errors in covariates ......................................447
8.2.1 Regression dilution ................................448
8.2.2 Correction for measurement error in covariates ........452
A Appendix: Notation .......................................457
B Appendix: Use of logarithms...............................463
C Appendix: Some recommendations.........................473
D Programming in R, SAS and STATA...........................477
References.....................................................483
Index..........................................................487
1
Introduction
Supposewearestudyingbloodpressureinhumansbasedonarandomsample
from a specific population, say, inhabitants of some larger city. The very first
step in such a study may be to get a summary of the level and variation
of blood pressure, subject to criteria such as ethnicity, gender or age. The
purpose of studying blood pressure may be to establish normal references to
serve as future guidelines for when to start treatment for either too high or
too low a blood pressure.
In order to illustrate the distribution of the blood pressure measurements
from this sample, we usually calculate average and standard deviation and
possiblyproduceahistogramorsomeothergraphicalillustration.Thesequan-
tities are examples of descriptive statistics.
Asmallpartofthevariationinthebloodpressuremeasurementscanprob-
ablybeascribedtomeasurementerror,however,alargerpartofthevariation
is more likely due to individual fluctuations over time and topopulation vari-
ation, the true differences between subjects. Part of this population variation
may be due to characteristics of the subjects that are easily recognized. For
instance,menfrequentlyhaveasomewhathigherbloodpressurethanwomen,
and older people tend to have a higher blood pressure than younger people.
The example illustrates that, in many fields of research, information may
be collected on various features in a number of experimental units. Other
examples may be the serum bilirubin level in male and female patients with
liver cirrhosis, whether persons in different job categories working in a given
company have suffered from severe headaches in some specified period, the
survival time from diagnosis of cancer patients in different stages of disease,
the rise in blood glucose in experimental animals after feeding with different
diets, the number of claims in a year for insurance policies of different types,
the yield of some crop in differently treated field plots in an agricultural
experiment, or the annual cancer rates in successive years in some country.
Inthelastthreeexamplestheexperimentalunitsaretheinsurancepolicy,
the field plot, and the country. However, in this book we are mainly using
examples from medical and public health research and we denote the experi-