Professional Documents
Culture Documents
Rand R. Wilcox
Professor of Psychology
University of Southern California
Los Angeles, California, United States
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ISBN: 978-0-12-820098-8
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11.10.4
R Functions regpre, regpreCV, corREG.best.DO, and
PcorREG.best.DO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 759
11.10.5 Inferences About Which Predictors Are Best. . . . . . . . . . . . . . . . . . . . . . . . . 762
11.10.6 R Functions regIVcom, regIVcommcp, logIVcom, ts2str, and
sm2strv7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 767
11.11 Marginal Longitudinal Data Analysis: Comments on Comparing Groups . . 768
11.11.1 R Functions long2g, longreg, longreg.plot, and xyplot. . . . . . . . . . . . . . . 770
11.12 Exercises. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 771
Chapter 12: ANCOVA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 773
12.1 Methods Based on Specific Design Points and a Linear Model . . . . . . . . . . . . . 775
12.1.1 Method S1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 776
12.1.2 Method S2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 776
12.1.3 Linear Contrasts for a One-Way or Higher Design . . . . . . . . . . . . . . . . . . . 779
12.1.4 Dealing With Two or More Covariates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 780
12.1.5 R Functions ancJN, ancJNmp, ancJNmpcp, anclin, reg2plot,
reg2g.p2plot, and ancJN.LC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 781
12.2 Methods When There Is Curvature and a Single Covariate . . . . . . . . . . . . . . . . . . 784
12.2.1 Method Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 784
12.2.2 Method BB: Bootstrap Bagging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 787
12.2.3 Method UB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 788
12.2.4 Method TAP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 789
12.2.5 Method G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 790
12.2.6 A Method Based on Grids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 792
12.2.7 R Functions ancova, anc.ES.sum, anc.grid, anc.grid.bin,
anc.grid.cat, ancovaWMW, ancpb, rplot2g, runmean2g, lplot2g,
ancdifplot, ancboot, ancbbpb, qhdsm2g, ancovaUB, ancovaUB.pv,
ancdet, ancmg1, and ancGLOB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 792
12.3 Dealing With Two or More Covariates When There Is Curvature . . . . . . . . . . . 802
12.3.1 Method MC1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 802
12.3.2 Method MC2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 803
12.3.3 Methods MC3 and MC4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 805
12.3.4 R Functions ancovamp, ancovampG, ancmppb, ancmg, ancov2COV,
ancdes, ancdet2C, ancdetM4, and ancM.COV.ES . . . . . . . . . . . . . . . . . . . . 807
12.4 Some Global Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 815
12.4.1 Method TG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 815
12.4.2 R Functions ancsm and Qancsm. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 818
12.5 Methods for Dependent Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 819
12.5.1 Methods Based on a Linear Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 819
12.5.2 R Functions Dancts and Dancols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 820
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12.5.3
Dealing With Curvature: Methods DY, DUB, and DTAP and
a Method Based on Grids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 821
12.5.4 R Functions Dancova, Dancova.ES.sum, Dancovapb, DancovaUB,
Dancdet, Dancovamp, Danc.grid, and ancDEP.MULC.ES . . . . . . . . . . 822
12.6 Exercises. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 825
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 827
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 885
xxiii
Preface
There are many new and improved methods in this 5th edition. The R package written for
this book provides a crude indication of how much has been added. When the 4th edition was
published, it contained a little over 1200 R functions. With this 5th edition, there are now over
1700 R functions.
All of the chapters have been updated. For the first three chapters the changes deal with soft-
ware issues and some technical issues. Major changes begin in Chapter 4. One of the major
additions has to do with measuring effect size. Coverage of this topic has been expanded con-
siderably. For example, Chapter 5 now describes six robust measures of effect size when
comparing two independent groups. Confidence intervals for all six are returned by the R
function ES.summary.CI. Each provides a different perspective on how the groups compare.
When there is little or no difference between the groups, all six tend to give very similar re-
sults. But when the groups differ substantially there is a possibility that measures of effect
size can differ substantially. In effect, multiple measures of effect size can help provide a
deeper and more nuanced understanding of data, as illustrated in Section 5.3.5. Easy-to-use
R functions have been added for measuring effect size when dealing with multiple groups.
There have been advances even at the most basic level. Consider, for example, the goal of
computing a confidence interval for the probability of success when dealing with a binomial
distribution. There are now clearer guidelines on when it is advantageous to use the Schilling–
Doi method versus the Agresti–Coull method. When comparing two independent binomial
distributions, more recent results point to using a method derived by Kulinskaya et al. (2010).
A related issue is computing a confidence interval for the probability of success given the
value of a covariate. It is known that when this is done via a logistic regression model, a slight
departure from this model can yield inaccurate results. A method for dealing with this concern
is covered in Chapter 11.
New functions related to regression have been added that include robust methods for dealing
with multicollinearity and robust analogs of the lasso method. The coverage of classification
(machine learning) methods has been expanded. Included is a function making it a simple
matter to compare the false positive and false negative rates of a collection of techniques.
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Preface
There are new results on comparing measures of association as well as measures of varia-
tion. New techniques related to ANOVA-type methods are covered in Chapters 7 and 8 and
new ANCOVA techniques are covered in Chapter 12. A variety of new plots have been added
as well.
As was the case in previous editions, this book focuses on the practical aspects of modern,
robust statistical methods. The increased accuracy and power of modern methods, versus con-
ventional approaches to ANOVA and regression, is remarkable. Through a combination of
theoretical developments, improved and more flexible statistical methods, and the power of
the computer, it is now possible to address problems with standard methods that seemed in-
surmountable only a few years ago.
Consider classic, routinely taught and used methods for comparing groups based on means. A
basic issue is how well these methods perform when dealing with heteroscedasticity and non-
normal distributions. Based on a vast body of literature published over the last 60 years, the
situation can be briefly summarized as follows. When comparing groups that have identical
distributions, classic methods work well in terms of controlling the Type I error probability.
When distributions differ, they might continue to perform well, but under general conditions
they can yield inaccurate confidence intervals and have relatively poor power. Even a small
departure from a normal distribution can destroy power and yield measures of effect size, sug-
gesting a small effect when in fact for the bulk of the population there is a large effect. The
result is that important differences between groups are often missed, and the magnitude of
the difference is poorly characterized. Put another way, groups probably differ when null hy-
potheses are rejected with standard methods, but in many situations, standard methods are the
least likely to find a difference, and they offer a poor summary of how groups differ and the
magnitude of the difference. A related concern is that the population mean and variance are
not robust, roughly meaning that an arbitrarily small change in a distribution can have an in-
ordinate impact on their values. In particular, under arbitrarily small shifts from normality,
their values can be substantially altered and potentially misleading. For example, a small shift
toward a heavy-tailed distribution, roughly meaning a distribution that tends to generate out-
liers, can inflate the variance, resulting in low power. Thus, even with arbitrarily large sample
sizes, the sample mean and variance might provide an unsatisfactory summary of the data.
When dealing with regression, the situation is even worse. That is, there are even more ways
in which analyses, based on conventional assumptions, can be misleading. The very founda-
tion of standard regression methods, namely estimation via the least squares principle, leads
to practical problems, as do violations of other standard assumptions. For example, if the error
term in the standard linear model has a normal distribution, but is heteroscedastic, the least
squares estimator can be highly inefficient, and the conventional confidence interval for the
xxvi
Preface
regression parameters can be extremely inaccurate. Another concern is assuming that a lin-
ear model adequately models the association under study. It is well established that this is not
always the case. New advances aimed at dealing with this issue are described.
A seemingly natural way of justifying classic methods is to test assumptions, for example, test
the assumption that data are sampled from a normal distribution. But all indications are that
this strategy is unsatisfactory. Roughly, methods for testing assumptions can have inadequate
power to detect situations where it is beneficial to use a robust method instead.
In 1960, it was unclear how to formally develop solutions to the many problems that have
been identified. It was the theory of robustness developed by P. Huber and F. Hampel that
paved the road for finding practical solutions. Today, there are many asymptotically cor-
rect ways of substantially improving on standard ANOVA and regression methods. That is,
they converge to the correct answer as the sample sizes get large, but simulation studies have
shown that when sample sizes are small, not all methods should be used. Moreover, for many
methods, it remains unclear how large the sample sizes must be before reasonably accurate re-
sults are obtained. One of the goals in this book is to identify those methods that perform well
in simulation studies, as well as those that do not.
Although the goal is to focus on the applied aspects of robust methods, it is important to dis-
cuss the foundations of modern methods, which is done in Chapters 2 and 3, and to some
extent in Chapter 4. One general point is that modern methods have a solid mathematical
foundation. Another goal is to impart the general flavor and aims of robust methods. This is
important because misconceptions are rampant. For example, some individuals take the term
robust to mean that a method controls the Type I error probability. This is just one component
of modern robust methods.
A practical concern is applying the methods described in this book. To deal with this prob-
lem, easy-to-use R functions are supplied, many of which are not readily available when using
other software packages. The package of R functions written for this book can be obtained
as indicated in Section 1.8 of Chapter 1. With one command, all of the functions described
in this book become a part of your version of R. Illustrations, using these functions, are in-
cluded.
The book assumes that the reader has had an introductory statistics course. That is, all that
is required is some knowledge about the basics of ANOVA, hypothesis testing, and regres-
sion. The foundations of robust methods, described in Chapter 2, are written at a relatively
non-technical level, but the exposition is much more technical than the rest of the book, and it
might be too technical for some readers. It is recommended that Chapter 2 be read or at least
skimmed, but those who are willing to accept certain results can skip to Chapter 3. One of the
main points in Chapter 2 is that the robust measures of location and scale that are used are not
xxvii
Preface
arbitrary, but were chosen to satisfy specific criteria. Moreover, these criteria eliminate from
consideration the population mean, variance, and Pearson’s correlation.
From an applied point of view, Chapters 4–12, which include methods for addressing com-
mon problems in ANOVA and regression, form the heart of the book. Technical details are
kept to a minimum. The goal is to provide a simple description of the best methods available,
based on theoretical and simulation studies, and to provide advice on which methods to use.
Usually, no single method dominates all others, one reason being that there are multiple crite-
ria for judging a particular technique. Accordingly, the relative merits of the various methods
are discussed. Although no single method dominates, standard methods are typically the least
satisfactory, and many alternative methods can be eliminated.
Finally, the author would like to thank James Algina, Gui Bao, James Jaccard, H. Keselman,
Boaz Levy, J. Magadia, and Allan Campopiano for catching typos in earlier editions as well
as bugs in earlier versions of the R software. A special thanks goes to Patrick Mair and Fe-
lix Schönbrodt, whose efforts helped provide easy access to the R functions described in this
book.
Ancillary links:
Students can access accompanying information on the companion site located here:
https://www.elsevier.com/books-and-journals/book-companion/9780128200988
Registered instructors can request to access electronic review copies and teaching resources
here:
https://educate.elsevier.com/9780128200988
xxviii
CHAPTER 1
Introduction
Introductory statistics courses describe methods for computing confidence intervals and test-
ing hypotheses about means and regression parameters based on the assumption that observa-
tions are randomly sampled from normal distributions. When comparing independent groups,
standard methods also assume that groups have a common variance, even when the means are
unequal, and a similar homogeneity of variance assumption is made when testing hypotheses
about regression parameters. Currently, these methods form the backbone of most applied re-
search. There is, however, a serious practical problem: Many journal articles have illustrated
that these standard methods can be highly unsatisfactory. Often, the result is a poor under-
standing of how groups differ and the magnitude of the difference. Power can be relatively
low compared to recently developed methods, least squares regression and Pearson’s correla-
tion can yield a highly misleading summary of how two or more random variables are related,
the probability coverage of standard methods for computing confidence intervals can differ
substantially from the nominal value, and the usual sample variance can give a distorted view
of the amount of dispersion among a population of participants. Even the population mean, if
it could be determined exactly, can give a distorted view of what the typical participant is like.
Although the problems just described are well known in the statistics literature, many text-
books written for non-statisticians still claim that standard techniques are completely satis-
factory. Consequently, it is important to review the problems that can arise and why these
problems were missed for so many years. As will become evident, several pieces of misin-
formation have become part of statistical folklore, resulting in a false sense of security when
using standard statistical techniques. The remainder of this chapter focuses on some basic is-
sues related to assuming normality, as well as some basic issues associated with the classic
analysis of variance (ANOVA) test and least squares regression. But it is stressed that there
are additional issues that will be discussed in subsequent chapters. One appeal of modern
robust methods is that under general conditions they can have substantially higher power com-
pared to more traditional techniques. But from a broader perspective, the main message is that
a collection of new and improved methods is now available that provides a more accurate and
more nuanced understanding of data.
»Vai niin, ette siis ole vielä esiintynyt missään… Te haluatte ensi-
esiintymistä. Se onkin vaikeampaa. Missä olette opiskellut ja minkä
ohjelmiston olette valmistanut?»
»Salonkinaisen…»
Hän meni ovea kohden. »Vielä kerran, suokaa anteeksi, että olen
vaivannut… hyvästi!»
»Haen paikkaa.»
»Minkälaista?»
»Entä te, neiti Durand?» kysyi rouva Berg kääntyen nuoren melko
kiemailevan näköisen neidin puoleen. »Miksi tulette tänne? Ettekö
kenties ole tyytyväinen paikkaanne?»
»Miten hyvä te olette, rouva Berg! Minä tuon heti paperit. Hyvästi!»
»Opettajattaren?»
»En.»
»Hiukan böhminkieltä.»
»Oletteko musikaalinen?»
»Pianolla on nuotteja.»
»Miks'ette?»
»Oi, isäni on ollut rikas, mutta hän meni ensin konkurssiin ja kuoli
sittemmin. Hän oli Alsergrundin rikkaimpia lihakauppiaita. Ja teistä
minun tulisi ruveta palvelijattareksi?»
»Lopettakaa jo, sillä muuten kai sanotte, että sekin on liian hyvää
minulle. Kadun, että tulin ensinkään näin kurjaan toimistoon. Minun
olisi pitänyt suoraa päätä mennä rouva Reisnerin luo, jolla on hienoin
opettajatartoimisto Wienissä. Hyvästi!»
»Ymmärrän.»
Kreivitär nousi.
»Oh… I see.»