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“How and why is computational statistics taking over the world? In this serious work
of synthesis that is also fun to read, Efron and Hastie, two pioneers in the integration of
parametric and nonparametric statistical ideas, give their take on the unreasonable effec-
tiveness of statistics and machine learning in the context of a series of clear, historically
informed examples.”
— Andrew Gelman, Columbia University

“This unusual book describes the nature of statistics by displaying multiple examples
of the way the field has evolved over the past 60 years, as it has adapted to the rapid
increase in available computing power. The authors’ perspective is summarized nicely
when they say, ‘Very roughly speaking, algorithms are what statisticians do, while
inference says why they do them.’ The book explains this ‘why’; that is, it explains
the purpose and progress of statistical research, through a close look at many major
methods, methods the authors themselves have advanced and studied at great length.
Both enjoyable and enlightening, Computer Age Statistical Inference is written espe-
cially for those who want to hear the big ideas, and see them instantiated through the
essential mathematics that defines statistical analysis. It makes a great supplement to
the traditional curricula for beginning graduate students.”
— Rob Kass, Carnegie Mellon University

“This is a terrific book. It gives a clear, accessible, and entertaining account of the
interplay between theory and methodological development that has driven statistics in
the computer age. The authors succeed brilliantly in locating contemporary algorithmic
methodologies for analysis of ‘big data’ within the framework of established statistical
theory.”
— Alastair Young, Imperial College London

“This is a guided tour of modern statistics that emphasizes the conceptual and compu-
tational advances of the last century. Authored by two masters of the field, it offers just
the right mix of mathematical analysis and insightful commentary.”
— Hal Varian, Google

“Efron and Hastie guide us through the maze of breakthrough statistical methodologies
following the computing evolution: why they were developed, their properties, and how
they are used. Highlighting their origins, the book helps us understand each method’s
roles in inference and/or prediction. The inference–prediction distinction maintained
throughout the book is a welcome and important novelty in the landscape of statistics
books.”
— Galit Shmueli, National Tsing Hua University

“A masterful guide to how the inferential bases of classical statistics can provide a
principled disciplinary frame for the data science of the twenty-first century.”
— Stephen Stigler, University of Chicago, author of
Seven Pillars of Statistical Wisdom
“Computer Age Statistical Inference offers a refreshing view of modern statistics. Algo-
rithmics are put on equal footing with intuition, properties, and the abstract arguments
behind them. The methods covered are indispensable to practicing statistical analysts
in today’s big data and big computing landscape.”
— Robert Gramacy, The University of Chicago Booth School of Business

“Every aspiring data scientist should carefully study this book, use it as a reference, and
carry it with them everywhere. The presentation through the two-and-a-half-century
history of statistical inference provides insight into the development of the discipline,
putting data science in its historical place.”
— Mark Girolami, Imperial College London

“Efron and Hastie are two immensely talented and accomplished scholars who have
managed to brilliantly weave the fiber of 250 years of statistical inference into the more
recent historical mechanization of computing. This book provides the reader with a
mid-level overview of the last 60-some years by detailing the nuances of a statistical
community that, historically, has been self-segregated into camps of Bayes, frequentist,
and Fisher yet in more recent years has been unified by advances in computing. What is
left to be explored is the emergence of, and role that, big data theory will have in bridg-
ing the gap between data science and statistical methodology. Whatever the outcome,
the authors provide a vision of high-speed computing having tremendous potential to
enable the contributions of statistical inference toward methodologies that address both
global and societal issues.”
— Rebecca Doerge, Carnegie Mellon University

“In this book, two masters of modern statistics give an insightful tour of the intertwined
worlds of statistics and computation. Through a series of important topics, Efron and
Hastie illuminate how modern methods for predicting and understanding data are rooted
in both statistical and computational thinking. They show how the rise of computational
power has transformed traditional methods and questions, and how it has pointed us to
new ways of thinking about statistics.”
— David Blei, Columbia University

Absolutely brilliant. This beautifully written compendium reviews many big statistical
ideas, including the authors’ own. A must for anyone engaged creatively in statistics
and the data sciences, for repeated use. Efron and Hastie demonstrate the ever-growing
power of statistical reasoning, past, present, and future.
— Carl Morris, Harvard University
Computer Age Statistical Inference

The twenty-first century has seen a breathtaking expansion of statistical methodology,

both in scope and in influence. “Big data,” “data science,” and “machine learning” have
become familiar terms in the news, as statistical methods are brought to bear upon the
enormous data sets of modern science and commerce. How did we get here? And where
are we going?
This book takes us on an exhilarating journey through the revolution in data analy-
sis following the introduction of electronic computation in the 1950s. Beginning with
classical inferential theories – Bayesian, frequentist, Fisherian – individual chapters
take up a series of influential topics: survival analysis, logistic regression, empirical
Bayes, the jackknife and bootstrap, random forests, neural networks, Markov chain
Monte Carlo, inference after model selection, and dozens more. The distinctly modern
approach integrates methodology and algorithms with statistical inference. The book
ends with speculation on the future direction of statistics and data science.

B R A D L E Y E F R O N is Max H. Stein Professor, Professor of Statistics, and Professor of

Biomedical Data Science at Stanford University. He has held visiting faculty appoint-
ments at Harvard, UC Berkeley, and Imperial College London. Efron has worked
extensively on theories of statistical inference, and is the inventor of the bootstrap sam-
pling technique. He received the National Medal of Science in 2005 and the Guy Medal
in Gold of the Royal Statistical Society in 2014.
T R E V O R H A S T I E is John A. Overdeck Professor, Professor of Statistics, and Profes-
sor of Biomedical Data Science at Stanford University. He is coauthor of Elements of
Statistical Learning, a key text in the field of modern data analysis. He is also known for
his work on generalized additive models and principal curves, and for his contributions
to the R computing environment. Hastie was awarded the Emmanuel and Carol Parzen
prize for Statistical Innovation in 2014.
 I N S T I T U T E O F M AT H E M AT I C A L S TAT I S T I C S
MONOGRAPHS

Editorial Board
D. R. Cox (University of Oxford)
B. Hambly (University of Oxford)
S. Holmes (Stanford University)
J. Wellner (University of Washington)

IMS Monographs are concise research monographs of high quality on any branch of
statistics or probability of sufficient interest to warrant publication as books. Some
concern relatively traditional topics in need of up-to-date assessment. Others are on
emerging themes. In all cases the objective is to provide a balanced view of the field.

Other Books in the Series

1. Large-Scale Inference, by Bradley Efron

2. Nonparametric Inference on Manifolds, by Abhishek Bhattacharya and Rabi
Battacharya
3. The Skew-Normal and Related Families, by Adelchi Azzalini
4. Case-Control Studies, by Ruth H. Keogh and D. R. Cox
5. Computer Age Statistical Inference, by Bradley Efron and Trevor Hastie
Computer Age Statistical Inference
Algorithms, Evidence, and Data Science

B R A D L E Y E F RO N
Stanford University, California

T R E VO R H A S T I E
Stanford University, California
 32 Avenue of the Americas, New York NY 10013-2473, USA

Cambridge University Press is part of the University of Cambridge.

It furthers the University’s mission by disseminating knowledge in the pursuit of
education, learning and research at the highest international levels of excellence.

www.cambridge.org
Information on this title: www.cambridge.org/9781107149892

c Bradley Efron and Trevor Hastie 2016
This publication is in copyright. Subject to statutory exception
and to the provisions of relevant collective licensing agreements,
no reproduction of any part may take place without the written
permission of Cambridge University Press.
First published 2016
Printed in the United Kingdom by Clays, St Ives plc
A catalogue record for this publication is available from the British Library
ISBN 978-1-107-14989-2 Hardback
Cambridge University Press has no responsibility for the persistence or accuracy of
URLs for external or third-party internet websites referred to in this publication,
and does not guarantee that any content on such websites is, or will remain,
accurate or appropriate.
To Donna and Lynda
 Contents

Preface xv
Acknowledgments xviii
Notation xix

Part I Classic Statistical Inference 1

1 Algorithms and Inference 3

1.1 A Regression Example 4
1.2 Hypothesis Testing 8
1.3 Notes 11

2 Frequentist Inference 12
2.1 Frequentism in Practice 14
2.2 Frequentist Optimality 18
2.3 Notes and Details 20

3 Bayesian Inference 22
3.1 Two Examples 24
3.2 Uninformative Prior Distributions 28
3.3 Flaws in Frequentist Inference 30
3.4 A Bayesian/Frequentist Comparison List 33
3.5 Notes and Details 36

4 Fisherian Inference and Maximum Likelihood Estimation 38

4.1 Likelihood and Maximum Likelihood 38
4.2 Fisher Information and the MLE 41
4.3 Conditional Inference 45
4.4 Permutation and Randomization 49
4.5 Notes and Details 51

5 Parametric Models and Exponential Families 53

ix
x Contents

5.1 Univariate Families 54

5.2 The Multivariate Normal Distribution 55
5.3 Fisher’s Information Bound for Multiparameter Families 59
5.4 The Multinomial Distribution 61
5.5 Exponential Families 64
5.6 Notes and Details 69

Part II Early Computer-Age Methods 73

6 Empirical Bayes 75
6.1 Robbins’ Formula 75
6.2 The Missing-Species Problem 78
6.3 A Medical Example 84
6.4 Indirect Evidence 1 88
6.5 Notes and Details 88

7 James–Stein Estimation and Ridge Regression 91

7.1 The James–Stein Estimator 91
7.2 The Baseball Players 94
7.3 Ridge Regression 97
7.4 Indirect Evidence 2 102
7.5 Notes and Details 104

8 Generalized Linear Models and Regression Trees 108

8.1 Logistic Regression 109
8.2 Generalized Linear Models 116
8.3 Poisson Regression 120
8.4 Regression Trees 124
8.5 Notes and Details 128

9 Survival Analysis and the EM Algorithm 131

9.1 Life Tables and Hazard Rates 131
9.2 Censored Data and the Kaplan–Meier Estimate 134
9.3 The Log-Rank Test 139
9.4 The Proportional Hazards Model 143
9.5 Missing Data and the EM Algorithm 146
9.6 Notes and Details 150

10 The Jackknife and the Bootstrap 155

10.1 The Jackknife Estimate of Standard Error 156
10.2 The Nonparametric Bootstrap 159
10.3 Resampling Plans 162
 Contents xi

10.4 The Parametric Bootstrap 169

10.5 Influence Functions and Robust Estimation 174
10.6 Notes and Details 177

11 Bootstrap Confidence Intervals 181

11.1 Neyman’s Construction for One-Parameter Problems 181
11.2 The Percentile Method 185
11.3 Bias-Corrected Confidence Intervals 190
11.4 Second-Order Accuracy 192
11.5 Bootstrap-t Intervals 195
11.6 Objective Bayes Intervals and the Confidence Distribution 198
11.7 Notes and Details 204

12 Cross-Validation and Cp Estimates of Prediction Error 208

12.1 Prediction Rules 208
12.2 Cross-Validation 213
12.3 Covariance Penalties 218
12.4 Training, Validation, and Ephemeral Predictors 227
12.5 Notes and Details 230

13 Objective Bayes Inference and MCMC 233

13.1 Objective Prior Distributions 234
13.2 Conjugate Prior Distributions 237
13.3 Model Selection and the Bayesian Information Criterion 243
13.4 Gibbs Sampling and MCMC 251
13.5 Example: Modeling Population Admixture 256
13.6 Notes and Details 261

14 Postwar Statistical Inference and Methodology 264

Part III Twenty-First-Century Topics 269

15 Large-Scale Hypothesis Testing and FDRs 271

15.1 Large-Scale Testing 272
15.2 False-Discovery Rates 275
15.3 Empirical Bayes Large-Scale Testing 278
15.4 Local False-Discovery Rates 282
15.5 Choice of the Null Distribution 286
15.6 Relevance 290
15.7 Notes and Details 294

16 Sparse Modeling and the Lasso 298

xii Contents

16.1 Forward Stepwise Regression 299

16.2 The Lasso 303
16.3 Fitting Lasso Models 308
16.4 Least-Angle Regression 309
16.5 Fitting Generalized Lasso Models 313
16.6 Post-Selection Inference for the Lasso 317
16.7 Connections and Extensions 319
16.8 Notes and Details 321

17 Random Forests and Boosting 324

17.1 Random Forests 325
17.2 Boosting with Squared-Error Loss 333
17.3 Gradient Boosting 338
17.4 Adaboost: the Original Boosting Algorithm 341
17.5 Connections and Extensions 345
17.6 Notes and Details 347

18 Neural Networks and Deep Learning 351

18.1 Neural Networks and the Handwritten Digit Problem 353
18.2 Fitting a Neural Network 356
18.3 Autoencoders 362
18.4 Deep Learning 364
18.5 Learning a Deep Network 368
18.6 Notes and Details 371

19 Support-Vector Machines and Kernel Methods 375

19.1 Optimal Separating Hyperplane 376
19.2 Soft-Margin Classifier 378
19.3 SVM Criterion as Loss Plus Penalty 379
19.4 Computations and the Kernel Trick 381
19.5 Function Fitting Using Kernels 384
19.6 Example: String Kernels for Protein Classification 385
19.7 SVMs: Concluding Remarks 387
19.8 Kernel Smoothing and Local Regression 387
19.9 Notes and Details 390

20 Inference After Model Selection 394

20.1 Simultaneous Confidence Intervals 395
20.2 Accuracy After Model Selection 402
20.3 Selection Bias 408
20.4 Combined Bayes–Frequentist Estimation 412
20.5 Notes and Details 417
 Contents xiii

21 Empirical Bayes Estimation Strategies 421

21.1 Bayes Deconvolution 421
21.2 g-Modeling and Estimation 424
21.3 Likelihood, Regularization, and Accuracy 427
21.4 Two Examples 432
21.5 Generalized Linear Mixed Models 437
21.6 Deconvolution and f -Modeling 440
21.7 Notes and Details 444

Epilogue 446
References 453
Author Index 463
Subject Index 467
 Preface

Statistical inference is an unusually wide-ranging discipline, located as it is

at the triple-point of mathematics, empirical science, and philosophy. The
discipline can be said to date from 1763, with the publication of Bayes’
rule (representing the philosophical side of the subject; the rule’s early ad-
vocates considered it an argument for the existence of God). The most re-
cent quarter of this 250-year history—from the 1950s to the present—is
the “computer age” of our book’s title, the time when computation, the tra-
ditional bottleneck of statistical applications, became faster and easier by a
factor of a million.
The book is an examination of how statistics has evolved over the past
sixty years—an aerial view of a vast subject, but seen from the height of a
small plane, not a jetliner or satellite. The individual chapters take up a se-
ries of influential topics—generalized linear models, survival analysis, the
jackknife and bootstrap, false-discovery rates, empirical Bayes, MCMC,
neural nets, and a dozen more—describing for each the key methodologi-
cal developments and their inferential justification.
Needless to say, the role of electronic computation is central to our
story. This doesn’t mean that every advance was computer-related. A land
bridge had opened to a new continent but not all were eager to cross.
Topics such as empirical Bayes and James–Stein estimation could have
emerged just as well under the constraints of mechanical computation. Oth-
ers, like the bootstrap and proportional hazards, were pureborn children of
the computer age. Almost all topics in twenty-first-century statistics are
now computer-dependent, but it will take our small plane a while to reach
the new millennium.
Dictionary definitions of statistical inference tend to equate it with the
entire discipline. This has become less satisfactory in the “big data” era of
immense computer-based processing algorithms. Here we will attempt, not
always consistently, to separate the two aspects of the statistical enterprise:
algorithmic developments aimed at specific problem areas, for instance

xv
xvi Preface

random forests for prediction, as distinct from the inferential arguments

offered in their support.
Very broadly speaking, algorithms are what statisticians do while infer-
ence says why they do them. A particularly energetic brand of the statisti-
cal enterprise has flourished in the new century, data science, emphasizing
algorithmic thinking rather than its inferential justification. The later chap-
ters of our book, where large-scale prediction algorithms such as boosting
and deep learning are examined, illustrate the data-science point of view.
(See the epilogue for a little more on the sometimes fraught statistics/data
science marriage.)
There are no such subjects as Biological Inference or Astronomical In-
ference or Geological Inference. Why do we need “Statistical Inference”?
The answer is simple: the natural sciences have nature to judge the ac-
curacy of their ideas. Statistics operates one step back from Nature, most
often interpreting the observations of natural scientists. Without Nature to
serve as a disinterested referee, we need a system of mathematical logic for
guidance and correction. Statistical inference is that system, distilled from
two and a half centuries of data-analytic experience.
The book proceeds historically, in three parts. The great themes of clas-
sical inference, Bayesian, frequentist, and Fisherian, reviewed in Part I,
were set in place before the age of electronic computation. Modern practice
has vastly extended their reach without changing the basic outlines. (An
analogy with classical and modern literature might be made.) Part II con-
cerns early computer-age developments, from the 1950s through the 1990s.
As a transitional period, this is the time when it is easiest to see the ef-
fects, or noneffects, of fast computation on the progress of statistical meth-
odology, both in its theory and practice. Part III, “Twenty-First-Century
topics,” brings the story up to the present. Ours is a time of enormously
ambitious algorithms (“machine learning” being the somewhat disquieting
catchphrase). Their justification is the ongoing task of modern statistical
inference.
Neither a catalog nor an encyclopedia, the book’s topics were chosen as
apt illustrations of the interplay between computational methodology and
inferential theory. Some missing topics that might have served just as well
include time series, general estimating equations, causal inference, graph-
ical models, and experimental design. In any case, there is no implication
that the topics presented here are the only ones worthy of discussion.
Also underrepresented are asymptotics and decision theory, the “math
stat” side of the field. Our intention was to maintain a technical level of
discussion appropriate to Masters’-level statisticians or first-year PhD stu-
 Preface xvii

dents. Inevitably, some of the presentation drifts into more difficult waters,
more from the nature of the statistical ideas than the mathematics. Readers
who find our aerial view circling too long over some topic shouldn’t hesi-
tate to move ahead in the book. For the most part, the chapters can be read
independently of each other (though there is a connecting overall theme).
This comment applies especially to nonstatisticians who have picked up
the book because of interest in some particular topic, say survival analysis
or boosting.
Useful disciplines that serve a wide variety of demanding clients run
the risk of losing their center. Statistics has managed, for the most part,
to maintain its philosophical cohesion despite a rising curve of outside de-
mand. The center of the field has in fact moved in the past sixty years, from
its traditional home in mathematics and logic toward a more computational
focus. Our book traces that movement on a topic-by-topic basis. An answer
to the intriguing question “What happens next?” won’t be attempted here,
except for a few words in the epilogue, where the rise of data science is
discussed.
 Acknowledgments

We are indebted to Cindy Kirby for her skillful work in the preparation of
this book, and Galit Shmueli for her helpful comments on an earlier draft.
At Cambridge University Press, a huge thank you to Steven Holt for his ex-
cellent copy editing, Clare Dennison for guiding us through the production
phase, and to Diana Gillooly, our editor, for her unfailing support.

Bradley Efron
Trevor Hastie
Department of Statistics
Stanford University
May 2016

xviii
 xix

Notation
Throughout the book the numbered  sign indicates a technical note or
reference element which is elaborated on at the end of the chapter. There,
next to the number, the page number of the referenced location is given in
parenthesis. For example, lowess in the notes on page 11 was referenced
via a 1 on page 6. Matrices such as † are represented in bold font, as
are certain vectors such as y, a data vector with n elements. Most other
vectors, such as coefficient vectors, are typically not bold. We use a dark
green typewriter font to indicate data set names such as prostate,
variable names such as prog from data sets, and R commands such as
glmnet or locfdr. No bibliographic references are given in the body of
the text; important references are given in the endnotes of each chapter.
 Part I

Classic Statistical Inference

 1

Algorithms and Inference

Statistics is the science of learning from experience, particularly experi-

ence that arrives a little bit at a time: the successes and failures of a new
experimental drug, the uncertain measurements of an asteroid’s path to-
ward Earth. It may seem surprising that any one theory can cover such an
amorphous target as “learning from experience.” In fact, there are two main
statistical theories, Bayesianism and frequentism, whose connections and
disagreements animate many of the succeeding chapters.
First, however, we want to discuss a less philosophical, more operational
division of labor that applies to both theories: between the algorithmic and
inferential aspects of statistical analysis. The distinction begins with the
most basic, and most popular, statistical method, averaging. Suppose we
have observed numbers x1 ; x2 ; : : : ; xn applying to some phenomenon of
interest, perhaps the automobile accident rates in the n D 50 states. The
mean
Xn
xN D xi =n (1.1)
iD1

summarizes the results in a single number.

How accurate is that number? The textbook answer is given in terms of
the standard error,
" n #1=2
X 2
ı
sbe D .xi  x/
N .n.n  1// : (1.2)
iD1

Here averaging (1.1) is the algorithm, while the standard error provides an
inference of the algorithm’s accuracy. It is a surprising, and crucial, aspect
of statistical theory that the same data that supplies an estimate can also
assess its accuracy.1
1
“Inference” concerns more than accuracy: speaking broadly, algorithms say what the
statistician does while inference says why he or she does it.

3
4 Algorithms and Inference

Of course, sbe (1.2) is itself an algorithm, which could be (and is) subject
to further inferential analysis concerning its accuracy. The point is that
the algorithm comes first and the inference follows at a second level of
statistical consideration. In practice this means that algorithmic invention
is a more free-wheeling and adventurous enterprise, with inference playing
catch-up as it strives to assess the accuracy, good or bad, of some hot new
algorithmic methodology.
If the inference/algorithm race is a tortoise-and-hare affair, then modern
electronic computation has bred a bionic hare. There are two effects at work
here: computer-based technology allows scientists to collect enormous data
sets, orders of magnitude larger than those that classic statistical theory
was designed to deal with; huge data demands new methodology, and the
demand is being met by a burst of innovative computer-based statistical
algorithms. When one reads of “big data” in the news, it is usually these
algorithms playing the starring roles.
Our book’s title, Computer Age Statistical Inference, emphasizes the tor-
toise’s side of the story. The past few decades have been a golden age of
statistical methodology. It hasn’t been, quite, a golden age for statistical
inference, but it has not been a dark age either. The efflorescence of am-
bitious new algorithms has forced an evolution (though not a revolution)
in inference, the theories by which statisticians choose among competing
methods. The book traces the interplay between methodology and infer-
ence as it has developed since the 1950s, the beginning of our discipline’s
computer age. As a preview, we end this chapter with two examples illus-
trating the transition from classic to computer-age practice.

1.1 A Regression Example

Figure 1.1 concerns a study of kidney function. Data points .xi ; yi / have
been observed for n D 157 healthy volunteers, with xi the i th volunteer’s
age in years, and yi a composite measure “tot” of overall function. Kid-
ney function generally declines with age, as evident in the downward scat-
ter of the points. The rate of decline is an important question in kidney
transplantation: in the past, potential donors past age 60 were prohibited,
though, given a shortage of donors, this is no longer enforced.
The solid line in Figure 1.1 is a linear regression

y D ˇO0 C ˇO1 x (1.3)

fit to the data by least squares, that is by minimizing the sum of squared

 1.1 A Regression Example 5

* *
4 * *
* ** * *
* * *
* * *
* * * *** * *
* **
2

* * * *
* * *
* * * * * * * ** *
* * * * * ** * * * *
* * ** *
*********** * *
0

**** * * * * * *
tot

* ** * ** * * **
** * * **
* * * ** * * * * * * * *
* * * * * * *
−2

** * * * *
* * **
* * * * *
* *
* * *
−4

*
*
* * *
*
−6

*
20 30 40 50 60 70 80 90

age

Figure 1.1 Kidney fitness tot vs age for 157 volunteers. The
line is a linear regression fit, showing ˙2 standard errors at
selected values of age.

deviations
n
X
.yi  ˇ0  ˇ1 xi /2 (1.4)
i D1

over all choices of .ˇ0 ; ˇ1 /. The least squares algorithm, which dates back
to Gauss and Legendre in the early 1800s, gives ˇO0 D 2:86 and ˇO1 D
0:079 as the least squares estimates. We can read off of the fitted line
an estimated value of kidney fitness for any chosen age. The top line of
Table 1.1 shows estimate 1.29 at age 20, down to 3:43 at age 80.
How accurate are these estimates? This is where inference comes in:
an extended version of formula (1.2), also going back to the 1800s, pro-
vides the standard errors, shown in line 2 of the table. The vertical bars in
Figure 1.1 are ˙ two standard errors, giving them about 95% chance of
containing the true expected value of tot at each age.
That 95% coverage depends on the validity of the linear regression model
(1.3). We might instead try a quadratic regression y D ˇO0 C ˇO1 x C ˇO2 x 2 ,
or a cubic, etc., all of this being well within the reach of pre-computer
statistical theory.
 6 Algorithms and Inference

Table 1.1 Regression analysis of the kidney data; (1) linear regression
estimates; (2) their standard errors; (3) lowess estimates; (4) their
bootstrap standard errors.

age 20 30 40 50 60 70 80
1. linear regression 1.29 .50 .28 1.07 1.86 2.64 3.43
2. std error .21 .15 .15 .19 .26 .34 .42

3. lowess 1.66 .65 .59 1.27 1.91 2.68 3.50

4. bootstrap std error .71 .23 .31 .32 .37 .47 .70

* *
* *
4

* ** * *
* *
* ** * ** *
*
* * * *
* **
2

* *
* * * ** * * * ** ** ** *
* * * * * ** * * * *
* * ** *
*********** * *
0

* * * * * *
* * *** ** *
tot

* * **
* * * * ** * * * * **
* ** *** * * *
* * * * * * *
−2

** * * * *
* * **
* * * * *
*
* * * *
−4

*
*
* * *
*
−6

*
20 30 40 50 60 70 80 90

age

Figure 1.2 Local polynomial lowess(x,y,1/3) fit to the

kidney-fitness data, with ˙2 bootstrap standard deviations.

A modern computer-based algorithm lowess produced the somewhat

1 bumpy regression curve in Figure 1.2. The lowess  2 algorithm moves
its attention along the x-axis, fitting local polynomial curves of differing
degrees to nearby .x; y/ points. (The 1/3 in the call3 lowess(x,y,1/3)
2
Here and throughout the book, the numbered  sign indicates a technical note or
reference element which is elaborated on at the end of the chapter.
3
Here and in all our examples we are employing the language R, itself one of the key
developments in computer-based statistical methodology.
 1.1 A Regression Example 7

determines the definition of local.) Repeated passes over the x-axis refine
the fit, reducing the effects of occasional anomalous points. The fitted curve
in Figure 1.2 is nearly linear at the right, but more complicated at the left
where points are more densely packed. It is flat between ages 25 and 35,
a potentially important difference from the uniform decline portrayed in
Figure 1.1.
There is no formula such as (1.2) to infer the accuracy of the lowess
curve. Instead, a computer-intensive inferential engine, the bootstrap, was
used to calculate the error bars in Figure 1.2. A bootstrap data set is pro-
duced by resampling 157 pairs .xi ; yi / from the original 157 with replace-
ment, so perhaps .x1 ; y1 / might show up twice in the bootstrap sample,
.x2 ; y2 / might be missing, .x3 ; y3 / present once, etc. Applying lowess
to the bootstrap sample generates a bootstrap replication of the original
calculation.
4
2
0
tot
−2
−4

20 30 40 50 60 70 80 90

age

Figure 1.3 25 bootstrap replications of lowess(x,y,1/3).

Figure 1.3 shows the first 25 (of 250) bootstrap lowess replications
bouncing around the original curve from Figure 1.2. The variability of the
replications at any one age, the bootstrap standard deviation, determined
the original curve’s accuracy. How and why the bootstrap works is dis-
cussed in Chapter 10. It has the great virtue of assessing estimation accu-
8 Algorithms and Inference

racy for any algorithm, no matter how complicated. The price is a hundred-
or thousand-fold increase in computation, unthinkable in 1930, but routine
now.
The bottom two lines of Table 1.1 show the lowess estimates and
their standard errors. We have paid a price for the increased flexibility of
lowess, its standard errors roughly doubling those for linear regression.

1.2 Hypothesis Testing

Our second example concerns the march of methodology and inference
for hypothesis testing rather than estimation: 72 leukemia patients, 45 with
ALL (acute lymphoblastic leukemia) and 27 with AML (acute myeloid leuk-
emia, a worse prognosis) have each had genetic activity measured for a
panel of 7,128 genes. The histograms in Figure 1.4 compare the genetic
activities in the two groups for gene 136.
8 10
6
4
2
0

0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6

ALL scores − mean .752

8 10
6
4
2
0

0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6

AML scores − mean .950

Figure 1.4 Scores for gene 136, leukemia data. Top ALL
(n D 47), bottom AML (n D 25). A two-sample t -statistic D 3:01
with p-value D :0036.

The AML group appears to show greater activity, the mean values being
ALL D 0:752 and AML D 0:950: (1.5)
 1.2 Hypothesis Testing 9

Is the perceived difference genuine, or perhaps, as people like to say, “a

statistical fluke”? The classic answer to this question is via a two-sample
t-statistic,
AML  ALL
tD ; (1.6)
b
sd
where sd b is an estimate of the numerator’s standard deviation.4
Dividing by sd b allows us (under Gaussian assumptions discussed in
Chapter 5) to compare the observed value of t with a standard “null” dis-
tribution, in this case a Student’s t distribution with 70 degrees of freedom.
We obtain t D 3:01 from (1.6), which would classically be considered very
strong evidence that the apparent difference (1.5) is genuine; in standard
terminology, “with two-sided significance level 0.0036.”
A small significance level (or “p-value”) is a statement of statistical sur-
prise: something very unusual has happened if in fact there is no difference
in gene 136 expression levels between ALL and AML patients. We are less
surprised by t D 3:01 if gene 136 is just one candidate out of thousands
that might have produced “interesting” results.
That is the case here. Figure 1.5 shows the histogram of the two-sample
t -statistics for the panel of 7128 genes. Now t D 3:01 looks less unusual;
400 other genes have t exceeding 3.01, about 5.6% of them.
This doesn’t mean that gene 136 is “significant at the 0.056 level.” There
are two powerful complicating factors:

1 Large numbers of candidates, 7128 here, will produce some large t -

values even if there is really no difference in genetic expression between
ALL and AML patients.
2 The histogram implies that in this study there is something wrong with
the theoretical null distribution (“Student’s t with 70 degrees of free-
dom”), the smooth curve in Figure 1.5. It is much too narrow at the
center, where presumably most of the genes are reporting unsignificant
results.

We will see in Chapter 15 that a low false-discovery rate, i.e., a low

chance of crying wolf over an innocuous gene, requires t exceeding 6.16
in the ALL/AML study. Only 47 of the 7128 genes make the cut. False-
discovery-rate theory is an impressive advance in statistical inference, in-
corporating Bayesian, frequentist, and empirical Bayesian (Chapter 6) el-
4 b might
Formally, a standard error is the standard deviation of a summary statistic, and sd
better be called sbe, but we will follow the distinction less than punctiliously here.
Another random document with
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"Here, Jack," said the mate, as he took the glass from the steward,
and filled it two thirds full of the reddish poison.
"Not any for me, thank your honor," replied Jack, to my
astonishment.
"What!" exclaimed the mate.
"None for me, sir."
"Don't you drink liquor?"
"Yes, sir; when I'm on shore I do; but I never was in the habit of
drinking it on board ship."
The mate looked very ugly.
"Here, Baxter," he added, turning to the next man.
"None for me, sir."
I was amazed at the self-denial and firmness of these men. The
others followed their example; not one of them would take the grog.
They understood that it was a bribe—that it was used to induce them
to comply with the new order of events. At that moment I felt that the
Michigan would not bear a cargo of shackled human beings over the
ocean, to be sold into bondage in Cuba or the Southern States. The
grog was served out to the rest of the crew, who did not refuse it.
"I suppose we are to understand that the bark is bound down the
coast of Africa, slaving," continued Jack, when the mate came aft
again.
"You can understand what you please," growled Waterford,
savagely; for his good humor had failed him with the defeat of his
scheme to win over the men.
"We are sorry for it, your honor, because we shipped for Palermo."
"Go forward, every one of you!" roared the mate.
"If this isn't a lawful voyage, Mr. Waterford—"
"Do you hear me?"
"We do, sir. We shipped for a lawful voyage, and—"
"Do you mean to get up a mutiny? Go forward, and attend to your
duty, or I'll put every mother's son of you in irons."
"If you say we are not going a slaving, we shall be satisfied."
"I won't say anything to you," said the mate, picking up a belaying-
pin.
The two passengers went below; but they immediately appeared
again with revolvers in their hands. Captain Farraday picked up a
handspike, and placed himself by the mate. At the same time the five
Spanish and Portuguese sailors came aft, each of them armed with
a handspike or some other weapon. The affair began to look serious
to us, who were provided with nothing to defend ourselves with.
"My men, this is mutiny," interposed Captain Farraday.
"We have a right to know whether this is a lawful voyage or not," said
Baxter.
"You will obey your officers, whether the voyage is lawful or not,"
added the captain.
"I'm not going to parley with mutineers," said Waterford, sternly, as
he moved forward towards us.
The two passengers cocked their pistols, and the five sailors who
were in the plot closed in before us. We were unprepared for a fight,
and we retreated in a body to the forecastle.
 CHAPTER XIV.
IN WHICH PHIL SPEAKS FOR TRUTH AND
JUSTICE, AND A SAIL IS DISCOVERED.
We had not gone aft to fight, only to talk; and we were not prepared
for the violent demonstration which was made against us. We
intended, after the fashion of sailors, to present our grievances, and
have an understanding in regard to the future. The seamen of our
party had refused to accept any liquor simply because it was offered
to them as the price of yielding to the wicked scheme of the officers.
This marvellous piece of self-denial on their part assured me that we
should be successful in the end. I had more respect for the virtue of
sailors than ever before; certainly more than when I first came on
board of the bark, and saw every man of the present crew drunk and
quarrelsome.
We were driven forward by the onslaught of the mate and his
supporters, and we halted forward of the windlass only when we
could go no farther. There was a plentiful supply of handspikes on the
forecastle; but, as the mate halted before we were compelled to
defend ourselves, no battle ensued.
"Now, my lads, I have you where I want you," said Waterford, casting
a triumphant glance over our party.
"We haven't tried to make any trouble, and we were respectful,"
replied Sanderson.
"I want you to understand that I call this mutiny, and I shall treat it as
such!" cried the mate, savagely. "I ordered you forward, and you
didn't go, till you were driven."
"When the ship is not on a lawful voyage, there's no such thing as
mutiny," said Baxter, boldly.
"I'll show you that there is," answered Waterford, shaking his weapon
at the discontented ones. "If you want to have trouble, we'll give you
enough of it."
"We don't want any trouble," added the more prudent Sanderson.
"All right, then; return to your duty. Obey your orders, and do your
work, and there will be no trouble. If you don't do it, I'll skin you alive,
every one of you!"
"We shipped for Palermo, sir; and, if we are not going there, we think
we have a right to know where we are going."
"You shipped for any port to which the vessel might go," added the
mate, doggedly.
"Will you tell us where we are bound, sir?"
"No; I will not be driven to tell you anything. In due time, if you behave
yourselves, I'll tell you all about it."
"Will you tell us whether we are engaged in a lawful voyage?"
"I tell you that every man who behaves himself shall have a thousand
dollars when the cruise is up, and have his grog three times a day,
and plum duff every day."
"That is just the same as saying that it is not a lawful voyage," I
added, in a low tone, to Sanderson.
"That's so, my hearty."
"Come out here, Phil Farringford!" shouted the mate. "You have made
all this trouble."
"No, he didn't, sir," replied Jack Sanderson. "One's as black as
another."
"Come out here, Phil! I'll teach you to get up a mutiny among the
men."
The mate made a demonstration forward, as though he intended to
drag me out from the midst of my companions. Probably he had
seen, and perhaps heard, my communications with the spokesman,
and his wrath against me was fanned into a blaze.
"Don't you go, Phil; we will stand by you," said Baxter.

The Crew stand by Phil.

"You will?" roared the mate.

"We are all in the same boat, sir."
"You would all have done very well, if his cant hadn't spoiled you. I
know him, and I'll put him in irons. Shove him out here and I will pass
over what you have done."
"No, sir; we won't give him up," answered Sanderson, decidedly.
"Then you will take the consequences."
"We are willing, sir."
The mate rolled up his sleeves, and glanced at his supporters, as
though he intended to make an assault upon the refractory crew; but
at this moment the captain and the two passengers spoke to him, and
they went aft together.
"We are in for it now, my lads," said old Jack Sanderson.
"We might as well be hung for a bull as a calf," added Baxter.
"If I'm the calf, I don't want you to get into trouble on my account," I
added.
"Phil's a good fellow, and we'll stand by him," replied Baxter.
"Ay, ay! stand by him," said half a dozen others.
"I say I don't want you to get yourselves into trouble for my sake; but I
would rather be hanged for mutiny than be hanged for being
concerned in the slave trade. It's piracy, you know, and there is no
law that can compel you to do duty in a vessel engaged in an illegal
voyage."
"That's so; Phil's a sea lawyer," said Walker.
"We won't let him have Phil," echoed Baxter, "or any other man. We'll
stick together, and go down together, if we can't get out of the
scrape."
"But what can we do?" asked one of the more timid of the men.
"We can only refuse to do duty, and take the consequences."
"I, for one, don't propose to take the consequences," I ventured to
say; for, though I had not said much thus far, I was decidedly in favor
of an aggressive policy.
"What do you think we ought to do?" demanded Baxter.
"Take the bark!" I replied emphatically, when I had satisfied myself
that no one was within hearing except our own party.
"That's just my idea," responded Baxter, bringing his fist down upon
the windlass to prove that he was in earnest. "I don't know what there
is in the hold, but I'll bet there is everything used in the slave trade—
the rice, the water, and the irons. If we should be overhauled by a
British or an American vessel, we should be captured, and sent into
an English or a United States port. If we are not hung, we shall lose
our wages, and be sent to prison."
"That's it!" exclaimed Sanderson.
"Our papers show that we are bound for Palermo, and they would
condemn us, if the stuff in the hold didn't. I'll never help carry a nigger
across the ocean, if I can help it, and I'll fight an honest fight, too, to
keep from doing it. I don't believe in fastening the door with a biled
parsnip."
Baxter was earnest and eloquent, and I honored him for his noble
and humane sentiments. His speech stiffened the backs of those who
were wavering. Twelve of us were of one mind, and we were sure
that York, the second mate, was with us, which made a majority.
Three of the crew still remained doubtful, ready to go with whichever
proved to be the winning side. Their very position showed them to be
weak, and of not much value to either party.
"We are all of one mind," said Sanderson; "but what can we do? It
isn't an easy thing to stand up against the officers, who are provided
with fire-arms."
"Never mind their fire-arms. Truth and justice are on our side, and
they will do us more good than all the guns and pistols that were ever
invented."
"That's all very pretty, but it don't always work so."
"We'll make it work so this time," said Baxter, stoutly. "It's no use to
refuse to do duty, and make a milk-and-water mess of it. When we do
something, we'll strike a blow that shall be felt."
"How are you going to do it?" asked Bilger, who was one of the timid
ones.
"We haven't decided that question yet; but where there's a will there's
a way. In the first place, we must stick together," replied Baxter. "We
will make a plan, and then we will put it through."
"Suppose we take the vessel; what can we do with it? We haven't a
navigator among us," suggested Walker.
"I can take an observation, and work up the reckoning," I replied.
"You!" exclaimed the doubter.
"I can. I have studied navigation, and I can lay down the position of
the bark on the chart every day that the sun shines."
"Good! York is a good sailor. In fact we have all the able and ordinary
seamen with us but the five Spaniards and Portuguese," said Baxter.
"But how shall we take the bark?"
"We'll watch our time, and strike when it comes. You have done some
fighting in your day, Phil; what do you say?"
"I never did any fighting on board of a ship, though I know something
about Indian strategy."
"It's all the same. How shall we go to work to make a sure thing of it?"
"I haven't looked the matter over yet, but I have an idea. In the first
place, we must organize."
"How organize?"
"We must have a leader, and all hands must obey his orders."
"That ought to be the second mate," suggested Sanderson.
"He has not taken part with us yet."
"But he has said he would when it was proved that the bark was
going a slaving," replied Baxter.
"All right," I added. "We must wait till night, if possible."
"There may be a row before night. The captain, mate, and the two
passengers are talking the matter over on the quarter-deck," said
Walker.
"Who's at the helm?"
"Schneider."
"He's one of the doubtful ones, and won't meddle as long as the thing
is undecided. The second mate has the first watch to-night," I
continued.
"Ay, ay," answered Baxter, deeply interested in my suggestion.
"At that time, the captain, mate, and the two passengers will be in
their state-rooms. I believe in taking them there."
"But we have Gorro and Martino in the starboard watch. What shall
we do with them?"
"We'll fix them," I replied. "Two of our stoutest hands must take care
of them. I'm not much more than a boy, but I can handle one of them."
"Plucky!" said Baxter.
"Two more must take care of the three in the forecastle. We can
fasten the door on them when we have got our own men out."
"Good! That will all work well," added Baxter.
"Who has the first trick at the wheel in our watch?" I asked.
"Martino," replied Sanderson.
"Then we must muzzle Gorro forward. Each man must have his own
job to do. Six men shall take off the forward hatch, and passing
through the between-decks, make their way to the cabin through the
steerage."
"Why not go down the cabin stairs?" asked Sanderson.
"Because Martino, at the helm, would give the alarm."
"I like the plan, Phil. We will go over it again, and give each man his
part of the work."
"Sail ho!" shouted Sylvio, one of the Spanish sailors, who was in the
waist.
The mate sprang into the weather mizzen rigging to examine the sail,
and in a few moments we all discovered a streak of black smoke on
the sky, which indicated a steamer.
 CHAPTER XV.
IN WHICH PHIL IS ASSIGNED TO AN IMPORTANT
POSITION BY HIS SHIPMATES.
The streak of smoke was on our weather bow, the wind being from
the north-east. The fact that the sail was a steamer rendered it
almost certain that she was a man-of-war; one of the cruisers on the
coast of Africa, on the lookout for slavers. If all hands had not been
busy attending to the exciting scenes on board, we might have
sooner discovered the sail.
"That's in our favor," said Dick Baxter, as soon as the steamer was
made out.
"I don't know about that," replied Jack Sanderson. "If we had taken
possession of the bark it would be in our favor. I don't like the idea of
being taken just yet, for the man-of-war won't be able to tell who's
guilty and who's innocent."
"The steamer will put an end to this cruise, at any rate," I added.
"I'm not so sure of that. The Michigan is a very fast sailer, and I
suppose that's the strongest reason why she happens to be in this
business. She's more'n a match for some of those old drogers of
steamers in the navy," continued Baxter. "She has logged more'n
fourteen knots on this cruise; and as the wind is to-day, she's good
for twelve, when she gets it on the quarter. That's a British steamer."
"What makes you think so?" I asked.
"Her black smoke. The English men-of-war use that kind of coal
which makes smoke as black as ink, and the American men-of-war
don't make any smoke."
"All hands on deck!" shouted the mate. "Stand by tacks and braces!"
"How's that? Shall we go to work?" said Baxter.
"Yes; let us wait for a proper time to carry out our plans," I replied.
All hands sprang to their stations, as though nothing had happened.
"Starboard the helm!" continued the mate, taking his order from the
captain, who appeared to be too drunk to handle the bark.
The order was given to ease off on the lee braces, and haul on the
weather.
"Steady as she is! Avast hauling! A small pull on the weather main-
topsail brace! That will do! A little more spanker-sheet. Belay, all!"
The bark was then headed about south-south-west, with the wind on
the port quarter, which Baxter had declared to be her best point in
sailing.
"The mate knows what that steamer is," said Sanderson, as we
gathered together again on the forecastle.
"That he does; he knows what black smoke means," responded
Baxter.
"Sartinly; he wouldn't run away from her, if he wasn't afraid of her.
That's what one puppy does when he's afraid of another."
"I don't want any more proof that this is an unlawful voyage."
"Even this was not needed," I added. "Can you see how the steamer
is headed?"
"No; you can hardly make her out at all. Her black smoke is about all
there is of her yet," answered Baxter. "But she will see us before
long, if she has not already. You may be sure that she will give
chase, for those men-of-war don't sail with their eyes shut."
"Are we alone now?" I asked, looking over the men to see that none
who did not belong to our party were present.
"Ay, ay, lad; we are all by ourselves," answered Baxter.
"Let us divide the work for to-night, then."
"The sooner the better."
"Six men must go into the cabin through the between-decks," I
continued. "Who shall they be?"
"You shall be one of them, Phil," said Baxter.
"Very well; I am willing. Sanderson shall be another."
"I'm agreed," responded the old salt.
"And Baxter shall look out for Martino at the helm. Walker shall lie
down upon Gorro, and Bilger shall see that only our own men come
out of the forecastle."
"Good, Phil!" exclaimed Baxter. "But what shall we do with York?"
"He must not commit himself till we have made a sure thing of the
job. Don't say a word to him; but he will not interfere," answered
Sanderson.
We stationed every man according to his ability for the great
enterprise, and I felt almost sure that it would be a success, if the
man-of-war did not overhaul us before we had time to put it in
operation. While we were thus engaged, the mate and the
passengers were busy watching the movements of the steamer with
a glass. They did not look forward to see what the crew were doing.
The Spanish and Portuguese sailors did not come near us. They had
already committed themselves on the side of the officers, and knew
that their shipmates had no good will towards them on this account.
They were in the waist, and seemed to be as busy as we were in
discussing the exciting affair which had occurred. I afterwards
learned that they had been engaged before in the slave trade, and
had been shipped by the Spanish passengers as willing agents in
the inhuman business.
I do not know what the mate had discovered in regard to the
steamer; but he ordered the studding-sails, alow and aloft, to be set
forward. The wind was fresh, and under this additional canvas the
bark flew through the water. The log was thrown; and Baxter, who
had charge of the operation, informed us that the Michigan was
making thirteen knots. I admired the vessel, and thought it a shame
and a pity that such a noble craft should be used in such a horrid
trade. She had been built to run up the Mediterranean as a fruiter,
and it was desirable that she should make quick passages. Some of
her carrying capacity had been sacrificed on this account; but she
could still carry negroes enough to make her voyage a very
profitable investment.
After we had set the studding-sails forward, our party again
discussed the details of our plan for the evening. The part of each
man, and each gang of men, was carefully considered. To each party
a leader was appointed, who was to be held responsible for the
share of the work assigned to him, and whom the others were to
obey without a question. I had the honor to be selected as the leader
of the largest gang, who were to do the job in the cabin. The fact that
I had been engaged in an Indian campaign seemed to give me a
great deal of credit for the service which we were to perform, and my
name was suggested for the important place by Jack Sanderson,
who was to be one of my party.
I found myself very popular with the crew; first, I suppose, because I
had been persecuted by the mate,—which was his fault, and not my
merit,—and second, because I had always tried to be kind and
obliging to my shipmates. I had read to them from the Bible every
Sunday, and always found them glad to hear the blessed word. I had
watched with those who were sick, and helped them whenever I had
an opportunity to do so. I told them all about the wilds of the Upper
Missouri, and related the story of the campaign with the Indians. I
had given them the history of Waterford in Chicago, so far as I knew
it. I had no intention of making myself popular with the men;
probably, if I had, I should have failed. I only wished to act the part of
a Christian towards them; and, for carrying out this simple and
sincere desire, I obtained a great deal more credit than I deserved.
Rude and rough as these men were, depraved even as a few of
them had become by the agency of that fiend which is the sailor's
direst curse, Rum, they were still men, and some of them had
received a fair education. Some of them were blessed with inquiring
minds, and many an hour of the silent watches of the night, as the
bark ploughed her way over the ocean, our discussions were upon
moral, religious, and scientific subjects. Though I was but eighteen,
my studies gave me a great advantage over my companions, and I
found myself consulted upon questions in which the men were
interested. I can only say, that whatever measure of regard and
respect I won from my shipmates was merited only by an earnest
and sincere desire to serve and benefit them.
Everything went along quietly on deck. The captain had
disappeared. Doubtless the excitement of the day had caused him to
drink deeper than usual, and I suppose he was asleep in his state-
room. Waterford was the real captain of the bark, though Farraday
sometimes acted as such. The mate must have been sadly disturbed
by the incipient mutiny which had appeared; but he took no further
steps to strengthen his position. He kept his eye on the streak of
black smoke over the lee quarter. Perhaps he felt that, as there was
no actual demonstration of mutiny on the part of the crew, he could
better afford to wait for the indications of the future than the crew
could. Certainly everything on board went along as usual, except
that the Spanish and Portuguese sailors separated themselves from
their shipmates, unless required, in the discharge of their duty, to
mingle with them.
Feeling that a great event was likely to occur within the next twenty-
four hours, I could not help considering the safety of my money, for I
hoped, by some means or other, that I should be able to reach
Europe, and find my mother. I looked all about the deck for a better
hiding-place for my treasure. While I was thinking of the matter, I was
ordered, with others, to get up a barrel of beef from the hold. I was
sure that I could find a safe place below for my gold; and, passing
into the forecastle, I put the bag into my pocket. After we had hoisted
up the barrel, I went aft to the temporary steerage which had been
built for this voyage. I noticed the position of the door, and satisfied
myself that it was not fastened; but I found no good place for my
money.
While the men were closing the hatch in the lower deck, I went
forward to the bow, where there was a pile of fire-wood. I climbed
over it, and found a crevice between the stem and the planking of
the deck, into which I jammed the bag. I was sure the mate would
not find it there; and, having disposed of my treasure, I hastened to
join my shipmates who were men of our party. They understood that
I was surveying the ground for the movement that night, and covered
my operations so that I was not noticed by any person on the other
side.
I felt easier after I had put my money in what I regarded as a safe
place. I did not expect to leave the vessel before we had captured
her; but, even if we failed, I could, with the assistance of my friends,
take off the fore scuttle, and recover the bag. I felt full of confidence
that we should succeed in our plan, and that, before eight bells in the
morning watch, the bark would be headed to the north. We actually
ran away from the steamer, if she discovered us at all. The mate
made no more trouble, and everything went along quietly till the first
dog watch, in which I had my trick at the wheel.
 CHAPTER XVI.
IN WHICH PHIL FINDS HIMSELF A PRISONER IN
THE STEERAGE.
Waterford certainly looked as ugly as ever, if he did not act so. He
planked the deck on the weather side, and occasionally glanced at
me, as though I was the cause of all the misfortunes that had
checkered the calendar of his existence. My party were all forward,
as there was nothing to do; for the mate, besides promising the men
plum duff and grog, had also given them "watch and watch." Before,
he had labored hard to make work for the men; now, he gave them an
easy time, and one watch was to be permitted to be below all the
time, except when heavy weather required all hands.
The five Spanish and Portuguese sailors were leaning against the
fiferail of the mainmast. They had drank their grog, and being in high
favor with the mate, were very cheerful. I paid little or no attention to
them, for I was obliged to keep my eye steadily on the binnacle. I saw
Waterford stop at the foot of the mainmast, and talk with these slave-
trading ruffians; but he soon resumed his walk, and took no further
notice of them.
The mate, as he came near the wheel, half an hour later, halted, and
looked at the spanker.
"Aft here, three of you, and give a pull on the spanker-sheet," said he.
Martino, Gorro, and Grego hastened upon the quarter-deck to obey
the order. They cast off the sheet, and gave it a pull.
"Avast—too much," interposed the mate. "Ease off again."
"Ease off," replied Martino; and I observed that they let out the sheet
till the sail was in exactly the same position as before.
"Avast; belay!" added the mate. "Take the helm, Gorro."
I looked up with astonishment when I heard this order, for it involved
a departure from the ordinary routine of the vessel. The Portuguese
took the helm; and while I was waiting for further commands, a pair of
hands were placed over my mouth, and I was suddenly and violently
borne down upon the deck. In a word, I was garroted after the
Spanish fashion. Grego seized me by the legs, and I was unable
either to struggle or to cry out. The two men picked me up, and
hastened into the cabin with me. Waterford walked forward as far as
the mainmast, and that was the last I saw of him. It was evident that
none of my shipmates forward had seen the trick played upon me, for
they were all behind the house on deck.
My captors bore me to the steerage, where they tied me hand and
foot, and made me fast to a stanchion. I began to understand why the
mate had been so quiet and peaceful since the row on deck. He had
concluded to fight his enemies in detail, instead of in the aggregate. I
was helpless now, and my companions in the forecastle did not even
know that any misfortune had happened to me. But I was sure they
would miss me when the helm was relieved, and I was more afraid
that they would go to work rashly than that they would do nothing.
 Phil a Prisoner in the Steerage.

"You'll hold still now, Phil," said Martino.

"I suppose I shall as long as these ropes hold out," I replied.
"You made the trouble, and now you will have to take it. If the men
don't want to obey orders now, they will catch pistol balls, instead of
plum duff and grog."
"What does the mate mean to do with me?" I asked.
"He means to make you work when we get the niggers on board. You
will have to feed them, and clean them out," laughed the Spaniard.
"Come; he is safe where he is now," added Grego.
My persecutors left me alone, and went on deck to report to the mate
what they had done. They had certainly done their work well, for my
wrists ached, the line was so tight upon them. My situation looked
very hopeless; and, after I had tested the strength of the cords that
bound me, I felt very much like giving up in despair. But, in the cause
of truth and justice, I felt that I had no right to despair. I was one of
those upon whom devolved the duty of preventing the Michigan from
being turned into a slave ship. We were to act not alone for our own
safety and comfort, but in the interests of humanity. God would bless
our efforts in his own way, and we were in duty bound to do our best,
without regard to consequences.
Though I did not know till afterwards, what followed on deck, I shall
relate it now, in the order of the events. Martino and Grego returned
to the waist, and reported to the mate that the prisoner was safe.
Martino then went forward, and told the men what had happened to
me. They had no suspicion of it before, so skilfully and silently had
the ruffians done their work. They were shocked and confounded.
They immediately took counsel among themselves; and at the
suggestion of Baxter, they decided to appear to yield to the
circumstances.
While the conference was in progress, the steward went forward with
the grog. This time they drank, and Sanderson took my allowance.
Every man seemed to be happy and cheerful; and the mate called all
hands to brace up the bark; for, as the steamer had not been seen for
several hours, it was decided to resume the course. The mate then
spoke to the hands, as he had in the forenoon, and they yielded the
point. They were willing to make a thousand dollars, and glad to have
"watch and watch," plum duff, and grog. The mate was satisfied; and,
when the starboard watch came on duty in the second dog watch, he
went below. I knew the sound of his step, and I heard him coming
towards the steerage.
"Mr. Waterford," said the captain, calling to him from his state-room,
which was near the open door leading into the steerage.
"Well, captain," replied the mate.
"What's the matter?"