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Statistics

Like the best-selling first two editions, A Hand-

book of Statistical Analyses using R, Third Edi-
tion provides an up-to-date guide to data analysis
using the R system for statistical computing. The
book explains how to conduct a range of statisti-
cal analyses, from simple inference to recursive
partitioning to cluster analysis.

New to the Third Edition

• Three new chapters on quantile regression,
missing values, and Bayesian inference
• Extra material in the logistic regression
chapter that describes a regression model
for ordered categorical response variables
• Additional exercises
• More detailed explanations of R code
• New section in each chapter summarizing
the results of the analyses
• Updated version of the HSAUR package
(HSAUR3), which includes some slides
Torsten Hothorn that can be used in introductory statistics
courses
Brian S. Everitt
Whether you’re a data analyst, scientist, or stu-
dent, this handbook shows you how to easily use

Hothorn and Everitt

R to effectively evaluate your data. With numer-
ous real-world examples, it emphasizes the prac-
tical application and interpretation of results.

Features
• Presents straightforward descriptions of
how to use R and interpret the results
• Gives an introduction to R for novices,
covering basic concepts and common data
manipulation techniques
• Shows how to obtain informative graphical
output by applying the appropriate R func-
tions
• Includes more examples and exercises that
encourage hands-on practice with R
• Offers the data, R code, and lecture slides in
the HSAUR3 package available from CRAN THIRD
EDITION Torsten Hothorn and Brian S. Everitt
K21384
 Contents

Preface to Third Edition xi

Preface to Second Edition xiii

Preface to First Edition xv

1 An Introduction to R 1
1.1 What is R? 1
1.2 Installing R 2
1.3 Help and Documentation 4
1.4 Data Objects in R 5
1.5 Data Import and Export 9
1.6 Basic Data Manipulation 11
1.7 Computing with Data 14
1.8 Organizing an Analysis 20
1.9 Summary of Findings 21
1.10 Final Comments 23

2 Data Analysis Using Graphical Displays 25

2.1 Introduction 25
2.2 Initial Data Analysis 27
2.3 Analysis Using R 29
2.4 Summary of Findings 40
2.5 Final Comments 41

3 Simple Inference 47
3.1 Introduction 47
3.2 Statistical Tests 51
3.3 Analysis Using R 55
3.4 Summary of Findings 65
3.5 Final Comments 66

4 Conditional Inference 69
4.1 Introduction 69
4.2 Conditional Test Procedures 72
4.3 Analysis Using R 74

vii
viii CONTENTS
4.4 Summary of Findings 81
4.5 Final Comments 81

5 Analysis of Variance 83
5.1 Introduction 83
5.2 Analysis of Variance 86
5.3 Analysis Using R 87
5.4 Summary of Findings 98
5.5 Final Comments 99

6 Simple and Multiple Linear Regression 101

6.1 Introduction 101
6.2 Simple Linear Regression 103
6.3 Multiple Linear Regression 104
6.4 Analysis Using R 107
6.5 Summary of Findings 118
6.6 Final Comments 119

7 Logistic Regression and Generalized Linear Models 121

7.1 Introduction 121
7.2 Logistic Regression and Generalized Linear Models 124
7.3 Analysis Using R 127
7.4 Summary of Findings 145
7.5 Final Comments 147

8 Density Estimation 149

8.1 Introduction 149
8.2 Density Estimation 151
8.3 Analysis Using R 156
8.4 Summary of Findings 164
8.5 Final Comments 165

9 Recursive Partitioning 171

9.1 Introduction 171
9.2 Recursive Partitioning 174
9.3 Analysis Using R 175
9.4 Summary of Findings 186
9.5 Final Comments 186

10 Scatterplot Smoothers and Additive Models 187

10.1 Introduction 187
10.2 Scatterplot Smoothers and Generalized Additive Models 191
10.3 Analysis Using R 196
10.4 Summary of Findings 205
10.5 Final Comments 206
CONTENTS ix
11 Survival Analysis 209
11.1 Introduction 209
11.2 Survival Analysis 210
11.3 Analysis Using R 216
11.4 Summary of Findings 223
11.5 Final Comments 224

12 Quantile Regression 227

12.1 Introduction 227
12.2 Quantile Regression 228
12.3 Analysis Using R 230
12.4 Summary of Findings 241
12.5 Final Comments 242

13 Analyzing Longitudinal Data I 243

13.1 Introduction 243
13.2 Analyzing Longitudinal Data 246
13.3 Linear Mixed Effects Models 247
13.4 Analysis Using R 249
13.5 Prediction of Random Effects 253
13.6 The Problem of Dropouts 253
13.7 Summary of Findings 256
13.8 Final Comments 258

14 Analyzing Longitudinal Data II 261

14.1 Introduction 261
14.2 Methods for Non-normal Distributions 263
14.3 Analysis Using R: GEE 268
14.4 Analysis Using R: Random Effects 277
14.5 Summary of Findings 280
14.6 Final Comments 280

15 Simultaneous Inference and Multiple Comparisons 283

15.1 Introduction 283
15.2 Simultaneous Inference and Multiple Comparisons 286
15.3 Analysis Using R 287
15.4 Summary of Findings 294
15.5 Final Comments 295

16 Missing Values 297

16.1 Introduction 297
16.2 The Problems of Missing Data 298
16.3 Dealing With Missing Values 299
16.4 Imputing Missing Values 300
16.5 Analyzing Multiply Imputed Data 301
x CONTENTS
16.6 Analysis Using R 303
16.7 Summary of Findings 311
16.8 Final Comments 311

17 Meta-Analysis 313
17.1 Introduction 313
17.2 Systematic Reviews and Meta-Analysis 315
17.3 Statistics of Meta-Analysis 317
17.4 Analysis Using R 319
17.5 Meta-Regression 322
17.6 Publication Bias 323
17.7 Summary of Findings 325
17.8 Final Comments 325

18 Bayesian Inference 331

18.1 Introduction 331
18.2 Bayesian Inference 333
18.3 Analysis Using R 337
18.4 Summary of Findings 344
18.5 Final Comments 344

19 Principal Component Analysis 347

19.1 Introduction 347
19.2 Principal Component Analysis 347
19.3 Analysis Using R 350
19.4 Summary of Findings 357
19.5 Final Comments 357

20 Multidimensional Scaling 361

20.1 Introduction 361
20.2 Multidimensional Scaling 361
20.3 Analysis Using R 367
20.4 Summary of Findings 372
20.5 Final Comments 373

21 Cluster Analysis 377

21.1 Introduction 377
21.2 Cluster Analysis 380
21.3 Analysis Using R 387
21.4 Summary of Findings 394
21.5 Final Comments 397

Bibliography 399

Index 415
 Preface to Third Edition

Again like the first two editions, this third edition of A Handbook of Statistical
Analyses using R is intended as a guide to data analysis with the R system for
statistical computing. In this edition we have added three new chapters, one
on quantile regression, one on missing values, and one on Bayesian inference.
There is also extra material in several chapters, for example, the chapter on
logistic regression now includes a description of a regression model for ordered
categorical response variables. And many chapters contain extra exercises and
more detailed explanation of the R code. Lastly every chapter now has a
penultimate section summarizing the results of the analyses carried out in
the chapter. A new version of the HSAUR package, now called HSAUR3
for obvious reasons, is available from the Comprehensive R Archive Network
(http://CRAN.R-project.org).
Many readers told us that they use the book as course material when
they teach introductory statistics courses. For some selected chapters, Sweave
sources of slides are now available in the HSAUR3 source package that can
be used as additional material in such courses.
We would like to thank Nora Fenske and Leonhard Held for providing feed-
back on the new Chapters 12 and 18.

Torsten Hothorn and Brian S. Everitt

Zürich and London, Easter 2014

xi
 Preface to Second Edition

Like the first edition this book is intended as a guide to data analysis with
the R system for statistical computing. New chapters on graphical displays,
generalized additive models, and simultaneous inference have been added to
this second edition and a section on generalized linear mixed models completes
the chapter that discusses the analysis of longitudinal data where the response
variable does not have a normal distribution. In addition, new examples and
additional exercises have been added to several chapters. We have also taken
the opportunity to correct a number of errors that were present in the first
edition. Most of these errors were kindly pointed out to us by a variety of peo-
ple to whom we are very grateful, especially Guido Schwarzer, Mike Cheung,
Tobias Verbeke, Yihui Xie, Lothar Häberle, and Radoslav Harman.
We learned that many instructors use our book successfully for introductory
courses in applied statistics. We have had the pleasure to give some courses
based on the first edition of the book ourselves and we are happy to share
slides covering many sections of particular chapters with our readers. LATEX
sources and PDF versions of slides covering several chapters are available from
the second author upon request.
A new version of the HSAUR package, now called HSAUR2 for obvious
reasons, is available from CRAN. Basically the package vignettes have been
updated to cover the new and modified material as well. Otherwise, the tech-
nical infrastructure remains as described in the preface to the first edition,
with two small exceptions: names of R add-on packages are now printed in
bold font and we refrain from showing significance stars in model summaries.
Lastly we would like to thank Thomas Kneib and Achim Zeileis for com-
menting on the newly added material and again the CRC Press staff, in par-
ticular Rob Calver, for their support during the preparation of this second
edition.

Brian S. Everitt and Torsten Hothorn

London and München, April 2009

xiii
 Preface to First Edition

This book is intended as a guide to data analysis with the R system for sta-
tistical computing. R is an environment incorporating an implementation of
the S programming language, which is powerful and flexible and has excellent
graphical facilities (R Development Core Team, 2014b). In the Handbook we
aim to give relatively brief and straightforward descriptions of how to conduct
a range of statistical analyses using R. Each chapter deals with the analy-
sis appropriate for one or several data sets. A brief account of the relevant
statistical background is included in each chapter along with appropriate ref-
erences, but our prime focus is on how to use R and how to interpret results.
We hope the book will provide students and researchers in many disciplines
with a self-contained means of using R to analyze their data.
R is an open-source project developed by dozens of volunteers for more than
ten years now and is available from the Internet under the General Public Li-
cense. R has become the lingua franca of statistical computing. Increasingly,
implementations of new statistical methodology first appear as R add-on pack-
ages. In some communities, such as in bioinformatics, R already is the primary
workhorse for statistical analyses. Because the sources of the R system are open
and available to everyone without restrictions and because of its powerful lan-
guage and graphical capabilities, R has started to become the main computing
engine for reproducible statistical research (Leisch, 2002a,b, 2003, Leisch and
Rossini, 2003, Gentleman, 2005). For a reproducible piece of research, the orig-
inal observations, all data preprocessing steps, the statistical analysis as well
as the scientific report form a unity and all need to be available for inspection,
reproduction, and modification by the readers.
Reproducibility is a natural requirement for textbooks such as the Handbook
of Statistical Analyses Using R and therefore this book is fully reproducible
using an R version greater or equal to 2.2.1. All analyses and results, including
figures and tables, can be reproduced by the reader without having to retype
a single line of R code. The data sets presented in this book are collected
in a dedicated add-on package called HSAUR accompanying this book. The
package can be installed from the Comprehensive R Archive Network (CRAN)
via
R> install.packages("HSAUR")
and its functionality is attached by
R> library("HSAUR")
The relevant parts of each chapter are available as a vignette, basically a

xv
xvi PREFACE TO FIRST EDITION
document including both the R sources and the rendered output of every
analysis contained in the book. For example, the first chapter can be inspected
by
R> vignette("Ch_introduction_to_R", package = "HSAUR")
and the R sources are available for reproducing our analyses by
R> edit(vignette("Ch_introduction_to_R", package = "HSAUR"))
An overview on all chapter vignettes included in the package can be obtained
from
R> vignette(package = "HSAUR")
We welcome comments on the R package HSAUR, and where we think these
add to or improve our analysis of a data set we will incorporate them into the
package and, hopefully at a later stage, into a revised or second edition of the
book.
Plots and tables of results obtained from R are all labeled as ‘Figures’ in
the text. For the graphical material, the corresponding figure also contains
the ‘essence’ of the R code used to produce the figure, although this code may
differ a little from that given in the HSAUR package, since the latter may
include some features, for example thicker line widths, designed to make a
basic plot more suitable for publication.
We would like to thank the R Development Core Team for the R system, and
authors of contributed add-on packages, particularly Uwe Ligges and Vince
Carey for helpful advice on scatterplot3d and gee. Kurt Hornik, Ludwig A.
Hothorn, Fritz Leisch and Rafael Weißbach provided good advice with some
statistical and technical problems. We are also very grateful to Achim Zeileis
for reading the entire manuscript, pointing out inconsistencies or even bugs,
and for making many suggestions which have led to improvements. Lastly we
would like to thank the CRC Press staff, in particular Rob Calver, for their
support during the preparation of the book. Any errors in the book are, of
course, the joint responsibility of the two authors.

Brian S. Everitt and Torsten Hothorn

London and Erlangen, December 2005
 List of Figures

1.1 Histograms of the market value and the logarithm of the

market value for the companies contained in the Forbes 2000
list. 19
1.2 Raw scatterplot of the logarithms of market value and sales. 20
1.3 Scatterplot with transparent shading of points of the loga-
rithms of market value and sales. 21
1.4 Boxplots of the logarithms of the market value for four
selected countries, the width of the boxes is proportional to
the square roots of the number of companies. 22

2.1 Histogram (top) and boxplot (bottom) of malignant melanoma

mortality rates. 30
2.2 Parallel boxplots of malignant melanoma mortality rates by
contiguity to an ocean. 31
2.3 Estimated densities of malignant melanoma mortality rates
by contiguity to an ocean. 32
2.4 Scatterplot of malignant melanoma mortality rates by geo-
graphical location. 33
2.5 Scatterplot of malignant melanoma mortality rates against
latitude. 34
2.6 Map of the United States of America showing malignant
melanoma mortality rates. 36
2.7 Bar chart of happiness. 37
2.8 Spineplot of health status and happiness. 38
2.9 Spinogram (left) and conditional density plot (right) of
happiness depending on log-income. 39
2.10 Scatterplot of jittered log-income of wife and husband,
conditional on the wife’s education. 40

3.1 Boxplots of estimates of room width in feet and meters (after

conversion to feet) and normal probability plots of estimates
of room width made in feet and in meters. 57
3.2 R output of the independent samples t-test for the roomwidth
data. 58
3.3 R output of the independent samples Welch test for the
roomwidth data. 58

xvii
xviii LIST OF FIGURES
3.4 R output of the Wilcoxon rank sum test for the roomwidth
data. 59
3.5 Boxplot and normal probability plot for differences between
the two mooring methods. 60
3.6 R output of the paired t-test for the waves data. 61
3.7 R output of the Wilcoxon signed rank test for the waves
data. 61
3.8 Enhanced scatterplot of water hardness and mortality,
showing both the joint and the marginal distributions and,
in addition, the location of the city by different plotting
symbols. 62
3.9 R output of Pearsons’ correlation coefficient for the water
data. 63
3.10 R output of the chi-squared test for the pistonrings data. 63
3.11 Association plot of the residuals for the pistonrings data. 64
3.12 R output of McNemar’s test for the rearrests data. 65
3.13 R output of an exact version of McNemar’s test for the
rearrests data computed via a binomial test. 65

4.1 An approximation for the conditional distribution of the

difference of mean roomwidth estimates in the feet and
meters group under the null hypothesis. The vertical lines
show the negative and positive absolute value of the test
statistic T obtained from the original data. 75
4.2 R output of the exact permutation test applied to the
roomwidth data. 76
4.3 R output of the exact conditional Wilcoxon rank sum test
applied to the roomwidth data. 77
4.4 R output of Fisher’s exact test for the suicides data. 77

5.1 Plot of mean weight gain for each level of the two factors. 88
5.2 R output of the ANOVA fit for the weightgain data. 89
5.3 Interaction plot of type and source. 90
5.4 Plot of mean litter weight for each level of the two factors for
the foster data. 91
5.5 Graphical presentation of multiple comparison results for the
foster feeding data. 94
5.6 Scatterplot matrix of epoch means for Egyptian skulls data. 96

6.1 Scatterplot of velocity and distance. 108

6.2 Scatterplot of velocity and distance with estimated regression
line (left) and plot of residuals against fitted values (right). 109
6.3 Boxplots of rain. 111
6.4 Scatterplots of rain against the continuous covariates. 112
6.5 R output of the linear model fit for the clouds data. 113
LIST OF FIGURES xix
6.6 Regression relationship between S-Ne criterion and rainfall
with and without seeding. 115
6.7 Plot of residuals against fitted values for clouds seeding
data. 116
6.8 Normal probability plot of residuals from cloud seeding model
clouds_lm. 117
6.9 Index plot of Cook’s distances for cloud seeding data. 118

7.1 Conditional density plots of the erythrocyte sedimentation

rate (ESR) given fibrinogen and globulin. 128
7.2 R output of the summary method for the logistic regression
model fitted to ESR and fibrigonen. 129
7.3 R output of the summary method for the logistic regression
model fitted to ESR and both globulin and fibrinogen. 130
7.4 Bubbleplot of fitted values for a logistic regression model
fitted to the plasma data. 131
7.5 R output of the summary method for the logistic regression
model fitted to the womensrole data. 132
7.6 Fitted (from womensrole_glm_1) and observed probabilities
of agreeing for the womensrole data. The size of the symbols
is proportional to the sample size. 134
7.7 R output of the summary method for the logistic regression
model fitted to the womensrole data. 135
7.8 Fitted (from womensrole_glm_2) and observed probabilities
of agreeing for the womensrole data. 136
7.9 Plot of deviance residuals from logistic regression model fitted
to the womensrole data. 137
7.10 R output of the summary method for the Poisson regression
model fitted to the polyps data. 138
7.11 R output of the print method for the conditional logistic
regression model fitted to the backpain data. 141
7.12 R output of the summary method for the proportional odds
model fitted to the CHFLS data. 143
7.13 R output of the cftest function for the proportional odds
model fitted to the CHFLS data. 144
7.14 Predicted distribution of happiness for hypothetical women
with health conditions rating from poor to excellent, with
the remaining explanatory variables being the same as for
the woman corresponding to the first row in the CHFLS data
frame. The levels of happiness have been abbreviated (A:
very unhappy, B: not too happy, C: somewhat happy; D: very
happy). 146

8.1 Three commonly used kernel functions. 154

xx LIST OF FIGURES
8.2 Kernel estimate showing the contributions of Gaussian kernels
evaluated for the individual observations with bandwidth
h = 0.4. 155
8.3 Epanechnikov kernel for a grid between (−1.1, −1.1) and
(1.1, 1.1). 156
8.4 Density estimates of the geyser eruption data imposed on a
histogram of the data. 158
8.5 A contour plot of the bivariate density estimate of the
CYGOB1 data, i.e., a two-dimensional graphical display for a
three-dimensional problem. 159
8.6 The bivariate density estimate of the CYGOB1 data, here shown
in a three-dimensional fashion using the persp function. 160
8.7 Fitted normal density and two-component normal mixture
for geyser eruption data. 162
8.8 Bootstrap distribution and confidence intervals for the mean
estimates of a two-component mixture for the geyser data. 165

9.1 Initial tree for the body fat data with the distribution of body
fat in terminal nodes visualized via boxplots. 176
9.2 Pruned regression tree for body fat data. 177
9.3 Observed and predicted DXA measurements. 178
9.4 Pruned classification tree of the glaucoma data with class
distribution in the leaves. 179
9.5 Estimated class probabilities depending on two important
variables. The 0.5 cut-off for the estimated glaucoma proba-
bility is depicted as a horizontal line. Glaucomateous eyes are
plotted as circles and normal eyes are triangles. 182
9.6 Conditional inference tree with the distribution of body fat
content shown for each terminal leaf. 184
9.7 Conditional inference tree with the distribution of glaucoma-
teous eyes shown for each terminal leaf. 184
9.8 Conditional inference tree with the distribution of self-
reported happiness shown for each terminal leaf. The levels
of happiness have been abbreviated (A: very unhappy, B:
not too happy, C: somewhat happy; D: very happy). The
justmin argument ensures that split descriptions longer than
10 characters are displayed over two lines. 185

10.1 A linear spline function with knots at a = 1, b = 3, and

c = 5. 193
10.2 Scatterplot of year and winning time. 197
10.3 Scatterplot of year and winning time with fitted values from
a simple linear model. 198
10.4 Scatterplot of year and winning time with fitted values from
a smooth non-parametric model. 199
LIST OF FIGURES xxi
10.5 Scatterplot of year and winning time with fitted values from
a quadratic model. 200
10.6 Partial contributions of six exploratory covariates to the
predicted SO2 concentration. 202
10.7 Residual plot of SO2 concentration. 203
10.8 Spinograms of the three exploratory variables and response
variable kyphosis. 204
10.9 Partial contributions of three exploratory variables with
confidence bands. 205
10.10 Effects of level of education for males (right) and females
(left) on the log-odds scale derived from an additive logistic
regression model. The shaded area denotes confidence bands. 206
10.11 Effects of level of education for males (right) and females
(left) on the log-odds scale derived from an additive logistic
regression model. The shaded area denotes confidence bands. 207

11.1 ‘Bath tub’ shape of a hazard function. 214

11.2 Survival times comparing treated and control patients. 217
11.3 Kaplan-Meier estimates for breast cancer patients who either
received hormonal therapy or not. 219
11.4 R output of the summary method for GBSG2_coxph. 220
11.5 Estimated regression coefficient for age depending on time
for the GBSG2 data. 221
11.6 Martingale residuals for the GBSG2 data. 222
11.7 Conditional inference tree for the GBSG2 data with the
survival function, estimated by Kaplan-Meier, shown for
every subgroup of patients identified by the tree. 223

12.1 Scatterplot of age and head circumference for 5101 Dutch

boys. 232
12.2 Scatterplot of age and head circumference for 5101 Dutch
boys with superimposed normal quantiles. 237
12.3 Scatterplot of age and head circumference for 5101 Dutch
boys with superimposed regression quantiles (solid lines) and
normal quantiles (dashed lines). 239
12.4 Scatterplot of age and head circumference for 5101 Dutch
boys with superimposed non-linear regression quantiles. 241

13.1 Boxplots for the repeated measures by treatment group for

the BtheB data. 250
13.2 R output of the linear mixed-effects model fit for the BtheB
data. 252
13.3 R output of the asymptotic p-values for linear mixed-effects
model fit for the BtheB data. 253
xxii LIST OF FIGURES
13.4 Quantile-quantile plots of predicted random intercepts and
residuals for the random intercept model BtheB_lmer1 fitted
to the BtheB data. 254
13.5 Distribution of BDI values for patients that do (circles) and
do not (bullets) attend the next scheduled visit. 257

14.1 Simulation of a positive response in a random intercept

logistic regression model for 20 subjects. The thick line is the
average over all 20 subjects. 267
14.2 R output of the summary method for the btb_gee model
(slightly abbreviated). 269
14.3 R output of the summary method for the btb_gee1 model
(slightly abbreviated). 270
14.4 R output of the summary method for the resp_glm model. 271
14.5 R output of the summary method for the resp_gee1 model
(slightly abbreviated). 272
14.6 R output of the summary method for the resp_gee2 model
(slightly abbreviated). 273
14.7 Boxplots of numbers of seizures in each two-week period post
randomization for placebo and active treatments. 274
14.8 Boxplots of log of numbers of seizures in each two-week period
post randomization for placebo and active treatments. 275
14.9 R output of the summary method for the epilepsy_glm
model. 276
14.10 R output of the summary method for the epilepsy_gee1
model (slightly abbreviated). 277
14.11 R output of the summary method for the epilepsy_gee2
model (slightly abbreviated). 278
14.12 R output of the summary method for the epilepsy_gee3
model (slightly abbreviated). 279
14.13 R output of the summary method for the resp_lmer model
(abbreviated). 279

15.1 Distribution of levels of expressed alpha synuclein mRNA in

three groups defined by the NACP -REP1 allele lengths. 288
15.2 Simultaneous confidence intervals for the alpha data based
on the ordinary covariance matrix (left) and a sandwich
estimator (right). 291
15.3 Probability of damage caused by roe deer browsing for five
tree species. Sample sizes are given in brackets. 293
15.4 Regression relationship between S-Ne criterion and rainfall
with and without seeding. The confidence bands cover the
area within the dashed curves. 295

16.1 Scatterplots of the complete cases of the bp data. 304

LIST OF FIGURES xxiii
16.2 R output of the complete-case linear model for the bp data. 305
16.3 Scatterplots of the imputed bp data. Imputed observations
are depicted as triangles. 307
16.4 R output of the mean imputation linear model for the bp
data. 308
16.5 Scatterplots of the multiple imputed bp data (first iteration).
Imputed observations are depicted as triangles. 309
16.6 R output of the multiple imputed linear model for the bp
data. 310

17.1 R output of the summary method for smokingOR. 320

17.2 Forest plot of observed effect sizes and 95% confidence
intervals for the nicotine gum studies. 321
17.3 R output of the summary method for BCG_OR. 323
17.4 R output of the summary method for BCG_DSL. 324
17.5 R output of the summary method for BCG_mod. 325
17.6 Plot of observed effect size for the BCG vaccine data against
latitude, with a weighted least squares regression fit shown in
addition. 326
17.7 Example funnel plots from simulated data. The asymmetry
in the lower plot is a hint that a publication bias might be a
problem. 327
17.8 Funnel plot for nicotine gum data. 328

19.1 Scatterplot matrix for the heptathlon data (all countries). 351
19.2 Scatterplot matrix for the heptathlon data after removing
observations of the PNG competitor. 353
19.3 Barplot of the variances explained by the principal compo-
nents (with observations for PNG removed). 356
19.4 Biplot of the (scaled) first two principal components (with
observations for PNG removed). 357
19.5 Scatterplot of the score assigned to each athlete in 1988 and
the first principal component. 358

20.1 Two-dimensional solution from classical multidimensional

scaling of distance matrix for water vole populations. 368
20.2 Minimum spanning tree for the watervoles data. 370
20.3 Two-dimensional solution from non-metric multidimensional
scaling of distance matrix for voting matrix. 371
20.4 The Shepard diagram for the voting data shows some
discrepancies between the original dissimilarities and the
multidimensional scaling solution. 372

21.1 Bivariate data showing the presence of three clusters. 381

21.2 Example of a dendrogram. 383
21.3 Darwin’s Tree of Life. 384
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love a woman—so much, that I am happy to sacrifice the dearest
wish of my heart, because I think I will serve you better by leaving
you.”
He took her hand and held it between his two strong hands.
“Don’t you think,” she whispered, so that he had to bend closer to
hear what she said, “don’t you think I—I ought to be consulted?”
“You—you,” he cried in wonderment, “would you——”
She looked at him with a smile, and her eyes were radiant with
unspoken happiness.
“I want you, Jimmy,” she said. It was the first time she had called him
by name. “I want you, dear.”
His arms were about her, and her lips met his.
They did not hear the tinkle of the bell, but they heard the knock at
the door, and the girl slipped from his arms and was collecting the
tea-things when Angel walked in.
He looked at Jimmy inanely, fiddling with his watch chain, and he
looked at the girl.
“Awfully sorry to intrude again,” he said, “but I got a wire at the little
postoffice up the road telling me I needn’t take the case at
Newcastle, so I thought I’d come back and tell you, Jimmy, that I will
take what I might call a ‘cemetery drink’ with you to-night.”
“I am not going,” said Jimmy, recovering his calm.
“Not—not going?” said the astonished Angel.
“No,” said the girl, speaking over his shoulder, “I have persuaded him
to stay.”
“Ah, so I see!” said Angel, stooping to pick up two hairpins that lay
on the hearthrug.
THE END
 A New and Deadly Force is Introduced
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