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Fundamentals of
Causal Inference
with R
CHAPMAN & HALL/CRC
Texts in Statistical Science Series
Joseph K. Blitzstein, Harvard University, USA
Julian J. Faraway, University of Bath, UK
Martin Tanner, Northwestern University, USA
Jim Zidek, University of British Columbia, Canada
Bayesian Networks
With Examples in R, Second Edition
Marco Scutari and Jean-Baptiste Denis
Time Series
Modeling, Computation, and Inference, Second Edition
Raquel Prado, Marco A. R. Ferreira and Mike West
Sampling
Design and Analysis, Third Edition
Sharon L. Lohr
Bayes Rules!
An Introduction to Applied Bayesian Modeling
Alicia Johnson, Miles Ott and Mine Dogucu
Babette A. Brumback
First edition published 2022
by CRC Press
6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742
The right of Babette A. Brumback to be identified as author of this work has been asserted by him/
her/them in accordance with sections 77 and 78 of the Copyright, Designs and Patents Act 1988.
Reasonable efforts have been made to publish reliable data and information, but the author and pub-
lisher cannot assume responsibility for the validity of all materials or the consequences of their use.
The authors and publishers have attempted to trace the copyright holders of all material reproduced
in this publication and apologize to copyright holders if permission to publish in this form has not
been obtained. If any copyright material has not been acknowledged please write and let us know so
we may rectify in any future reprint.
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transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or
hereafter invented, including photocopying, microfilming, and recording, or in any information
storage or retrieval system, without written permission from the publishers.
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DOI: 10.1201/9781003146674
Typeset in CMR10
by KnowledgeWorks Global Ltd.
Preface xi
1 Introduction 1
1.1 A Brief History . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Data Examples . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.2.1 Mortality Rates by Country . . . . . . . . . . . . . . . 6
1.2.2 National Center for Education Statistics . . . . . . . . 8
1.2.3 Reducing Alcohol Consumption . . . . . . . . . . . . . 9
1.2.3.1 The What-If? Study . . . . . . . . . . . . . . 9
1.2.3.2 The Double What-If? Study . . . . . . . . . 10
1.2.4 General Social Survey . . . . . . . . . . . . . . . . . . 13
1.2.5 A Cancer Clinical Trial . . . . . . . . . . . . . . . . . 15
1.3 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
vii
viii Contents
12 Mediation 195
12.1 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
12.2 Traditional Parametric Methods . . . . . . . . . . . . . . . . 199
12.3 More Examples . . . . . . . . . . . . . . . . . . . . . . . . . 200
12.4 Exercise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
Appendix 223
Bibliography 225
Index 233
Preface
xi
xii Preface
dividing up the work of making a presentation for each one. Then, I randomly
called on students from the class to present their solutions. I made sure that
the groups were relatively balanced in terms of student levels. The pilot test
went well. The material is accessible to senior-level undergraduate students in
Statistics, and likely also in Data Science (the program at the University of
Florida was too new to have any of those). It is even more accessible to M.S.
students in Biostatistics and Statistics, and not too easy to avoid challenging
Ph.D. students from a variety of programs.
In my career, I have always been motivated by real examples. Therefore, I
worked hard to include as many real data examples as possible in the book and
in the exercises. I chose to analyze the data examples using R throughout the
book. Some familiarity with R is essential prior to beginning the textbook. The
appendix documents where to download R and which packages are necessary
for the R code presented in the book. Having been fortunate to teach very many
times out of the textbooks by J.J. Faraway that include R code and real data
examples, I thought his approach would also work well for causal inference.
Having said this, I also find it very helpful to learn and teach causal inference
methods using simulated data examples, for which the causal mechanisms are
known. Thus, I also make extensive use of simulations throught the text.
In very many of the examples, I do not really believe that the results can be
interpreted causally. Indeed, I am generally very cautious about interpreting
results causally, even when the required assumptions are more plausible. Nev-
ertheless, many methods in this book can also be applied when assumptions
do not hold, and in this case they have meaning as “adjusted associations,”
which are often still of interest to collaborators. Furthermore, I believe such
examples still have pedagogical value.
I have taught Causal Inference three times. First, in Fall of 1999 at the
University of Washington, when I was just starting out and did not know
much at all; furthermore, textbooks on the topic were virtually non-existent.
Second, in Spring of 2020 at the University of Florida, when I taught out of
the new textbook by M.A. Hernan and J.M. Robins. This motivated me to try
to present the material in my own way when I taught for the third time and
piloted this textbook in Spring of 2021 at the University of Florida. I wish to
thank all of my previous mentors and especially the students of those three
classes, who asked many good questions that taught me a lot. Students of the
third class pointed out many typos and errors in the textbook and also made
suggestions for how to improve it. I am grateful to all, but wish to specifically
acknowledge those who gave me written permission: Seungjun Ahn, Saurabh
Bhandari, James Colee, Amy M. Crisp, Deborah Rozum, Jeremy Sanchez,
Jake Shannin, Eric A. Wright, Dongyuan Wu, Xiulin Xie, Kai Yang, Xiaomeng
Yuan, Wenjie Zeng, Runzhi Zhang, and Xinyi Zhang. Many thanks also to
Edward Kennedy, Nandita Mitra, and Ronghui Xu for their helpful reviews.
A website for the book with datasets, R code, solutions to the
odd exercises, and more is available by searching for the textbook at
www.routledge.com.
1
Introduction
DOI: 10.1201/9781003146674-1 1
2 Introduction
“We have no other notion of cause and effect, but that of certain objects,
which have been always conjoined together, and which in all past instances
have been found inseparable. We cannot penetrate into the reason of the
conjunction. We only observe the thing itself, and always find that, from
the constant conjunction, the objects require a union in the imagination...
Thus, though causation be a philosophical relation, as implying contiguity,
succession, and constant conjunction, yet it is only so far as it is a natural
relation, and produces a union among our ideas, that we are able to reason
upon it, or draw any inference from it.”
It is noteworthy that Hume did not propose any methods to verify a causal
relationship other than to observe contiguity, succession, and constant con-
junction. Nevertheless, shortly afterwards in 1747, James Lind undertook what
is widely recognized today as one of the very first medical trials, proving a
causal relationship between eating oranges and lemon and recovering from
scurvy. From Brown (2005), we read that Lind took aside twelve men with
advanced symptoms of scurvy “as similar as I could have them.” Six pairs of
men aboard the HMS Salisbury were thus experimented upon. The first pair
were given slightly alcoholic cider. The second were given an elixir of vitriol.
The third pair took vinegar. The fourth drank sea water. The fifth were fed
two oranges and one lemon daily for six days, when the meager supply ran
out. The sixth were given a medicinal paste and cream of tartar, which is a
mild laxative. The pair who were fed the oranges and the lemons were nearly
recovered after only a week. Those who had drunk the cider responded favor-
ably, but at the end of two weeks they were still too weak to return to duty.
The other four pairs did not experience good effects.
By 1846, Mill (1846), in his five canons, proposed five methods for proving
cause and effect:
“First Canon (the Method of Agreement): If two or more instances of the
phenomenon under investigation have only one circumstance in common,
the circumstance in which alone all the instances agree, is the cause (or
effect) of the given phenomenon.
Second Canon (the Method of Difference): If an instance in which the
phenomenon-under investigation occurs, and an instance in which it does
not occur, have every circumstance save one in common, that one occurring
only in the former; the circumstance in which alone the two instances differ,
is the effect, or cause, or a necessary part off the cause, off the phenomenon.
Third Canon (the Joint Method of Agreement and Difference): If two or
more instances in which the phenomenon occurs have only one circum-
stance in common, while two or more instances in which it does not occur
have nothing in common save the absence of that circumstance; the cir-
cumstance in which alone the two sets of instances differ, is the effect, or
cause, or a necessary part of the cause, of the phenomenon.
Discovering Diverse Content Through
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expectation that the particle will permanently adhere to the surface of
the filter.
Incendiary Devices
The incendiary devices used during the late war included: bombs,
shell, tracer shell and bullets, grenades, and flame throwers.
Bombs
Later the Germans used a scatter type of bomb (Fig. 109) which
was designed to give 46 points of conflagration. Each of these 46
small cylinders contained 50 grams of an air incendiary material.
They were arranged in layers, packed in with very fine gun powder.
The bomb is ignited by a friction lighter which is pulled automatically
when the bomb is released from the aeroplane. The bomb is
constructed to burst in the air and not on striking the ground. The
upper part of the projectile consists of a cast iron nose riveted to the
sheet iron body of the bomb. When the explosion occurs, the nose is
blown away and the small incendiary cylinders are scattered in the
air.
The incendiary material appears to be a mixture of barium nitrate
and tar. Its incendiary power is very low because combustion takes
the form of a small flame of very short duration. It should, however,
be very valuable for firing inflammable materials.
British Bombs. The early British bombs were petrol bombs,
which were used without great success for crop burning. Phosphorus
bombs were then used for attacking aircraft. But the most successful
incendiary is the so-called “Baby Incendiary Bomb.” This is a 6.5-
ounce bomb with an incendiary charge of special thermit. These
small bombs are carried in containers holding either 144 or 272
bombs. The former container approximates in size and weight one
50-pound H.E. bomb and the latter one 120-pound H.E. bomb. The
bomb contains a cartridge very much like a shot gun shell which, on
impact, sets down on the striker point in the base of the body, and
causes the ignition of the charge. It is claimed that the cartridge of
the B.I. bomb burns when totally immersed in any liquid (water
included) and in depths up to two feet the flame breaks through the
surface.
French Bombs. The French used three types of incendiary
bombs, a special thermit (calonite), the Chenard and the Davidsen.
The Chenard bomb is a true intensive type and is thought to be very
successful. It functions by means of a time fuse operated by the
unscrewing of a propeller, before striking the ground, and reaches its
target in flames. Its chief disadvantage is the small amount of
incendiary material which it carries. The Davidsen bomb expels its
charge as a single unit and is not considered as valuable or as
successful as the Chenard.
American Bombs. The program of the Chemical Warfare
Service included three types of bombs:
Mark II Incendiary drop bomb
Mark III Incendiary drop bomb
Mark I Scatter bomb
Mark II Bomb. The incendiary Mark II drop bomb is designed to
be dropped from an aeroplane and is intended for use against
buildings, etc., when penetrating effect followed by an intensive
incendiary action is sought.
The bomb case consists of two parts: a body and a nose. The
body is a tapering zinc shell which carries the firing mechanism and
stabilizing tail fin at the small end and at the large end a threaded
ring which screws into the nose. The nose is of drawn steel of such
shape as to have low end-on resistance and is sufficiently strong to
penetrate frame structures.
Incendiary Darts