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Chapter 0 Preface
0.1 My theory, which is mine
The premise of this book, and the other books in the Think X series, is that if you know how to program, you can use that skill to learn other topics.
Most books on Bayesian statistics use mathematical notation and present ideas in terms of mathematical concepts like calculus. This book uses Python code instead of math, and discrete approximations instead of continuous mathematics. As a result, what would be an integral in a math book becomes a summation, and most operations on probability distributions are simple loops.
I think this presentation is easier to understand, at least for people with programming skills. It is also more general, because when we make modeling decisions, we can choose the most appropriate model without worrying too much about whether the model lends itself to conventional analysis.
Also, it provides a smooth development path from simple examples to real-world problems. Chapter 3 is a good example. It starts with a simple example involving dice, one of the staples of basic probability. From there it proceeds in small steps to the locomotive problem, which I borrowed from Mosteller’s Fifty Challenging Problems in Probability with Solutions, and from there to the German tank problem, a famously successful application of Bayesian methods during World War II.
0.2 Modeling and approximation
Most chapters in this book are motivated by a real-world problem, so they involve some degree of modeling. Before we can apply Bayesian methods (or any other analysis), we have to make decisions about which parts of the real-world system to include in the model and which details we can abstract away.
For example, in Chapter 7, the motivating problem is to predict the winner of a hockey game. I model goal-scoring as a Poisson process, which implies that a goal is equally likely at any point in the game. That is not exactly true, but it is probably a good enough model for most purposes.
In Chapter 12 the motivating problem is interpreting SAT scores (the SAT is a standardized test used for college admissions in the United States). I start with a simple model that assumes that all SAT questions are equally difficult, but in fact the designers of the SAT deliberately include some questions that are relatively easy and some that are relatively hard. I present a second model that accounts for this aspect of the design, and show that it doesn’t have a big effect on the results after all.
I think it is important to include modeling as an explicit part of problem solving because it reminds us to think about modeling errors (that is, errors due to simplifications and assumptions of the model).
Many of the methods in this book are based on discrete distributions, which makes some people worry about numerical errors. But for real-world problems, numerical errors are almost always smaller than modeling errors.
Furthermore, the discrete approach often allows better modeling decisions, and I would rather have an approximate solution to a good model than an exact solution to a bad model.
On the other hand, continuous methods sometimes yield performance advantages—for example by replacing a linear- or quadratic-time computation with a constant-time solution.
So I recommend a general process with these steps:
One benefit of this process is that Steps 1 and 2 tend to be fast, so you can explore several alternative models before investing heavily in any of them.
Another benefit is that if you get to Step 3, you will be starting with a reference implementation that is likely to be correct, which you can use for regression testing (that is, checking that the optimized code yields the same results, at least approximately).
0.3 Working with the code
The code and sound samples used in this book are available from https://github.com/AllenDowney/ThinkBayes. Git is a version control system that allows you to keep track of the files that make up a project. A collection of files under Git’s control is called a “repository”. GitHub is a hosting service that provides storage for Git repositories and a convenient web interface.
The GitHub homepage for my repository provides several ways to work with the code:
The code for the first edition of the book works with Python 2. If you are using Python 3, you might want to use the updated code in https://github.com/AllenDowney/ThinkBayes2 instead.
I developed this book using Anaconda from Continuum Analytics, which is a free Python distribution that includes all the packages you’ll need to run the code (and lots more). I found Anaconda easy to install. By default it does a user-level installation, not system-level, so you don’t need administrative privileges. You can download Anaconda from http://continuum.io/downloads.
If you don’t want to use Anaconda, you will need the following packages:
Although these are commonly used packages, they are not included with all Python installations, and they can be hard to install in some environments. If you have trouble installing them, I recommend using Anaconda or one of the other Python distributions that include these packages.
Many of the examples in this book use classes and functions defined in thinkbayes.py. Some of them also use thinkplot.py, which provides wrappers for some of the functions in pyplot, which is part of matplotlib.
0.4 Code style
Experienced Python programmers will notice that the code in this book does not comply with PEP 8, which is the most common style guide for Python (http://www.python.org/dev/peps/pep-0008/).
Specifically, PEP 8 calls for lowercase function names with
underscores between words,
I broke this rule because I developed some of the code while I was a Visiting Scientist at Google, so I followed the Google style guide, which deviates from PEP 8 in a few places. Once I got used to Google style, I found that I liked it. And at this point, it would be too much trouble to change.
Also on the topic of style, I write “Bayes’s theorem” with an s after the apostrophe, which is preferred in some style guides and deprecated in others. I don’t have a strong preference. I had to choose one, and this is the one I chose.
And finally one typographical note: throughout the book, I use PMF and CDF for the mathematical concept of a probability mass function or cumulative distribution function, and Pmf and Cdf to refer to the Python objects I use to represent them.
There are several excellent modules for doing Bayesian statistics in Python, including pymc and OpenBUGS. I chose not to use them for this book because you need a fair amount of background knowledge to get started with these modules, and I want to keep the prerequisites minimal. If you know Python and a little bit about probability, you are ready to start this book.
Chapter 1 is about probability and Bayes’s theorem; it has no code. Chapter 2 introduces Pmf, a thinly disguised Python dictionary I use to represent a probability mass function (PMF). Then Chapter 3 introduces Suite, a kind of Pmf that provides a framework for doing Bayesian updates.
In some of the later chapters, I use analytic distributions including the Gaussian (normal) distribution, the exponential and Poisson distributions, and the beta distribution. In Chapter 15 I break out the less-common Dirichlet distribution, but I explain it as I go along. If you are not familiar with these distributions, you can read about them on Wikipedia. You could also read the companion to this book, Think Stats, or an introductory statistics book (although I’m afraid most of them take a mathematical approach that is not particularly helpful for practical purposes).
If you include at least part of the sentence the error appears in, that makes it easy for me to search. Page and section numbers are fine, too, but not as easy to work with. Thanks!
Other people who spotted typos and small errors include Tom Pollard, Paul A. Giannaros, Jonathan Edwards, George Purkins, Robert Marcus, Ram Limbu, James Lawry, Ben Kahle, Jeffrey Law, and Alvaro Sanchez.
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