(Ebook) A Biostatistics Toolbox For Data Analysis by Steve Selvin ISBN 9781107113084, 1107113083 Online PDF
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A Biostatistics Toolbox for Data Analysis
This sophisticated package of statistical methods is for advanced master’s degree and
Ph.D. students in public health and epidemiology who are involved in the analysis
of data. It makes the link from statistical theory to data analysis, focusing on the
methods and data types most common in public health and related fields. Like most
toolboxes, the statistical tools in this book are organized into sections with similar
objectives. Unlike most toolboxes, however, these tools are accompanied by com-
plete instructions, explanations, detailed examples, and advice on relevant issues and
potential pitfalls – conveying skills, intuition, and experience.
The only prerequisite is a first-year statistics course and familiarity with a com-
puting package such as R, Stata, SPSS, or SAS. Though the book is not tied to
a particular computing language, its figures and analyses were all created using
R. Relevant R code, data sets, and links to public data sets are available from
www.cambridge.org/9781107113084.
Steve Selvin
University of California, Berkeley
32 Avenue of the Americas, New York, NY 10013-2473, USA
www.cambridge.org
Information on this title: www.cambridge.org/9781107113084
C Steve Selvin 2015
A catalog record for this publication is available from the British Library.
Preface xv
Basics
1 Statistical Distributions 3
The Normal Probability Distribution 3
The t-Distribution 7
The Chi-Square Probability Distribution 9
Illustration of the Pearson Chi-Square Statistic – Simplest Case 12
The f-Distribution 13
The Uniform Probability Distribution 13
The p-value 15
A Few Relationships among Probability Distributions 16
2 Confidence Intervals 19
Four Properties of an Estimated Confidence Interval 20
Confidence Intervals for a Function of an Estimate 21
Confidence Intervals Based on Estimates near Zero 21
Exact Confidence Interval (Computer-Estimated) 22
A Confidence Interval Based on an Estimated Median Value 23
A Confidence Interval and a Confidence Band 25
Details: A Confidence Interval and a Statistical Test 27
3 A Weighted Average 29
A Basic Application 29
Ratios and Weighted Averages 30
Estimates Weighted by Reciprocal Variances 32
A Puzzle 37
Age-Adjusted Rates Using Weighted Averages 39
Smoothing – A Weighted Average Approach 40
Example: Weighted Average Smoothing of Hodgkin’s Disease
Mortality Data 44
vii
viii Contents
5 Correlation 69
Spearman’s Rank Correlation Coefficient 73
Point Biserial Correlation Coefficient 74
Nonparametric Measure of Association: The γ -Coefficient 77
A Special Case: The 2 × k Table 80
Chi-Square–Based Measures of Association 81
Proportional Reduction in Error Criterion 83
Applications
6 The 2 × 2 Table 87
The Analysis of a 2 × 2 Table 89
Measures of Association in a 2 × 2 Table 92
Odds Ratio and Relative Risk Ratio 94
A Correction to Improve the Normal Distribution Approximation 96
The Hypergeometric Probability Distribution 98
Fisher’s Exact Test 101
Correlation in a 2 × 2 Table 102
A 2 × 2 Table with a Structural Zero 106
Assessing the Accuracy of a Diagnostic Test 107
Survival
16 Rates 309
An Average Mortality Rate 309
Contents xi
Epidemiology
Genetics
Theory
Books on statistical methods largely fall into two categories: elementary books that describe
statistical techniques and mathematically advanced texts that describe the theory underling
these techniques. This text is about the art and science of applying statistical methods to
the analysis of collected data and provides an answer to the question, after a first course in
statistics, What next? Like most toolboxes, the statistical tools in the text are loosely organized
into sections of similar objectives. Unlike most toolboxes, these tools are accompanied by
complete instructions, explanations, detailed examples, and advice on relevant issues and
potential pitfalls. Thus, the text is a sophisticated introduction to statistical analysis and a
necessary text for master’s and Ph.D. students in epidemiology programs as well as others
whose research requires the analysis of data.
The text employs a pattern of describing sampled data and providing examples followed
by a discussion of the appropriate analytic strategies. This approach introduces the reader to
data and analytic issues and then explores the logic and statistical details. A large number of
examples and illustrations are included to appeal to a diverse audience. It is often the case
that examples produce substantial insight into the problem in hand. Most statistical texts
reverse this approach and describe the statistical method first followed by examples.
The level of this text is beyond introductory but far short of advanced.
Fundamental topics, such as the median values, simple linear regression methods, correla-
tion coefficients, and confidence intervals found in most introductory books are not repeated
but frequently reinforced. The explanations, illustrations, and examples require little or no
mathematics to completely understand the presented material. Nevertheless, simple mathe-
matical notation and arguments are included because they are unambiguous, and frequently
their clarity leads to better understanding.
The complexity of the mathematics that supports the discussion of the statistical tools is
no more than high school algebra. Mostly the symbols and notation from mathematics are
used to describe the various approaches to data analysis. An exception is the last chapter,
which is intended to enrich the applied nature of the text with a bit of statistical theory.
The choices of the statistical tools included in the text are largely based on two criteria:
the usefulness in the analysis of data from human populations as well as a variety of other
methods because they simply demonstrate general statistical data analysis strategies. The
level of presentation of the techniques discussed evolved from a second-year course in
biostatistics for epidemiology graduate students taught over the last decade at the University
of California, Berkeley. Also, much of the material has been presented in summer courses
at the Graduate Summer Session in Epidemiology at the University of Michigan School of
Public Health and more recently at The Johns Hopkins Bloomberg School of Public Health as
xv
xvi Preface
part of the Summer Institute of Epidemiology and Biostatistics. In other words, the material
has been thoroughly “classroom tested.”
The text is organized in six sections.
Section I: BASICS is a review of fundamental statistical distributions and methods: for exam-
ple, confidence intervals and correlation including important details not typically included
in introductory texts.
Section II: APPLICATIONS builds on these basic statistical tools to create more advanced
strategies used to analyze specific kinds of issues and data. Linear models, contingency
table analysis, graphical methods, and bootstrap estimation are examples of methods that are
frequently useful in unraveling the sometimes complicated issues that data are collected to
explore. Also included are parallel and often neglected nonparametric methods.
The next three sections continue to develop new methods as well as include further exten-
sions of basic statistical tools but applied to specific subject matter areas: survival, epidemi-
ologic, and genetic data. These sections are a “proving grounds” for statistical techniques
applied to a variety of challenging kinds of data.
Section III: SURVIVAL contains discussions of three important statistical techniques
designed for the analysis of survival time data. Specifically, they consist of an extensive
exploration of rates and their properties, followed by descriptions of nonparametric methods
and regression models specifically designed to analyze survival data.
Section IV: EPIDEMIOLOGY similarly explores statistical methods particularly designed
for analysis of epidemiologic data such as attributable risk analysis, cluster analysis, ROC
curves, and reclassification methods.
Section V: GENETICS presents statistical tools applied to several fundamental topics to
give a sense of the role of statistics and data analysis in a genetics context. Topics include
a statistical description of selection/mutation dynamics, sibship analysis, and application to
several ways that statistical tools identify the consequences of nonrandom mating.
Section VI: THEORY is focused on the underlying principles of a few statistical tools
frequently used in data analysis settings. This last section, however, is not about data analysis
but is a “user friendly” introduction to how important data analysis tools work. Many
“tools” of modern society are effectively used without even a hint of how and why they
work. Statistical methods are not an exception. This readily accessible “beginner’s guide to
statistical theory” is intended to enrich the focus on applications. Primarily, these theoretical
details demystify the sometimes baffling expressions that appear when the focus is entirely
on description and application. With surprisingly little effort, such mysterious expressions
and the sometimes obscure logic of statistical techniques disappear with use of high school
algebra and a bit of first semester calculus.
Key Features
The text examples mostly consist of small subsets of real data so that the analytic results
described are easily verified or explored with alternative analyses. These examples also
range over a number of methods and kinds of data, from estimating missing values to special
Preface xvii
techniques potentially useful in the analysis of genetic data. Several statistical methods are
illustrated with the analysis of complete and again real data in terms of comprehensive case
studies.
The introduction of many of the statistical methods discussed begins with an example
made up of only a few artificial observations. These miniature examples allow simple “hands-
on” illustrations of the more complicated computational and technical details. In addition,
more than 150 figures provide visual displays of analytic concepts, and issues adding yet
another important dimension to the use of statistical tools to analyze data. The distinguished
statistician John W. Tukey stated, “The greatest value of a picture is it forces us to notice
what we never see.”
It is not possible to characterize statistical methods in a definite linear or logical sequence.
The discussed techniques are indexed to create a “road map” so that the interconnections
among the discussed material can be traced back and forth throughout the text.
Nonparametric methods are typically treated as a separate topic. These methods are
integrated into the text where they are natural partners to parallel parametric methods. These
important techniques enrich the practice and understanding of most statistical approaches
and are particularly important when small sample sizes are encountered.
The text does not contain references to parallel published material. The ability to use
online searches to locate references certainly replaces the tradition of annotating a text.
Using Google, for example, easily produces not only specific material referenced in the text
but a wide range of other perhaps worthwhile sources on the same topic.
An appendix contains the computer code that produced the worked-out examples in
the text. The statistical software used is entitled simply “R.” Free and easily downloaded,
it provides an extensive statistical analysis system. The explanations and details in the
appendix are not comprehensive and are left to manuals and books created exactly for
this purpose. The R system, however, is completely self-documenting with direct access
to descriptions of the R language, computer code, and examples. In addition, this pop-
ular data analysis system is well documented in numerous books, and a huge number
of online computer sites exist that provide specific instructions and illustrations. The
R analyses in the appendix can be used in variety of ways in conjunction with the text.
First, using the presented code to verify the text material provides an extremely detailed
description of the application of specific methods and statistical approaches. Furthermore,
with minor modification, additional data sets can be analyzed to furnish alternative examples
or assess results from larger sample sizes or gauge the influences of extreme values. The
text does not refer to or depend on the R code, and the appendix can be completely ignored.
At the other extreme, this appendix presents the opportunity to be part of learning a useful
statistical analysis software language. R is available from www.r-project.org.
Remember, the study of statistics makes it possible to acquire the ability to state with great
certainty the degree of uncertainty.
Basics
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