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 Introductory Statistics for the
Life and Biomedical Sciences
First Edition

Julie Vu
Preceptor in Statistics
Harvard University

David Harrington
Professor of Biostatistics (Emeritus)
Harvard T.H. Chan School of Public Health
Dana-Farber Cancer Institute

A tablet-friendly version of this PDF

where margins have been minimized
can be found in the book's extra files.
Copyright © 2020. First Edition.
Version date: July 26th, 2020.

This textbook and its supplements, including slides and labs, may be downloaded for free at
openintro.org/book/biostat.

This textbook is a derivative of OpenIntro Statistics 3rd Edition by Diez, Barr, and Çetinkaya-
Rundel, and it is available under a Creative Commons Attribution-ShareAlike 3.0 Unported United
States license. License details are available at the Creative Commons website:
creativecommons.org.

Source files for this book may be found on Github at

github.com/OI-Biostat/oi_biostat_text.
 3

Table of Contents

1 Introduction to data 10
1.1 Case study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.2 Data basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
1.3 Data collection principles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
1.4 Numerical data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
1.5 Categorical data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
1.6 Relationships between two variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
1.7 Exploratory data analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
1.8 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
1.9 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

2 Probability 88
2.1 Defining probability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
2.2 Conditional probability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
2.3 Extended example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
2.4 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
2.5 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

3 Distributions of random variables 138

3.1 Random variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
3.2 Binomial distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
3.3 Normal distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
3.4 Poisson distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
3.5 Distributions related to Bernoulli trials . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
3.6 Distributions for pairs of random variables . . . . . . . . . . . . . . . . . . . . . . . . 177
3.7 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
3.8 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185

4 Foundations for inference 198

4.1 Variability in estimates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
4.2 Confidence intervals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
4.3 Hypothesis testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
4.4 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
4.5 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
4 TABLE OF CONTENTS

5 Inference for numerical data 236

5.1 Single-sample inference with the t-distribution . . . . . . . . . . . . . . . . . . . . . . 238
5.2 Two-sample test for paired data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
5.3 Two-sample test for independent data . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
5.4 Power calculations for a difference of means . . . . . . . . . . . . . . . . . . . . . . . . 257
5.5 Comparing means with ANOVA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
5.6 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
5.7 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274

6 Simple linear regression 290

6.1 Examining scatterplots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293
6.2 Estimating a regression line using least squares . . . . . . . . . . . . . . . . . . . . . . 295
6.3 Interpreting a linear model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298
6.4 Statistical inference with regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
6.5 Interval estimates with regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312
6.6 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316
6.7 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317

7 Multiple linear regression 330

7.1 Introduction to multiple linear regression . . . . . . . . . . . . . . . . . . . . . . . . . 332
7.2 Simple versus multiple regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 334
7.3 Evaluating the fit of a multiple regression model . . . . . . . . . . . . . . . . . . . . . 338
7.4 The general multiple linear regression model . . . . . . . . . . . . . . . . . . . . . . . 342
7.5 Categorical predictors with several levels . . . . . . . . . . . . . . . . . . . . . . . . . . 347
7.6 Reanalyzing the PREVEND data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350
7.7 Interaction in regression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
7.8 Model selection for explanatory models . . . . . . . . . . . . . . . . . . . . . . . . . . 358
7.9 The connection between ANOVA and regression . . . . . . . . . . . . . . . . . . . . . 368
7.10 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370
7.11 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372

8 Inference for categorical data 386

8.1 Inference for a single proportion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 388
8.2 Inference for the difference of two proportions . . . . . . . . . . . . . . . . . . . . . . 395
8.3 Inference for two or more groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401
8.4 Chi-square tests for the fit of a distribution . . . . . . . . . . . . . . . . . . . . . . . . 414
8.5 Outcome-based sampling: case-control studies . . . . . . . . . . . . . . . . . . . . . . 416
8.6 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 420
8.7 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421

A End of chapter exercise solutions 435

B Distribution tables 463

Index 469
 5

Foreword

The past year has been challenging for the health sciences in ways that we could not have imagined
when we started writing 5 years ago. The rapid spread of the SARS coronavirus (SARS-CoV-2)
worldwide has upended the scientific research process and highlighted the need for maintaining a
balance between speed and reliability. Major medical journals have dramatically increased the pace
of publication; the urgency of the situation necessitates that data and research findings be made
available as quickly as possible to inform public policy and clinical practice. Yet it remains essential
that studies undergo rigorous review; the retraction of two high-profile coronavirus studies 1, 2
sparked widespread concerns about data integrity, reproducibility, and the editorial process.
In parallel, deepening public awareness of structural racism has caused a re-examination of
the role of race in published studies in health and medicine. A recent review of algorithms used to
direct treatment in areas such as cardiology, obstetrics and oncology uncovered examples of race
used in ways that may lead to substandard care for people of color. 3 The SARS-CoV-2 pandemic
has reminded us once again that marginalized populations are disproportionately at risk for bad
health outcomes. Data on 17 million patients in England 4 suggest that Blacks and South Asians
have a death rate that is approximately 50% higher than white members of the population.
Understanding the SARS coronavirus and tackling racial disparities in health outcomes are
but two of the many areas in which Biostatistics will play an important role in the coming decades.
Much of that work will be done by those now beginning their study of Biostatistics. We hope this
book provides an accessible point of entry for students planning to begin work in biology, medicine,
or public health. While the material presented in this book is essential for understanding the
foundations of the discipline, we advise readers to remember that a mastery of technical details is
secondary to choosing important scientific questions, examining data without bias, and reporting
results that transparently display the strengths and weaknesses of a study.

1 Mandeep R. Mehra et al. “Retraction: Cardiovascular Disease, Drug Therapy, and Mortality in Covid-19. N Engl J
Med. DOI: 10.1056/NEJMoa2007621.” In: New England Journal of Medicine 382.26 (2020), pp. 2582–2582. doi: 10.1056/
NEJMc2021225.
2 Mandeep R Mehra et al. “RETRACTED:Hydroxychloroquine or chloroquine with or without a macrolide for treatment
of COVID-19: a multinational registry analysis”. In: The Lancet (2020). doi: https://doi.org/10.1016/S0140- 6736(20)
31180-6.
3 Darshali A. Vyas et al. “Hidden in Plain Sight — Reconsidering the Use of Race Correction in Clinical Algorithms”.
In: New England Journal of Medicine (2020). doi: 10.1056/NEJMms2004740.
4 Elizabeth J. Williamson et al. “OpenSAFELY: factors associated with COVID-19 death in 17 million patients”. In:
Nature (2020). issn: 1476-4687.
 6

Preface

This text introduces statistics and its applications in the life sciences and biomedical research. It is
based on the freely available OpenIntro Statistics, and, like OpenIntro, it may be downloaded at no
cost. 5 In writing Introduction to Statistics for the Life and Biomedical Sciences, we have added sub-
stantial new material, but also retained some examples and exercises from OpenIntro that illustrate
important ideas even if they do not relate directly to medicine or the life sciences. Because of its
link to the original OpenIntro project, this text is often referred to as OpenIntro Biostatistics in the
supplementary materials.
This text is intended for undergraduate and graduate students interested in careers in biology
or medicine, and may also be profitably read by students of public health or medicine. It cov-
ers many of the traditional introductory topics in statistics, in addition to discussing some newer
methods being used in molecular biology.
Statistics has become an integral part of research in medicine and biology, and the tools for
summarizing data and drawing inferences from data are essential both for understanding the out-
comes of studies and for incorporating measures of uncertainty into that understanding. An intro-
ductory text in statistics for students who will work in medicine, public health, or the life sciences
should be more than simply the usual introduction, supplemented with an occasional example
from biology or medical science. By drawing the majority of examples and exercises in this text
from published data, we hope to convey the value of statistics in medical and biological research. In
cases where examples draw on important material in biology or medicine, the problem statement
contains the necessary background information.
Computing is an essential part of the practice of statistics. Nearly everyone entering the
biomedical sciences will need to interpret the results of analyses conducted in software; many
will also need to be capable of conducting such analyses. The text and associated materials sepa-
rate those two activities to allow students and instructors to emphasize either or both skills. The
text discusses the important features of figures and tables used to support an interpretation, rather
than the process of generating such material from data. This allows students whose main focus
is understanding statistical concepts not to be distracted by the details of a particular software
package. In our experience, however, we have found that many students enter a research setting
after only a single course in statistics. These students benefit from a practical introduction to data
analysis that incorporates the use of a statistical computing language. The‘ self-paced learning labs
associated with the text provide such an introduction; these are described in more detail later in
this preface. The datasets used in this book are available via the R openintro package available on
CRAN 6 and the R oibiostat package available via GitHub.
5 PDF available at https://www.openintro.org/book/biostat/ and source available at https://github.com/
OI-Biostat/oi_biostat_text.
6 Diez DM, Barr CD, Çetinkaya-Rundel M. 2012. openintro: OpenIntro data sets and supplement functions. http:
//cran.r-project.org/web/packages/openintro.
 7

Textbook overview
The chapters of this book are as follows:

1. Introduction to data. Data structures, basic data collection principles, numerical and graphical
summaries, and exploratory data analysis.
2. Probability. The basic principles of probability.
3. Distributions of random variables. Introduction to random variables, distributions of discrete
and continuous random variables, and distributions for pairs of random variables.
4. Foundations for inference. General ideas for statistical inference in the context of estimating a
population mean.
5. Inference for numerical data. Inference for one-sample and two-sample means with the t-distribution,
power calculations for a difference of means, and ANOVA.
6. Simple linear regression. An introduction to linear regression with a single explanatory vari-
able, evaluating model assumptions, and inference in a regression context.
7. Multiple linear regression. General multiple regression model, categorical predictors with more
than two values, interaction, and model selection.
8. Inference for categorical data. Inference for single proportions, inference for two or more groups,
and outcome-based sampling.

Examples, exercises, and appendices

Examples in the text help with an understanding of how to apply methods:

EXAMPLE 0.1
This is an example. When a question is asked here, where can the answer be found?

The answer can be found here, in the solution section of the example.

When we think the reader would benefit from working out the solution to an example, we frame it
as Guided Practice.

GUIDED PRACTICE 0.2

The reader may check or learn the answer to any Guided Practice problem by reviewing the full
solution in a footnote. 7

There are exercises at the end of each chapter that are useful for practice or homework as-
signments. Solutions to odd numbered problems can be found in Appendix A. Readers will notice
that there are fewer end of chapter exercises in the last three chapters. The more complicated
methods, such as multiple regression, do not always lend themselves to hand calculation, and
computing is increasingly important both to gain practical experience with these methods and to
explore complex datasets. For students more interested in concepts than computing, however, we
have included useful end of chapter exercises that emphasize the interpretation of output from
statistical software.
Probability tables for the normal, t, and chi-square distributions are in Appendix B, and PDF
copies of these tables are also available from openintro.org for anyone to download, print, share, or
modify. The labs and the text also illustrate the use of simple R commands to calculate probabilities
from common distributions.
7 Guided Practice problems are intended to stretch your thinking, and you can check yourself by reviewing the footnote
solution for any Guided Practice.
8 CHAPTER 0. PREFACE

Self-paced learning labs

The labs associated with the text can be downloaded from github.com/OI-Biostat/oi_biostat_
labs. They provide guidance on conducting data analysis and visualization with the R statistical
language and the computing environment RStudio, while building understanding of statistical
concepts. The labs begin from first principles and require no previous experience with statistical
software. Both R and RStudio are freely available for all major computing operating systems, and
the Unit 0 labs (00_getting_started) provide information on downloading and installing them.
Information on downloading and installing the packages may also be found at openintro.org.
The labs for each chapter all have the same structure. Each lab consists of a set of three
documents: a handout with the problem statements, a template to be used for working through
the lab, and a solution set with the problem solutions. The handout and solution set are most
easily read in PDF format (although Rmd files are also provided), while the template is an Rmd
file that can be loaded into RStudio. Each chapter of labs is accompanied by a set of "Lab Notes",
which provides a reference guide of all new R functions discussed in the labs.
Learning is best done, of course, if a student attempts the lab exercises before reading the
solutions. The "Lab Notes" may be a useful resource to refer to while working through problems.

OpenIntro, online resources, and getting involved

OpenIntro is an organization focused on developing free and affordable education materials. The
first project, OpenIntro Statistics, is intended for introductory statistics courses at the high school
through university levels. Other projects examine the use of randomization methods for learning
about statistics and conducting analyses (Introductory Statistics with Randomization and Simulation)
and advanced statistics that may be taught at the high school level (Advanced High School Statistics).
We encourage anyone learning or teaching statistics to visit openintro.org and get involved by
using the many online resources, which are all free, or by creating new material. Students can test
their knowledge with practice quizzes, or try an application of concepts learned in each chapter
using real data and the free statistical software R. Teachers can download the source for course
materials, labs, slides, datasets, R figures, or create their own custom quizzes and problem sets for
students to take on the website. Everyone is also welcome to download the book’s source files to
create a custom version of this textbook or to simply share a PDF copy with a friend or on a website.
All of these products are free, and anyone is welcome to use these online tools and resources with
or without this textbook as a companion.

Acknowledgements
The OpenIntro project would not have been possible without the dedication of many people, in-
cluding the authors of OpenIntro Statistics, the OpenIntro team and the many faculty, students,
and readers who commented on all the editions of OpenIntro Statistics.
This text has benefited from feedback from Andrea Foulkes, Raji Balasubramanian, Curry
Hilton, Michael Parzen, Kevin Rader, and the many excellent teaching fellows at Harvard College
who assisted in courses using the book. The cover design was provided by Pierre Baduel.
9
 10

Chapter 1
Introduction to data

1.1 Case study

1.2 Data basics

1.3 Data collection principles

1.4 Numerical data

1.5 Categorical data

1.6 Relationships between two variables

1.7 Exploratory data analysis

1.8 Notes

1.9 Exercises
 11

Making observations and recording data form the backbone of empirical research,
and represent the beginning of a systematic approach to investigating scientific
questions. As a discipline, statistics focuses on addressing the following three
questions in a rigorous and efficient manner: How can data best be collected? How
should data be analyzed? What can be inferred from data?

This chapter provides a brief discussion on the principles of data collection, and
introduces basic methods for summarizing and exploring data.

For labs, slides, and other resources, please visit

www.openintro.org/book/biostat
12 CHAPTER 1. INTRODUCTION TO DATA

1.1 Case study: preventing peanut allergies

The proportion of young children in Western countries with peanut allergies has doubled in
the last 10 years. Previous research suggests that exposing infants to peanut-based foods, rather
than excluding such foods from their diets, may be an effective strategy for preventing the develop-
ment of peanut allergies. The "Learning Early about Peanut Allergy" (LEAP) study was conducted
to investigate whether early exposure to peanut products reduces the probability that a child will
develop peanut allergies. 1
The study team enrolled children in the United Kingdom between 2006 and 2009, selecting
640 infants with eczema, egg allergy, or both. Each child was randomly assigned to either the
peanut consumption (treatment) group or the peanut avoidance (control) group. Children in the
treatment group were fed at least 6 grams of peanut protein daily until 5 years of age, while chil-
dren in the control group avoided consuming peanut protein until 5 years of age.
At 5 years of age, each child was tested for peanut allergy using an oral food challenge (OFC): 5
grams of peanut protein in a single dose. A child was recorded as passing the oral food challenge if
no allergic reaction was detected, and failing the oral food challenge if an allergic reaction occurred.
These children had previously been tested for peanut allergy through a skin test, conducted at the
time of study entry; the main analysis presented in the paper was based on data from 530 children
with an earlier negative skin test. 2
Individual-level data from the study are shown in Figure 1.1 for 5 of the 530 children—each
row represents a participant and shows the participant’s study ID number, treatment group assign-
ment, and OFC outcome. 3

participant.ID treatment.group overall.V60.outcome

LEAP_100522 Peanut Consumption PASS OFC
LEAP_103358 Peanut Consumption PASS OFC
LEAP_105069 Peanut Avoidance PASS OFC
LEAP_994047 Peanut Avoidance PASS OFC
LEAP_997608 Peanut Consumption PASS OFC

Figure 1.1: Individual-level LEAP results, for five children.

The data can be organized in the form of a two-way summary table; Figure 1.2 shows the
results categorized by treatment group and OFC outcome.

FAIL OFC PASS OFC Sum

Peanut Avoidance 36 227 263
Peanut Consumption 5 262 267
Sum 41 489 530

Figure 1.2: Summary of LEAP results, organized by treatment group (either

peanut avoidance or consumption) and result of the oral food challenge at 5 years
of age (either pass or fail).

1 Du Toit, George, et al. Randomized trial of peanut consumption in infants at risk for peanut allergy. New England
Journal of Medicine 372.9 (2015): 803-813.
2 Although a total of 542 children had an earlier negative skin test, data collection did not occur for 12 children.
3 The data are available as LEAP in the R package oibiostat.
1.1. CASE STUDY 13

The summary table makes it easier to identify patterns in the data. Recall that the question
of interest is whether children in the peanut consumption group are more or less likely to develop
peanut allergies than those in the peanut avoidance group. In the avoidance group, the proportion
of children failing the OFC is 36/263 = 0.137 (13.7%); in the consumption group, the proportion
of children failing the OFC is 5/267 = 0.019 (1.9%). Figure 1.3 shows a graphical method of dis-
playing the study results, using either the number of individuals per category from Figure 1.2 or
the proportion of individuals with a specific OFC outcome in a group.

1.0
FAIL OFC FAIL OFC
250
PASS OFC PASS OFC
0.8
200
0.6
150

0.4
100

50 0.2

0 0.0
Peanut Avoidance Peanut Consumption Peanut Avoidance Peanut Consumption

(a) (b)

Figure 1.3: (a) A bar plot displaying the number of individuals who failed or
passed the OFC in each treatment group. (b) A bar plot displaying the proportions
of individuals in each group that failed or passed the OFC.

The proportion of participants failing the OFC is 11.8% higher in the peanut avoidance group
than the peanut consumption group. Another way to summarize the data is to compute the ratio of
the two proportions (0.137/0.019 = 7.31), and conclude that the proportion of participants failing
the OFC in the avoidance group is more than 7 times as large as in the consumption group; i.e.,
the risk of failing the OFC was more than 7 times as great for participants in the avoidance group
relative to the consumption group.
Based on the results of the study, it seems that early exposure to peanut products may be
an effective strategy for reducing the chances of developing peanut allergies later in life. It is
important to note that this study was conducted in the United Kingdom at a single site of pediatric
care; it is not clear that these results can be generalized to other countries or cultures.
The results also raise an important statistical issue: does the study provide definitive evidence
that peanut consumption is beneficial? In other words, is the 11.8% difference between the two
groups larger than one would expect by chance variation alone? The material on inference in later
chapters will provide the statistical tools to evaluate this question.
14 CHAPTER 1. INTRODUCTION TO DATA

1.2 Data basics

Effective organization and description of data is a first step in most analyses. This section
introduces a structure for organizing data and basic terminology used to describe data.

1.2.1 Observations, variables, and data matrices

In evolutionary biology, parental investment refers to the amount of time, energy, or other
resources devoted towards raising offspring. This section introduces the frog dataset, which orig-
inates from a 2013 study about maternal investment in a frog species. 4 Reproduction is a costly
process for female frogs, necessitating a trade-off between individual egg size and total number of
eggs produced. Researchers were interested in investigating how maternal investment varies with
altitude and collected measurements on egg clutches found at breeding ponds across 11 study sites;
for 5 sites, the body size of individual female frogs was also recorded.

altitude latitude egg.size clutch.size clutch.volume body.size

1 3,462.00 34.82 1.95 181.97 177.83 3.63
2 3,462.00 34.82 1.95 269.15 257.04 3.63
3 3,462.00 34.82 1.95 158.49 151.36 3.72
150 2,597.00 34.05 2.24 537.03 776.25 NA

Figure 1.4: Data matrix for the frog dataset.

Figure 1.4 displays rows 1, 2, 3, and 150 of the data from the 431 clutches observed as part
of the study. 5 Each row in the table corresponds to a single clutch, indicating where the clutch
was collected (altitude and latitude), egg.size, clutch.size, clutch.volume, and body.size of
the mother when available. "NA" corresponds to a missing value, indicating that information on
an individual female was not collected for that particular clutch. The recorded characteristics are
referred to as variables; in this table, each column represents a variable.

variable description
altitude Altitude of the study site in meters above sea level
latitude Latitude of the study site measured in degrees
egg.size Average diameter of an individual egg to the 0.01 mm
clutch.size Estimated number of eggs in clutch
clutch.volume Volume of egg clutch in mm3
body.size Length of mother frog in cm

Figure 1.5: Variables and their descriptions for the frog dataset.

It is important to check the definitions of variables, as they are not always obvious. For ex-
ample, why has clutch.size not been recorded as whole numbers? For a given clutch, researchers
counted approximately 5 grams’ worth of eggs and then estimated the total number of eggs based
on the mass of the entire clutch. Definitions of the variables are given in Figure 1.5. 6

4 Chen, W., et al. Maternal investment increases with altitude in a frog on the Tibetan Plateau. Journal of evolutionary
biology 26.12 (2013): 2710-2715.
5 The frog dataset is available in the R package oibiostat.
6 The data discussed here are in the original scale; in the published paper, some values have undergone a natural log
transformation.
1.2. DATA BASICS 15

The data in Figure 1.4 are organized as a data matrix. Each row of a data matrix corresponds
to an observational unit, and each column corresponds to a variable. A piece of the data matrix for
the LEAP study introduced in Section 1.1 is shown in Figure 1.1; the rows are study participants
and three variables are shown for each participant. Data matrices are a convenient way to record
and store data. If the data are collected for another individual, another row can easily be added;
similarly, another column can be added for a new variable.

1.2.2 Types of variables

The Functional polymorphisms Associated with human Muscle Size and Strength study (FA-
MuSS) measured a variety of demographic, phenotypic, and genetic characteristics for about 1,300
participants. 7 Data from the study have been used in a number of subsequent studies,8 such as
one examining the relationship between muscle strength and genotype at a location on the ACTN3
gene. 9
The famuss dataset is a subset of the data for 595 participants. 10 Four rows of the famuss
dataset are shown in Figure 1.6, and the variables are described in Figure 1.7.

sex age race height weight actn3.r577x ndrm.ch

1 Female 27 Caucasian 65.0 199.0 CC 40.0
2 Male 36 Caucasian 71.7 189.0 CT 25.0
3 Female 24 Caucasian 65.0 134.0 CT 40.0
595 Female 30 Caucasian 64.0 134.0 CC 43.8

Figure 1.6: Four rows from the famuss data matrix.

variable description
sex Sex of the participant
age Age in years
race Race, recorded as African Am (African American), Caucasian, Asian,
Hispanic or Other
height Height in inches
weight Weight in pounds
actn3.r577x Genotype at the location r577x in the ACTN3 gene.
ndrm.ch Percent change in strength in the non-dominant arm, comparing strength
after to before training

Figure 1.7: Variables and their descriptions for the famuss dataset.

The variables age, height, weight, and ndrm.ch are numerical variables. They take on numer-
ical values, and it is reasonable to add, subtract, or take averages with these values. In contrast,
a variable reporting telephone numbers would not be classified as numerical, since sums, differ-
ences, and averages in this context have no meaning. Age measured in years is said to be discrete,
since it can only take on numerical values with jumps; i.e., positive integer values. Percent change
in strength in the non-dominant arm (ndrm.ch) is continuous, and can take on any value within a
specified range.

7 Thompson PD, Moyna M, Seip, R, et al., 2004. Functional Polymorphisms Associated with Human Muscle Size and
Strength. Medicine and Science in Sports and Exercise 36:1132 - 1139.
8 Pescatello L, et al. Highlights from the functional single nucleotide polymorphisms associated with human muscle
size and strength or FAMuSS study, BioMed Research International 2013.
9 Clarkson P, et al., Journal of Applied Physiology 99: 154-163, 2005.
10 The subset is from Foulkes, Andrea S. Applied statistical genetics with R: for population-based association studies.
Springer Science & Business Media, 2009. The full version of the data is available at http://people.umass.edu/foulkes/
asg/data.html.
16 CHAPTER 1. INTRODUCTION TO DATA

Figure 1.8: Breakdown of variables into their respective types.

The variables sex, race, and actn3.r577x are categorical variables, which take on values that
are names or labels. The possible values of a categorical variable are called the variable’s levels. 11
For example, the levels of actn3.r577x are the three possible genotypes at this particular locus:
CC, CT, or TT. Categorical variables without a natural ordering are called nominal categorical
variables; sex, race, and actn3.r577x are all nominal categorical variables. Categorical variables
with levels that have a natural ordering are referred to as ordinal categorical variables. For exam-
ple, age of the participants grouped into 5-year intervals (15-20, 21-25, 26-30, etc.) is an ordinal
categorical variable.

EXAMPLE 1.1
Classify the variables in the frog dataset: altitude, latitude, egg.size, clutch.size,
clutch.volume, and body.size.

The variables egg.size, clutch.size, clutch.volume, and body.size are continuous numerical
variables, and can take on all positive values.
In the context of this study, the variables altitude and latitude are best described as categorical
variables, since the numerical values of the variables correspond to the 11 specific study sites where
data were collected. Researchers were interested in exploring the relationship between altitude and
maternal investment; it would be reasonable to consider altitude an ordinal categorical variable.

GUIDED PRACTICE 1.2

Characterize the variables treatment.group and overall.V60.outcome from the LEAP study (dis-
cussed in Section 1.1). 12

GUIDED PRACTICE 1.3

Suppose that on a given day, a research assistant collected data on the first 20 individuals visiting a
walk-in clinic: age (measured as less than 21, 21 - 65, and greater than 65 years of age), sex, height,
weight, and reason for the visit. Classify each of the variables. 13

11 Categorical variables are sometimes called factor variables.

12 These variables measure non-numerical quantities, and thus are categorical variables with two levels.
13 Height and weight are continuous numerical variables. Age as measured by the research assistant is ordinal categorical.
Sex and the reason for the visit are nominal categorical variables.
1.2. DATA BASICS 17

1.2.3 Relationships between variables

Many studies are motivated by a researcher examining how two or more variables are related.
For example, do the values of one variable increase as the values of another decrease? Do the values
of one variable tend to differ by the levels of another variable?
One study used the famuss data to investigate whether ACTN3 genotype at a particular lo-
cation (residue 577) is associated with change in muscle strength. The ACTN3 gene codes for a
protein involved in muscle function. A common mutation in the gene at a specific location changes
the cytosine (C) nucleotide to a thymine (T) nucleotide; individuals with the TT genotype are un-
able to produce any ACTN3 protein.
Researchers hypothesized that genotype at this location might influence muscle function. As
a measure of muscle function, they recorded the percent change in non-dominant arm strength
after strength training; this variable, ndrm.ch, is the response variable in the study. A response
variable is defined by the particular research question a study seeks to address, and measures the
outcome of interest in the study. A study will typically examine whether the values of a response
variable differ as values of an explanatory variable change, and if so, how the two variables are
related. A given study may examine several explanatory variables for a single response variable. 14
The explanatory variable examined in relation to ndrm.ch in the study is actn3.r557x, ACTN3
genotype at location 577.

EXAMPLE 1.4
In the maternal investment study conducted on frogs, researchers collected measurements on egg
clutches and female frogs at 11 study sites, located at differing altitudes, in order to investigate
how maternal investment varies with altitude. Identify the response and explanatory variables in
the study.

The variables egg.size, clutch.size, and clutch.volume are response variables indicative of ma-
ternal investment.
The explanatory variable examined in the study is altitude.
While latitude is an environmental factor that might potentially influence features of the egg
clutches, it is not a variable of interest in this particular study.
Female body size (body.size) is neither an explanatory nor response variable.

GUIDED PRACTICE 1.5

Refer to the variables from the famuss dataset described in Figure 1.7 to formulate a question about
the relationships between these variables, and identify the response and explanatory variables in
the context of the question. 15

14 Response variables are sometimes called dependent variables and explanatory variables are often called independent
variables or predictors.
15 Two sample questions: (1) Does change in participant arm strength after training seem associated with race? The
response variable is ndrm.ch and the explanatory variable is race. (2) Do male participants appear to respond differently to
strength training than females? The response variable is ndrm.ch and the explanatory variable is sex.
18 CHAPTER 1. INTRODUCTION TO DATA

1.3 Data collection principles

The first step in research is to identify questions to investigate. A clearly articulated research
question is essential for selecting subjects to be studied, identifying relevant variables, and deter-
mining how data should be collected.

1.3.1 Populations and samples

Consider the following research questions:

1. Do bluefin tuna from the Atlantic Ocean have particularly high levels of mercury, such that
they are unsafe for human consumption?
2. For infants predisposed to developing a peanut allergy, is there evidence that introducing
peanut products early in life is an effective strategy for reducing the risk of developing a
peanut allergy?
3. Does a recently developed drug designed to treat glioblastoma, a form of brain cancer, appear
more effective at inducing tumor shrinkage than the drug currently on the market?

Each of these questions refers to a specific target population. For example, in the first ques-
tion, the target population consists of all bluefin tuna from the Atlantic Ocean; each individual
bluefin tuna represents a case. It is almost always either too expensive or logistically impossible to
collect data for every case in a population. As a result, nearly all research is based on information
obtained about a sample from the population. A sample represents a small fraction of the popu-
lation. Researchers interested in evaluating the mercury content of bluefin tuna from the Atlantic
Ocean could collect a sample of 500 bluefin tuna (or some other quantity), measure the mercury
content, and use the observed information to formulate an answer to the research question.

GUIDED PRACTICE 1.6

Identify the target populations for the remaining two research questions. 16

16 In Question 2, the target population consists of infants predisposed to developing a peanut allergy. In Question 3, the
target population consists of patients with glioblastoma.
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