Tomás J.

Aragón

Field Epidemiology with R

 For my wife, Irene, and my children Ángela Isabel,
Luis Miguel and Tomás Martín, whose unconditional
love and support make the impossible possible.
For my staff, students, colleagues and community
residents who teach, mentor and coach me every day.
Contents

List of Tables v

List of Figures vii

Preface ix

About the Author xi

1 Introduction 1

2 Epidemiologic concepts for controlling infectious diseases 3

2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.2 Transmission mechanisms . . . . . . . . . . . . . . . . . . . . 3
2.3 Transmission dynamics . . . . . . . . . . . . . . . . . . . . . 3
2.4 Transmission containment . . . . . . . . . . . . . . . . . . . 3

3 Epidemiologic measures 5

4 Conducting an outbreak investigation in 7 steps (or less) 7

5 Step 1: Case investigations 9

6 Step 2: Continue or start surveillance 11

7 Step 3: Cause investigations (and root cause analysis) 13

8 Step 4: Control and prevention strategies (do early) 15

9 Step 5: Conduct an analytic study (if necessary) 17

10 Step 6: Conclusions (enhancing valid inferences) 19

11 Step 7: Communicate findings 21

11.1 Prepare written communications . . . . . . . . . . . . . . . . 21
11.1.1 Interim/final report template . . . . . . . . . . . . . . 21
11.1.2 Prepare manuscript . . . . . . . . . . . . . . . . . . . 21
11.2 Crisis and emergency risk communication . . . . . . . . . . . 21
11.3 Media communication basics . . . . . . . . . . . . . . . . . . 21

iii
iv Contents

Appendix 23

A More to Say 23
List of Tables

v
List of Figures

vii
Preface

The document format “R Markdown” was first introduced in the knitr package
(Xie, 2015, 2018) in early 2012. The idea was to embed code chunks (of R or
other languages) in Markdown documents. In fact, knitr supported several
authoring languages from the beginning in addition to Markdown, including
LaTeX, HTML, AsciiDoc, reStructuredText, and Textile. Looking back over
the five years, it seems to be fair to say that Markdown has become the
most popular document format, which is what we expected. The simplicity of
Markdown clearly stands out among these document formats.

ix
About the Author

Tomás J. Aragón is the health officer of the City and County of San Francisco,
and director of the Population Health Division (PHD) at the San Francisco
Department of Public Health.1 As health officer, he exercises leadership and
legal authority to protect and promote health. As PHD director, he directs
public health services. His focus areas include health equity, lean enterprise
transformation, collective impact, data science, and leadership development.
He teaches population health data science (with R) at the University of Cali-
fornia, Berkeley School of Public Health, and maintains a public health blog
with a practiced-based focus on population health leadership, lean, and data
science at https://taragonmd.github.io/.

1 https://www.sfdph.org

xi
1
Introduction

There is no single education and training activity that prepares public health
trainees and graduate students for the rigors, depth, breadth, and diversity
of public health science and practice than conducting outbreak investigations.
The science and art of conducting outbreak investigations provides learning op-
portunities. Outbreak investigations are complex, fast-paced, and conducted
by a multidisciplinary team operating in a high-pressure, rapidly changing, and
uncertain environment. Investigators must be agile, open-minded, and flexi-
ble, yet tenacious and methodologically rigorous in pursuing evasive causal
explanations in order to intervene and protect the public.
Conducting an outbreak investigation is commonly summarized in ten steps
(Gregg, 2008): (1) Determine the existence of the epidemic; (2) Confirm the
diagnosis; (3) Define a case and count cases; (4) Orient the data interms of
time, place, and person; (5) Determine who is at risk of becoming ill; (6)
Develop a hypothesis that explains the specific exposure that caused disease
and test this hypothesis by appropriate statistical methods; (7) Compare the
hypothesis with the established facts; (8) Plan a more systematic study; (9)
Prepare a written report; and (10) Execute control and prevention measures.
Alternatively, one can use an eight step approach (MacDonald, 2011): (1)
Verify the diagnosis and confirm the outbreak; (2) Define a case and conduct
case finding; (3) Tabulate and orient data: time, place, and person; (4) Take
immediate control measures; (5) Formulate and test hypothesis; (6) Plan and
execute additional studies; (7) Implement and evaluate control measures; and
(8) Communicate findings.
The Centers for Disease Control and Prevention uses 13 steps (?).1 In this
book, we cover the same material but organized under seven conceptual steps
based on how disease intervention specialists (DISs) work at local health de-
partments. On a daily basis, DISs investigate and manage individual “cases.”
Now, in an outbreak investigation, they investigate a group of cases (case
investiation) with the purpose of drawing conclusions about what is causing
this outbreak in order to control it. Here are the seven conceptual steps:
Table: Conducting an outbreak investigation in 7 steps (or less)
1 Also see https://www.cdc.gov/ophss/csels/dsepd/ss1978/lesson6/section2.html

1
2 1 Introduction

1. Case investigations |
2. Continue (or start) surveillance |
3. Cause investigations |
4. Control and prevention measures (do early) |
5. Conduct analytic study (if necessary) |
6. Conclusions (enhancing valid inferences) |
7. Communicate findings |
2
Epidemiologic concepts for controlling
infectious diseases

2.1 Introduction

2.2 Transmission mechanisms

2.3 Transmission dynamics

2.4 Transmission containment

3
3
Epidemiologic measures

tbd

5
4
Conducting an outbreak investigation in 7
steps (or less)

tbd

7
5
Step 1: Case investigations

tbd

9
6
Step 2: Continue or start surveillance

tbd

11
7
Step 3: Cause investigations (and root cause
analysis)

tbd

13
8
Step 4: Control and prevention strategies (do
early)

tbd

15
9
Step 5: Conduct an analytic study (if
necessary)

tbd

17
10
Step 6: Conclusions (enhancing valid
inferences)

tbd

19
11
Step 7: Communicate findings

11.1 Prepare written communications

11.1.1 Interim/final report template

11.1.2 Prepare manuscript

11.2 Crisis and emergency risk communication

11.3 Media communication basics

21
A
More to Say

Yeah! I have finished my book, but I have more to say about some topics. Let
me explain them in this appendix.
To know more about bookdown, see https://bookdown.org.

23
Bibliography

Gregg, M. (2008). Field Epidemiology. Oxford University Press.

MacDonald, P. D. (2011). Methods in Field Epidemiology. Jones & Bartlett
Learning.

25