An Introduction to Stata for Health Researchers - Third Edition

by Svend Juul

Svend Juul and Morten Frydenberg’s An Introduction to Stata for Health Researchers, Third Edition is distinguished in its careful attention to detail. The reader will learn not only how to use Stata for statistical analysis but also the skills needed to make the analysis reproducible. The authors use a friendly, down-to-earth tone and include tips gained from a lifetime of collaboration and consulting.

The book is based on the assumption that the reader has some basic knowledge of statistics but no knowledge of Stata. The authors build the reader’s abilities as a builder would build a house: laying a firm foundation in Stata; framing a general structure in which good work can be accomplished; adding the details that are particular to various types of statistical analyses; and finally, trimming with a thorough treatment of graphics.

Juul and Frydenberg start by teaching the reader how to communicate with Stata, not just through its unified syntax, but also by demonstrating how Stata thinks about its basic building blocks. The authors show how Stata views data, thus allowing the reader to see the variety of possible data structures. They also show how to manipulate data to create a dataset that is well documented. When demonstrating analysis techniques, the authors show how to think of analysis in terms of estimation and postestimation. They make the book easy to use as a learning tool and easy to refer back to for useful techniques.

Once they introduce Stata to new users, Juul and Frydenberg fill in the details for performing analysis in Stata. As would be expected from a book addressing health researchers, Juul and Frydenberg mostly demonstrate the statistical techniques that are common in biostatistics and epidemiology: case–control, matched case–control, and incidence-rate data analysis, which can be stratified or not; linear and generalized linear models, including logistic, Poisson, and binomial regression; survival analysis with proportional hazards; and classification using receiver operating characteristic curves. While presenting general estimation techniques, the authors also spend time with interactions and techniques for checking model assumptions.

While teaching Stata implementation, Juul and Frydenberg reinforce habits that allow reproducible research and graceful backtracking in case of errors. Early in the book, they introduce how to use do-files for creating sequences and log files for tracking work. At the end of the book, they introduce some useful programming techniques, such as loops and branching, that simplify repetitive tasks.

Table of contents

List of Tables

List of Figures

Preface to the third edition

Preface to the second edition

Preface to the first edition

Online supplements

Notations in this book

I The basics

1 Getting started

1.1 Installing and updating Stata

1.2 Starting and exiting Stata

1.3 Customizing Stata (Windows)

1.4 Windows in Stata

1.5 Issuing commands

1.6 managing Output

2 Getting help—and more

22.1 The manuals

2.2 Online help

2.3 Other resources

2.4 Errors and error messages

3 Stata file types and names

4 Command syntax

4.1 General syntax rules

4.2 Syntax diagrams

4.3 Lists of variables and numbers

4.4 Qualifiers

4.5 Weights

4.6 Options

4.7 Prefixes

4.8 Other syntax elements

4.9 Version control

II Data management

5 Variables

5.1 Types of Variables

5.2 Numeric formats

5.3 Decimal periods and commas 

5.4 Missing values 

5.5 Storage types and precision 

5.6 Date and time variables 

5.7 String variables

5.8 Memory considerations

6 Getting data in and out of Stata

6.1 Opening and saving Stata data

6.2 Entering data

6.3 Reading ASCII data

6.4 Exchanging data with other programs

7 Documentation commands

7.1 Labels

7.2 Working with labels: An example

8 Calculations

8.1 generate and replace

8.2 Operators and functions in calculations

8.3 Extended functions: egen

8.4 Recoding variables

8.5 Checking correctness of calculations

8.6 Giving numbers to observations

9 Commands affecting data structure

9.1 Selecting observations and variables

9.2 Renaming and reordering variables

9.3 Sorting data

9.4 Combining files

9.5 Reshaping data

10 Taking good care of your data

10.1 The audit trail

10.2 Data collection

10.3 Entering data in the computer

10.4 Data management

10.5 Analysis

10.6 Protect your data

          10.7 Archiving the project

III Analysis

11 Description and simple analysis

11.1 Overview of a dataset

11.2 Listing observations

11.3 Simple tables for categorical variables

11.4 Analyzing continuous variables

11.5 Finding confidence intervals

11.6 Immediate commands

12 Stratified analysis

12.1 Cohort data without censorings

12.2 Incidence-rate data

12.3Case–control data

13 Regression analysis

13.1 Linear regression

13.2 Regression postestimation

13.3 Categorical predictors—factor variables

13.4 Interactions in regression models

          13.5 Logistic regression

13.6 Other regression models

          13.7 Nonindependent observations

14 Incidence, mortality, and survival

14.1 Setting the time scale and event: The stset command

14.2 The Kaplan–Meier survival function

14.3 Cox proportional hazards regression

14.4 Preparing data for advanced survival analyses

14.5 Advanced survival modeling

14.6 Tabulating rates

14.7 Poisson regression

          14.8 Standardization

15 Measurement and diagnosis

15.1 Comparing two measurements

15.2 Reproducibility of measurements

15.3 Using tests for diagnosis

16 Miscellaneous

16.1 Random samples, simulations

16.2 Sample-size and study power estimation

16.3 Other analyses

IV Graphs

17 Graphs

           17.1 Anatomy of a graph
           17.2 Anatomy of graph commands
           17.3 Graph size
           17.4 Schemes
           17.5 Graph options: Axes
           17.6 Graph options: Text elements
           17.7 Plot options: Markers, lines, etc.
           17.8 Graph examples
           17.9 By-graphs and combined graphs
           17.10 Using dialogs to generate commands
           17.11 The Graph Editor
           17.12 Saving, displaying, and printing graphs

V Advanced topics

18 Advanced topics

 18.1 Using saved results

 18.2 Macros and scalars

 18.3 Programs

 18.4 Useful programming commands

 18.5 Do-files and ado-files useful for handling output

           18.6 Ado-files useful for handling output

VI Appendixes

A Manuals and other good books

  A.1 Stata manuals

  A.2 Other good books

B Exercises

  B.1 The user interface

  B.2 Managing output

  B.3 Calculations

  B.4 Working with missing values

  B.5 Working with date variables

  B.6 Description and simple analysis

  B.7 Taking good care of your data

C Advice on working with Windows

            C.1 Create a smart folder structure
            C.2 How to select a default working folder for a program
            C.3 Make Windows display filename extensions
            C.4 Creating a new folder
            C.5 Renaming a folder or a file
            C.6 Copying a file or a folder to another folder or to an external drive
            C.7 How to move a file or a folder to another folder
            C.8 Write-protect your files

References

Author index

Subject index