Epi Info, Version 6 A Word-Processing, Database, and Statistics Program for Public Health on IBM-compatible Microcomputers Program design by Andrew G. Dean, Jeffrey A. Dean, Denis Coulombier, Anthony H. Burton, Karl A. Brendel, Donald C. Smith, Richard C. Dicker, Kevin M. Sullivan, Robert F. Fagan, Programming by Jeffrey A. Dean, Denis Coulombier, Donald C. Smith, Karl A. Brendel, Thomas G. Arner, and Andrew G. Dean Manual by Andrew G. Dean Revised for Version 6.03, January 1996 Produced by: The Division of Surveillance and Epidemiology Epidemiology Program Office Centers for Disease Control and Prevention (CDC) Atlanta, Georgia 30333 in collaboration with The Global Programme on AIDS World Health Organization (WHO) Geneva, Switzerland This manual and the programs are in the public domain and may be freely copied, translated, and distributed without restriction. They are available on the Internet at ftp.cdc.gov Suggested citation: Dean AG, Dean JA, Coulombier D, Brendel KA, SmithDC, Burton AH, Dicker RC, Sullivan K, Fagan RF, Arner, TG. Epi Info, Version 6: a word processing, database, and statistics program for public health on IBM- compatible microcomputers. Centers for Disease Control and Prevention, Atlanta, Georgia, U.S.A., 1996. Epi Info Hotline for Technical Assistance (404) 728-0545 FAX (404) 315-6440 [email protected] 2 Acknowledgements Dr. David Martin, Brookline, Mass, and A. Ray Simons, Atlanta, Georgia, provided Turbo Pascal procedures for exact confidence limits. Ruth A. Etzel, M.D., and Daniel C. Rodrigue, M.D., of the Centers for Disease Control and Prevention provided the materials for Chapter 12. S. Kathleen Egan of the Epidemiology Program Office produced portions of the EPED tutorials. Stuart H. Burri developed PRN files for using EPED with several printers. The authors of the CSAMPLE program and documentation are acknowledged in Chapter 14. We are grateful to Robert K. Jung for contributing a license to use his ARJSFX compression software for installing Epi Info. We thank the users of Epi Info, Version 5, who provided suggestions and the many people who participated in official or unofficial "beta testing," especially Marc A. Strassburg, Ph.D., of the Los Angeles County Department of Health Services. Notes These programs were produced by the Epidemiology Program Office, Centers for Disease Control and Prevention, and the Global Programme on AIDS, World Health Organization, and are provided for use by the public health community. You are encouraged to give copies of the programs and the manual to your friends and colleagues. No warranty is made or implied for use of the software for any particular purpose. Epi Info is written in Turbo Pascal from Borland International and uses GRAF/DRIVE PLUS ((C) 1989, 90 M.K.Fleming) printer drivers. The manual was written and indexed in Microsoft Word on a Macintosh computer. The cover art is by Mr. Marlon Wolcott. The master disks were tested for computer viruses with the McAfee virus-detection software.(McAfee Associates, (408) 988-3832) Trade names are used for identification only or for examples; no endorsement of particular products is intended or implied. The use of trade names or trademarks in this manual does not imply that such names, as understood by the Trade Marks and Merchandise Marks Act, may be used freely by anyone. Telephone Assistance Line Telephone assistance will be provided if a problem is not solved by reference to the manual. Information for obtaining Epi Info technical assistance is given on the preceding page. Please send comments and suggestions for future versions to: Andrew G. Dean, M.D., M.P.H. Epidemiology Program Office, Mailstop C08 Centers for Disease Control and Prevention Atlanta, GA 30333 Telephone (404) 639-2693 Home Telephone (770) 458-2271 (Emergencies only please) Fax (404) 639-1546 Internet [email protected] Contents Introduction: Chapter 1 How To Use This Manual.........................................................................7 Chapter 2 What Is Epi Info, Version 6?..................................................................11 Chapter 3 What's New in Version 6?......................................................................17 Chapter 4 Installing Epi Info...................................................................................35 Chapter 5 Running Epi Info.....................................................................................45 Level I: Word Processing Functions Chapter 6 Using EPED, the Epidemiologist’s Editor, As a General Word Processor.........................................................................51 Chapter 7 Creating Questionnaires Using EPED....................................................73 Level I: Entering and Analyzing Data Without Programming Chapter 8 Entering Data Using the ENTER Program.............................................83 Chapter 9 ANALYSIS: Producing Lists, Frequencies, Tables, Statistics, and Graphs from Epi Info Files.................................97 Level II: More Refined Data Entry and Analysis Chapter 10 The CHECK Program: Optional Error Checking, Coding, and Skip Patterns During Data Entry....................................................111 Chapter 11 Writing Programs and Preparing Data for ANALYSIS .......................121 Chapter 12 Example of Epidemic Investigation : an Epidemic of Paralytic Shellfish Poisoning............................................................137 Chapter 13 More ANALYSIS: Writing New Files; Restructuring Records; Communicating with the Screen and Printer; Summary Records.................................................................................145 CHAPTER 1 USING THIS MANUAL Chapter 14 CSAMPLE: Analyzing Data from Complex Survey Samples.....................................................................................157 Level II: Other Epi Info Functions Chapter 15 STATCALC and EPITABLE: Two Statistical Calculators.................185 Chapter 16 EXPORT: Producing Files for Use in Other Database and Statistical Systems..........................................................191 Chapter 17 IMPORTing Data Files from Other Programs......................................197 Chapter 18 MERGE: Merging and Updating Files and Records.............................203 Chapter 19 Duplicate Data Entry and Validation--Two Approaches......................211 Chapter 20 EPIGLUE/EPI6: Menuing and Executive Health Information Shell with Hypertext.............................................................................215 Chapter 21 EPIAID, the Tutorial and Interactive Text Function in EPED.................................................................................239 Level III: Advanced Features of Epi Info Chapter 22 Programming the Data Entry Process with .CHK Files........................245 Chapter 23 Example: Programs For Nutritional Anthropometry............................267 Chapter 24 Precise Control of Tables: the REPORT Command.............................291 Chapter 25 Linking Files Together: Relational Features of ANALYSIS, MERGE, and ENTER.................................................307 Chapter 26 Example: NETSS, a Disease Surveillance System, using Relational File Structure and Hypertext Output...................................321 Chapter 27 Generating Artificial Data Files and Random Numbers;......................341 Chapter 28 Writing EPIAID Programs....................................................................347 Using Epi Info in Special Environments Chapter 29 Using Epi Info with Languages Other Than English............................353 Chapter 30 Portable Computers and Epidemiologic Field Investigation................359 Reference Section Chapter 31 Limitations of Speed and Memory, Debugging, and What To Do When Problems Occur.....................................................367 Chapter 32 Statistics: Understanding the Results....................................................373 Chapter 33 EPED Commands.................................................................................415 Chapter 34 EPIAID Commands..............................................................................437 Chapter 35 ENTER and CHECK Commands.........................................................453 Chapter 36 ANALYSIS Commands........................................................................487 Chapter 37 Epi Info File Structure...........................................................................547 Chapter 38 Epi Info and Local Area Networks (LANs)..........................................565 Chapter 39 The Programmer’s Toolkit and the REC2QES and MAKELIST Utilities..................................................................................................569 Functional Index Epidemic Investigation.................................................................................................577 Disease Surveillance.....................................................................................................579 Alphabetic Index.....................................................................................................................581 CHAPTER 1 USING THIS MANUAL 1 Chapter How To Use This Manual Tutorial For a quick introduction to Epi Info, read Chapter 2, install the system as described in Chapter 4, and follow the tutorial instructions in bold type (like this one) at the beginning of each chapter. Epi Info can be used at several levels depending on your level of experience and needs. The elementary level I allows word processing and entry and analysis of questionnaire data. Classes of students usually reach this level with a few hours of practice. Learning aids of several kinds are provided. The menu and major programs have help sections, some of which contain major portions of reference Chapters 33, 35, and 36 in this manual. Major programs have interactive tutorials that lead you through major concepts. Extensive examples are provided in the chapters headed "Example" and as actual programs on the Epi Info disks. These include: • An Investigation of Paralytic Shellfish Poisoning in Central America • A Program To Do Nutritional Anthropometric Calculations within a Survey Questionnaire • A Multi-file Automated Disease Surveillance System with Customized Reporting Formats and Relational File Handling • Numerous smaller examples represented in the EXAMPLE and TUTORIAL sections of the EPI6 menu Each of these programs can be modified for use in your own setting and will provide a "flying start" to persons responsible for setting up such systems. CHAPTER 1 USING THIS MANUAL Shorter examples are provided throughout the manual. When a topic is discussed, software examples elsewhere in the manual are cited so that you can see actual applications. This manual provides several different approaches for learning Epi Info. There are tutorial sections at the beginning of most chapters that provide quick summaries of the material in the chapter. Chapters in the book are arranged in experience levels I through III. Levels I and II are useful for both epidemic investigation and disease surveillance. Level III offers features designed for permanent or research-oriented systems and some aspects require programming skill. Those that require more than simple persistence and experimentation are clearly marked. If you intend to use Epi Info mainly for processing data rather than for word processing, you can skip Chapter 6 temporarily and proceed to make a questionnaire as described in Chapter 7. Users of all levels who have not used Epi Info before should begin by reading Chapters 6 or 7-9 and doing the tutorials. More advanced features can be learned as needed by approaching the appropriate chapters through the table of contents, the topical index, or the two functional indices at the end of the manual. Some experienced users will make heaviest use of the reference chapters 33-36, where essential facts about commands are presented in somewhat technical but complete form. Users of Epi Info, Version 5, can begin using Version 6 by reading Chapter 3, "What's New in Version 6." This chapter lists new features and gives summaries of those for which descriptions are provided in other chapters. To learn about all features of Version 6, an experienced Version 5 user should read Chapters 3 and 19-28, and refer to Chapters 33-36 or the help files in the programs for reference. These chapters contain most of the new material added to the Version 5 manual, although many of the other chapters have been reorganized and, we hope, improved. Advanced techniques for entering and analyzing data are illustrated in application programs on the disks, as described in Chapters 12, 14, 23, and 26. Chapter 29 gives suggestions for those using Epi Info with languages other than English. Chapter 30 discusses equipment and procedures for using Epi Info on a portable computer in the investigation of outbreaks. Technical information on memory size and processing speed are given in Chapter 31. Formulas or references for the statistics in Epi Info are given in Chapter 32.