
             COMPUTER PROGRAMS FOR EPIDEMIOLOGIC ANALYSIS (PEPI)
            by Paul M. Gahlinger and J.H. Abramson.  Version 2.05
         
  These programs are for use in statistical analyses, especially of data on 
  health and disease.  They are designed to facilitate secondary calculations 
  after observations have been tabulated or counted.  Results are shown on 
  the screen, and in most cases can also be printed or saved as text in a 
  disk file.  Data must usually be entered at the keyboard. 

  ***************************************************************************
  For the latest versions (with installation programs for Windows and DOS and
  a menu program for DOS) and a 375-page manual that describes the uses of 
  the programs, with formulae, references, examples and a Program Finder to
  identify programs to meet specific needs, send $50 (U.S.$60 if outside the
  U.S) to USD Inc., 2075-A West Park Place, Stone Mountain, GA 30087, U.S.   
      Tel: 770-469-4098    Fax: 770-469-0681    E-mail: usd@usd-inc.com   
         URL: http://www.usd-inc.com (permits payment by credit card)
  ***************************************************************************
     N.B. Printing errors in the manual are listed at the end of this file.
         
                       FOR BASIC INSTRUCTIONS, READ ON.

  See FILELIST.TXT for a list of the programs and other files. Changes made 
  since publication of the manual for PEPI Version 2 are described in 
  UPDATE1.TXT, UPDATE2.TXT and UPDATE3.TXT.  You can read these files by 
  typing (e.g.) VIEW UPDATE1.TXT or (in Windows) by clicking on their icons.
 
  The programs are copyrighted, but may be freely copied and distributed for 
  personal (not institutional) use.  They may not be exploited commercially 
  without permission.  The programs are provided without any warranties, 
  whether expressed or implied, and without any liability to users. 

    Comments and suggestions are welcomed.  Please send them by mail, fax
    or e-mail to one of the authors, c/o USD Inc. (see addresses above).  
    All comments will be taken into account when the programs are revised. 
  
         
  IF YOU ACQUIRED PEPI205.ZIP:

    PEPI205.ZIP does not contain installation or menu programs.  After 
    unzipping the file you can run the statistical programs in DOS from a 
    diskette or your hard disk, as you would any other program. 
    
    If you used the INSTALL or WINSTAL program to install a previous version 
    of PEPI, copy the newer programs (obtained from PEPI205.ZIP) to the 
    directory containing the older versions (replacing the older ones).  You 
    can then go on using the PEPI menu (in DOS) or icons (in Windows).  
    Version numbers are shown in the "Time" column in DOS or File Manager 
    directory listings, as well as in each program's opening screen.  If you 
    have not installed PEPI with the INSTALL or WINSTAL program, most of the 
    following instructions are irrelevant.  
        
         
  CONTENTS:        Installing the programs
                   Installing new versions
                   Running the programs
                   Running the programs under Microsoft Windows
                   Printing and saving the results 
                   PEPI on the Internet
                   Problems
                   Printing errors in the manual

  INSTALLING THE PROGRAMS:

  - The programs need not be installed; they can be run from a diskette. 

  - You can use the INSTALL or WINSTALL program to copy the programs to a 
    directory of your choice on your hard disk.  Depending on your hard disk, 
    the space required is 1.5 to 1.7 megabytes for INSTALL, and 1.5 to 2.3 
    megabytes for WINSTALL.  

  - If you do not possess Microsoft Windows, use the INSTALL program:  

      Put distribution disk 1 in drive A or B and enter "A:INSTALL" {1} {2}" 
      or "B:INSTALL {1} {2}", where {1} is the drive you are installing FROM 
      and {2} is the full name of the directory you wish to install TO. 
      There must be a space between {1} and {2}. 
      Examples: A:INSTALL A: C:\STATPROG   (Install to C:\STATPROG from A) 
                B:INSTALL B: D:\STAT\PEPI  (Install to D:\STAT\PEPI from B)
      When you are asked to do so, insert distribution disk 2 in the same 
      drive. The hard disk directory will be created if it does not exist. If 
      there are older versions of the programs in the directory they will be 
      replaced. The installation program will not modify your AUTOEXEC.BAT 
      file; but it is advisable to ensure that the directory appears in the 
      search PATH.  
    
  - If you have Microsoft Windows (including Windows 95 and Windows NT), use 
    the WINSTALL program.  This will copy the programs to a directory where 
    they will be available for use both in DOS and in Windows. 
       
      Insert distribution disk 1 in drive A or B, load Windows, select
      "Run" from the Program Manager File menu, and enter "A:WINSTALL" or
      "B:WINSTALL". Insert distribution disk 2 in the same drive when you are
      asked to do so.  The program files will be copied to a hard disk
      directory of your choice.  The hard disk directory will be created if
      it does not exist. If there are older versions of the programs in the
      directory they will be replaced.  No changes will be made to
      CONFIG.SYS, AUTOEXEC.BAT, or WIN.INI.  A "Statistical Programs" program 
      group will be created, in which each program has an icon that can be 
      double-clicked to run the program.  If you wish you can "drag" the 
      Program Finder or Calculator icons to more prominent positions, or make 
      other changes, and then set the "Save settings on exit" option (see 
      your Windows manual). 
                                          

  INSTALLING NEW VERSIONS
           
  - If you wish to install new versions of the programs, and you have new 
    disks, run INSTALL or WINSTALL (with the new disks), specifying the 
    directory that contains the old versions.  If there is a new version of 
    any program, this will automatically replace the old version; if there is 
    no new version, the old version will remain intact; if there is a 
    completely new program, this will be installed.  New versions of the 
    UPDATE files and README.TXT will replace the old ones.  
           
  - If you do not have new disks, but have acquired a compressed (ZIP) file 
    containing new programs, you can copy the newer programs to the 
    directory containing the older ones (replacing the older ones). 


  RUNNING THE PROGRAMS 
                 
  The programs are easy to run.  Follow the instructions that appear on the 
  screen.  If extra explanations are wanted, they will be found in the manual. 

  - To run a program from the DOS prompt (e.g. A:>) type its name (e.g. 
    "TIMES") and press the <Enter> or <Return> key.  If you have copied the 
    program file to your hard disk, either operate it from the directory to 
    which you copied it, or make sure this directory is in your PATH.  

  - You can also run a program from the DOS prompt by typing "PEPI", which 
    brings up a menu.  Move the highlight bar with an arrow key or a mouse, 
    and select a program by pressing <Enter> or the left mouse button.  To 
    quit the menu, press <Escape> or the right mouse button.  The PEPI menu 
    will not work unless the directory to which the statistical and menu 
    programs have been copied is in your PATH, and SM.CFG is in the C:\ root 
    directory (where the installation programs put it).  Do not use the menu 
    while in Windows or in a DOS shell with little free memory; you may have 
    trouble running it from a diskette unless your computer has expanded or 
    extended memory. 

  - To run a program under Microsoft Windows: see next section.
                         
  - In the instructions, <Ent> refers to the <Enter> or <Return> key. 
    
  - You may be offered choices: e.g., "Type N if you want to enter numbers of 
    cases, or just <Ent> if you want to enter rates".  If your response is N, 
    you can type either "n" or "N".  When you make a choice by typing a letter 
    it is generally sufficient to tap the key, without pressing the <Enter> 
    key afterwards. 
    
  - After entering a number you will almost always have to press the <Enter> 
    key as well, to let the computer know your entry is complete. 
                   
  - When there are no further data to enter, you are generally instructed to 
    inform the computer of this by pressing <Enter>. 
    
  - When rates are entered, you will generally be asked what their base is; if 
    the rate is 4 per 1,000, enter 1000.  A proportion is always between 0 and 
    1, with a base of 1.  In the instructions the term "rate" is used both for 
    measures whose denominators are total numbers of individuals (prevalence, 
    cumulative incidence, "risk") and for rates whose denominators are person-
    time units (incidence density, mortality density). 

  - If you do something wrong - for example, if you enter a letter instead of 
    a numeral - the program will usually beep and ask you to try again. 

  - If you want to quit a program in the middle, you can usually do this 
    safely by pressing <Ctrl><Break> - i.e., the "Control" and "Break" keys 
    together.  If the computer is busy there may be a delay before it 
    responds.  In a real emergency, press <Ctrl><Alt><Del>. 

  - The programs do not store data or retrieve data from computer files, with 
    four exceptions: DIRST and INDIRST (which standardize rates, proportions 
    and means) can store and use standards entered at the keyboard, SURVIVAL 
    (life table analyses) can store and modify data, and WHATS stores results, 
    constants and formulae for later use. 


  RUNNING THE PROGRAMS UNDER MICROSOFT WINDOWS

  - The programs are DOS applications, but can be run under Windows (including 
    Windows 95 and Windows NT). 
         
  - The easiest way is to install the programs with WINSTALL (see above). This 
    creates a "Statistical Programs" program group, in which each program has 
    an icon.  Double-click on the icon to run the program.   Double-click on
    the "?" icon to run the Program Finder, which will help you to identify
    a program that meets your needs.
         
  - If you have not installed the programs with icons, you can use any of the 
    other methods available for launching a DOS program in Windows (see your 
    Windows manual). Remember to specify the PIF file (e.g. TIMES.PIF) rather 
    than the EXE file (e.g. TIMES.EXE), so as to enable the PrintScreen or 
    Selective PrintScreen features (see below); the latter functions will not 
    work in Windows 3.0 in standard mode. 
    
  - You can read the UPDATE*.TXT files and other .TXT files by clicking on the 
    file's icon (if there is one) or the file name in a File Manager directory 
    list, or by using the "Run" command and entering the file name. 
                                                               

  PRINTING AND SAVING THE RESULTS 

  - Most of the programs offer printing and saving options. 

  - If you wish to be discriminatory about what you print, do not select the 
    automatic printing option.  Instead, use the computer's "PrintScreen" 
    (<PrtSc>) key to print whatever is currently on the screen (this should 
    work in Windows also, if you use WINSTALL to install the programs).  
    However, keyboards and computers vary.  You may have to press 
    <Shift><PrtSc> - i.e., the "Shift" and "PrintScreen" keys together.  You 
    may find that if you press <Ctrl><PrtScr> everything that appears on the 
    screen will be printed until you press <Ctrl><PrtScr> again.  
                                         
  - For your convenience, a public-domain "Selective PrintScreen" program, 
    SPS, by Bob Montgomery (we have modified the prompt) is provided.  Run 
    this program in advance, by typing "SPS" or putting "SPS" in your 
    AUTOEXEC.BAT file.  Then (whether you use the automatic printing option or 
    the <PrtSc> key) you will be able to decide, before each results screen is 
    printed, whether to print the whole screen (by typing "P") or a chosen 
    part of it (to do this, put the cursor in the top left corner of the 
    required block, press <Enter>, move the cursor to the bottom right corner 
    of the block and press <Enter> again), or whether not to print the screen 
    at all (by pressing <Escape>).  Instructions are in SPS.TXT.  The SPS 
    program may give trouble in some systems.          


  PEPI ON THE INTERNET

  - A PEPI page is maintained on the InterNet by USD Inc.  It provides
    information on the latest version.  The URL is: 
               http://www.usd-inc.com

  - The latest version of PEPI can be downloaded free from the Simtel and 
    Garbo software repositories and their mirror sites, in the form of a 
    compressed file.  This contains the statistical programs, the README and 
    UPDATE files, and the updated Program Finder for Windows.  It does not 
    contain installation or menu programs. 
    
    The file is named pepiXXX.zip, where "XXX" is the latest version number 
    (currently 205). The Simtel directory is /pub/simtelnet/msdos/statstic/ 
    and the Garbo directory is /pc/math.  You can find a source by using 
    (say) the Virtual Software Library simple search, whose URL is 
               http://vsl.cnet.com/cgi-bin/vsl-master/QuickForm?
    and searching for "pepi" in the "DOS" category.


  PROBLEMS

  - Please inform one of the authors if you encounter a problem.  
  
  - After installing in Windows 3.x you may find that some of the icons are 
    missing; this may be because you are using a color mode - e.g. "high 
    color" or "true color" - that needs extra memory per icon, so that the 
    nominal ceiling of 50 icons per program group is reduced.  You will have 
    to create an extra program group manually, and insert the missing program 
    items (contact one of the authors for detailed help). 

  - If you have inserted a distribution disk and invoked the WINSTALL 
    installation program, but then get a message asking you to insert the 
    distribution disk (and specifying the name of one of your hard disk 
    directories), abort WINSTALL, use File Manager to select the drive that 
    contains the distribution disk (generally A: or B:), and try again.  

  - If your hard disk is full, WINSTALL may seem to complete the installation 
    program without actually doing so.  

  - If you re-install with WINSTALL after the addition of completely new 
    programs to the PEPI package, you may find that the program icons are not 
    shown in alphabetical order.  You can fix this by deleting STATISTI.GRP 
    (in your Windows directory) and using WINSTALL again. 

  - The name of POWER.EXE was changed to POWR.EXE. to avoid confusion with the 
    Microsoft DOS POWER.EXE program.  If you have an old version of the 
    POWER.EXE statistical program, you should delete it manually; if you use 
    Windows, also delete POWER.PIF and POWER.ICO, and the old icon. 


  ACKNOWLEDGEMENTS

  - SHOW.COM 2.1, by Gary M. Raymond, was used to prepare the self-displaying 
    README.COM file.  RFTGEN 2.03, by Dave Baldwin, was used to prepare the 
    Program Finder for Windows.  Other programs we used are listed in the 
    manual. To modify the menu program you must either guess the password or 
    obtain a modifiable copy (SMART MENU 2.6) from its author (John Campion), 
    using the form in the MENU.FRM file in one of the distribution disks. 

  
  
  PRINTING ERRORS IN THE MANUAL FOR PEPI VERSION 2:

  Several lines were accidentally omitted: 

  - The last sentence on page 17 should read:
      
      The number of tests may be the number performed, if they were based on 
      prior hypotheses, or the total number possible (whether actually 
      performed or not), if they were chosen after examination of the data 
      (Samuels 1991: 499-509). 
      
  - The last sentence on page 101 should read:
  
      If the probability of the array is the same as the probability of the 
      observed table, its value is included in Fisher's P, and half its 
      value in the mid-P estimate. 
      
  - The last sentence on page 138 should read:
  
      High and low estimates of S are calculated by computing the 
      probability of nonsurvival for each time period, applying this to the 
      number of subjects who are under observation at the beginning of the 
      interval and were not withdrawn during the period, and applying a 
      modified probability of nonsurvival (divided or multiplied by 2) to 
      the people who were withdrawn. 
                                                                
  Pages 198 and 199, which should have contained part of Example 3, were 
  accidentally left blank. 

  Page 225: "randomized" should be replaced by "randomization" in the 
  heading of Example 1. 

  Page 287: "reliability" should be replaced by "reproducibility" in the
  5th line from the bottom.
  
