
             COMPUTER PROGRAMS FOR EPIDEMIOLOGIC ANALYSIS (PEPI)
            by Paul M. Gahlinger and J.H. Abramson.  Version 2.07a
  --------------------------------------------------------------------------
         
  These programs are for use in statistical analyses, especially of data on 
  health and disease, mainly to facilitate secondary calculations after 
  observations have been tabulated or counted.  Results are shown on the 
  screen, and can also be printed or saved as text in a disk file.  Data are 
  entered at the keyboard (except for logistic regression analysis). 

  **************************************************************************
    For information on how to obtain the programs, run any of the programs 
    and press the "Information" key when the opening screen appears, or    
    visit the PEPI web site (http://www.usd-inc.com/pepi.html), which also 
    announces new versions.                                                 
  ***************************************************************************
                         
                       FOR BASIC INSTRUCTIONS, READ ON.

  Run PROGRAMS.COM for brief descriptions of the programs.  See FILELIST.TXT 
  for a list of the programs (with their latest version numbers) and other 
  files. Changes made since publication of the manual for PEPI Version 2 are 
  described in UPDATE1.TXT, UPDATE2.TXT and UPDATE3.TXT. 
 
  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 to one of the 
  authors, c/o USD Inc. (see addresses above).
  
  ***************************************************************************

  IF YOU ACQUIRED PEPI207a.ZIP:

    PEPI207a.ZIP does not contain installation or menu programs.  
    
    Installation is not essential.  After unzipping the file you can run the
    statistical programs in DOS from any disk or directory, as you would any
    other program.  In DOS, you can type FINDER to view the Program Finder,
    PROGRAMS to see thumbnail descriptions of all the programs, README to view
    this file, and VIEW UPDATE1.TXT, VIEW UPDATE2.TXT or VIEW UPDATE3.TXT for
    update information.

    If you previously used the INSTALL or WINSTALL program to install PEPI,
    substitute the new programs for the old ones.  To do this, unzip the file,
    copy the new SM.CFG to the C:\ root directory (to update the PEPI menu for
    DOS), and copy the other unzipped files to the directory containing the
    old files.  You can safely replace (overwrite) existing files; but this is
    unnecessary if the version number is the same.  Version numbers are shown
    in the "Time" column in DOS or other directory listings, as well as in
    each program's opening screen.
       
    If you have not previously installed LOGISTIK for Windows, create an icon
    by specifying LOGISTIK.PIF as a new program item or by "dragging"
    LOGISTIK.PIF to the "Statistical programs" program group or folder; if a
    "DOS" icon appears, you can change it to the "LOGISTIK" icon by specifying
    LOGISTIK.ICO.  Drag the icon to the position you want, and save the
    settings.  You can operate the program without creating an icon, by
    running LOGISTIK.PIF (if you run LOGISTIK.EXE, the "Print results" option
    and the PrintScreen function will not work).
    
    Follow the same steps to install LOGX for Windows, using LOGX.PIF and
    LOGX.ICO.
    
    POOLING was a separate program before Version 2.07, when it became part of
    COMBINE.  If you have previously installed POOLING, remove it manually:
    delete POOLING.EXE, POOLING.PIF and POOLING.ICO, and (in Windows) delete
    the icon.
    
    If you have not previously installed PEPI with the INSTALL or WINSTALL
    program, some of the following instructions are irrelevant.

    If you previously used PEPI207.ZIP, note that PEPI207A.ZIP contains 
    corrected versions of LOGISTIK.EXE and LOGX.EXE and a new UPDATE1.TXT. 
    These are the only changes. 
    
  ***************************************************************************
  
  CONTENTS:          Installing the programs
                     Installing new versions
                     Finding the program you need
                     Running the programs in DOS
                     Running the programs under Microsoft Windows
                     Using the programs: basic instructions
                     Printing and saving the results 
                     Errors in the manual
                     Problems
  
  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 2.1 to 2.5 megabytes for INSTALL, and 2.4 to 3.1 
    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 you should ensure that the directory is 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 either in DOS or 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; if necessary, this directory will be created.  
      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 or folder will be 
      created, with icons for all programs.  If you wish you can "drag" icons 
      to change their positions, and then save the settings (see your Windows 
      manual).  
                                          

  INSTALLING NEW VERSIONS
           
  - If you wish to install new versions of the programs, and you have new 
    diskettes, run INSTALL or WINSTALL (with the new diskettes), specifying 
    the directory that contains the old versions.  If there is a new version 
    of any program or other file this will automatically replace the old 
    version; if there is no new version the old one will remain intact; if 
    there is a completely new program, it will be installed.  
           
  - If you do not have new diskettes, but have acquired a compressed (ZIP)
    file containing a new version of PEPI, copy the newer programs to the
    directory containing the old ones (replacing the old ones).  See
    instructions above ("If you acquired PEPI207a.ZIP"),


  FINDING THE PROGRAM YOU NEED

  - A Program Finder is provided.  This is an index in which you can look up 
    a statistical procedure, or what you want to achieve (e.g. "smoothing of 
    curves") or compute (e.g. "odds ratio"), or the kind of study (e.g. 
    "case-control study").  

  - In DOS, type FINDER (or choose "Program finder" in the menu).  For 
    thumbnail descriptions of all the programs, type PROGRAMS (or choose "The 
    programs" in the menu).

  - In Windows, click on the Help ("?") icon to run the Windows Program 
    Finder, which includes thumbnail descriptions of all the programs. 
         

  RUNNING THE PROGRAMS IN DOS
    
  - To run a program from the DOS prompt (e.g. A:>) type its name (e.g. 
    "TIMES") and press <Enter> or <Return>.  Operate the program from the 
    directory in which it is situated, or make sure this directory is in your 
    PATH.  

  - You can also type "PEPI", which brings up a menu (if you have used 
    INSTALL or WINSTALL).  Move the highlight bar with an arrow key or a 
    mouse, and press <Enter> or the left mouse button to select a statistical 
    program (or see the program finder or program descriptions).  To quit the 
    menu, press <Escape> or the right mouse button.  The menu will work only 
    if the directory to which the programs have been copied is in your PATH, 
    and SM.CFG is in the C:\ root directory (where INSTALL and WINSTALL 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. 
    
                         
  RUNNING THE PROGRAMS UNDER MICROSOFT WINDOWS

  - The programs are DOS applications, but can be run under Windows (3.x, 95 
    or NT). 
         
  - If you have installed the programs and other files with icons (by using 
    WINSTALL), just click on the icon.  
                                 
  - You can also use any other method of launching a DOS program in Windows 
    (see your Windows manual).  Launch the PIF file (e.g. TIMES.PIF) rather 
    than the EXE file (e.g. TIMES.EXE), or the PrintScreen and Selective 
    PrintScreen features (see below) will not work. 
    

  USING THE PROGRAMS: BASIC INSTRUCTIONS
                 
  The programs are easy to use.  Follow the instructions shown on the screen.  
  Extra explanations will be found in the manual or UPDATE files. 

  - If you wish to quit a program at the data-entry stage (and no "quit the 
    program" option is offered), try pressing <Enter>.  You can quit a 
    program at any time by pressing <Ctrl><Break>; there maybe a delay.  In a 
    real emergency, press <Ctrl><Alt><Del>.  
     
  - In the instructions, <Ent> refers to the <Enter> or <Return> key. 

  - When choices are offered, e.g."Type A if .. or B if ..", it is generally 
    sufficient to tap the key, without pressing <Enter>.  You may use either 
    lower-case (a, b) or upper-case (A, B). 

  - After entering a number you will almost always have to press <Enter>.
    
  - When there are no further data to enter, you are generally asked to 
    signal 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 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. 

  - The programs do not store data or retrieve data from computer files, with 
    five exceptions: LOGISTIK can read data files and create and use 
    dictionary files, DIRST and INDIRST can store standards entered at the 
    keyboard, SURVIVAL can store and modify data for its own use, and WHATS 
    stores results, constants and formulae for later use.  


  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" 
    (<PrtScr>) key whenever you want to print what is on the screen (this 
    should work in Windows too, if you installed the programs with WINSTALL).  
    However, keyboards and computers vary.  You may have to press 
    <Shift><PrtScr>. 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, is provided.  Run this in advance by typing "SPS" 
    or putting "SPS" in your AUTOEXEC.BAT file.  Then (whether you use the 
    automatic printing option or the <PrtScr> 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 (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.          


  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. 

  Page 156: The program computes chi-square by formula 13 of Mantel 1963; 
  the formula printed is an application specific to case-control studies.
                                                                
  Pages 198 and 199, which should have contained part of Example 3, were 
  accidentally left blank.       
  
  Page 223, paragraph 4: "each5nd an" should be replaced by "each stratum
  (block) to the sample and a residual".

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

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

  - Please inform one of the authors if you encounter a problem.  
  
  - If your hard disk is full, WINSTALL may seem to complete the installation 
    program without actually doing so.  
 
  - After installing in Windows 3.x you may find that some icons are missing: 
    you may be using a color mode - e.g. "high color" or "true color" - that 
    needs extra memory per icon, so that the number of icons per program 
    group is reduced.  Create an extra program group or folder, and insert 
    the missing program items manually. 

 
  ACKNOWLEDGEMENTS

  - SHOW.COM 2.1, by Gary M. Raymond, was used to make the self-displaying 
    COM files.  RFTGEN 2.03, by Dave Baldwin, was used for the Program Finder 
    for Windows, and an adaptation of TXT2UNIT 2.0, by J.J. Arenzon, was 
    used for information displays.  We are grateful to Pat Anderson for 
    permission to use his EDITWIN word-processor unit.  Other programs we 
    used are listed in the manual and UPDATE files.  To modify the menu 
    program, 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. 


