


 RUN BMDP PROGRAM:  BIMED [(parameter| -command | #switch)...]| -F | -H
 
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                           BIMED HELP PACKAGE

 THE BIMED HELP PACKAGE WILL BE TYPED OUT IN 20 LINE SEGMENTS.   AT  THE
 END OF EACH SEGMENT, YOU WILL BE RECEIVE A PROMPT.
       *IF YOU WANT TO CONTINUE, MERELY TYPE A CARRIAGE RETURN
       *IF YOU WANT TO CONTINUE WITHOUT ANY MORE PROMPTS  AND  PRINT  TO
            THE BOTTOM OF THE HELP FILE, TYPE "G".
       *IF YOU WANT TO SKIP THE NEXT 20 LINES, TYPE "/".
       *TYPE ANYTHING ELSE TO LEAVE THE HELP PACKAGE.

 
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                           TABLE OF CONTENTS

  1.   DESCRIPTION OF PROGRAM
  2.   PARAMETERS
  3.   COMMANDS
  4.   SWITCHES
  5.   ERRORS
  6.   RUN YOUR PROGRAM ON BATCH MODE
  7.   USING YOUR OWN FORTRAN TRANSFORMATIONS

 
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                         DESCRIPTION OF PROGRAM

 THIS PROGRAM WILL RUN YOUR BMDP PROGRAMS FOR YOU.  IT WILL ALSO PROVIDE
 THE FOLLOWING SERVICES:

       INQUIRE FOR ALL PARAMETERS
       MAKE ALL FILE ASSIGNMENTS TO THE OPERATING SYSTEM
       ANNOTATE YOUR OUTPUT WITH THE ASSIGNMENTS

 THE PROGRAM HAS  SEVERAL  OPTIONS,  SET  BY  MEANS  OF  SWITCHES.   THE
 OPTIONS, AND THE DEFAULT VALUE FOR EACH OPTION, ARE:

       ASSUME YOUR BMDP PROGRAM HAS ONE (D) OR MANY PROBLEMS
       RUN BMDP INTERACTIVELY (D) OR ON THE BATCH QUEUE
       RUN BMDP WITHOUT (D) OR WITH USER-SUPPLIED FORTRAN 
             TRANSFORMATIONS
       EDIT AND EXECUTE (D) THE BMDP PROGRAM, OR ONLY EDIT IT
       SHOW DETAILED ERROR MESSAGES (D) OR ONLY TRUNCATED MESSAGES

 THE PROGRAM CAN ALSO RESPOND TO SEVERAL COMMANDS.  THESE COMMANDS ALLOW
 YOU TO:

       DISPLAY THE FORMAT OF THE BIMED COMMAND
       DISPLAY THIS HELP FILE
       SHOW THE STATUS OF ALL SWITCHES
       TERMINATE BIMED PREMATURELY
       READ INPUT FROM A FILE SPECIFIED BY YOU

 ALL SWITCHES START WITH A "#";  ALL COMMANDS START  WITH  A  "-".   ANY
 OTHER  INPUT  IS  ASSUMED  TO  BE A PARAMETER.  ONCE BIMED HAS ALL YOUR
 PARAMETERS, IT WILL COPY YOUR FILE CONTAINING BMDP  COMMANDS,  ANNOTATE
 IT,  AND MAKE ALL FILE ASSIGNMENTS.  IT WILL THEN RUN THE BMDP PROGRAM.
 WHEN BIMED RUNS BMDP WITH USER-SUPPLIED TRANSFORMATIONS OR ON THE BATCH
 QUEUE,  YOU  WILL  ALWAYS  RECEIVE  A  WARNING THAT TWO MODULES CONTAIN
 COMPILATION WARNINGS.  THIS IS A NORMAL STATE OF AFFAIRS, AND IS DUE TO
 THE STRUCTURE OF THE BMDP PROGRAMS THEMSELVES.  TO SIMPLIFY THE RUNNING
 OF BIMED, NOTE THAT YOU CAN SUPPLY UP TO YOUR FIRST EIGHT ANSWERS  WHEN
 YOU CALL FOR BIMED.  DO THIS BY INPUTTING THEM ON THE SAME COMMAND LINE
 AS THE COMMAND BIMED, SEPARATED BY SPACES.  FOR EXAMPLE:

       BIMED #TRANSFORMS BMDP1D MYFILE.FOR BMDP1D.INP

 CALLS FOR  BIMED,  SETS  THE  "#TRANSFORMS"  SWITCH  (SEE  BELOW),  AND
 SUPPLIES THE NAMES OF THE FIRST THREE FILES FOR WHICH BIMED ASKS.

 ONE IMPORTANT NOTE:  AS BIMED MAKES ALL FILE ASSIGNMENTS FOR  YOU,  YOU
 SHOULD  ***NOT***  INCLUDE  ANY  FILE  ASSIGNMENTS IN YOUR BMDP COMMAND
 LANGUAGE FILE.  IN OTHER WORDS, DO NOT USE THE BMDP COMMANDS  "FILE  ="
 OR  "UNIT  =".   ALSO,  AS  BIMED  WILL EDIT YOUR FILE (AND AS BIMED IS
 BASICALLY A RATHER SIMPLE-MINDED  PROGRAM),  YOU  SHOULD  FOLLOW  THESE
 RULES IN WRITING YOUR BMDP COMMAND FILE:

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       1.  DO NOT USE THE COMMANDS "FILE =" OR "UNIT =".
       2.  USE THE CONSTRUCTION /PARAGRAPH-NAME.
       3.  PLACE THE COMMANDS "/INPUT" AND "/SAVE" (IF USED) ON LINES
               BY THEMSELVES, WITH NO OTHER COMMANDS ON THOSE LINES.
               ALSO, START THOSE COMMANDS BEFORE COLUMN 30.

 BY FOLLOWING THESE RULES, YOU WILL NOT RUN INTO UNTOWARDS EVENTS CAUSED
 BY THE SIMPLICITY OF BOTH BIMED AND BMDP.

 
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                               PARAMETERS

 BIMED ASKS YOU FOR SEVERAL PARAMETERS INVOLVED WITH RUNNING  YOUR  BMDP
 PROGRAM.   IT  OFFERS DEFAULT VALUES WHICH ARE USED IF YOU ONLY ENTER A
 CARRIAGE RETURN IN REPLY TO ITS PROMPTS.  NATURALLY, NOT ALL PARAMETERS
 ARE  ASKED  EVERY  TIME,  BUT  RATHER  ONLY  THOSE PARAMETERS WHICH ARE
 APPROPRIATE TO  YOUR  PROGRAM,  AS  INDICATED  BY  THE  SWITCHES.   THE
 PARAMETERS ASKED, AND THE ORDER IN WHICH THEY ARE ASKED, ARE:


       BMDP PROGRAM TO RUN
       (ALWAYS ASKED)
       DEFAULT:  NONE AVAILABLE

       OBJECT FILE CONTAING YOUR BMDP TRANSFORMATIONS
       DEFAULT:  BMDPXX.OBJ (WHERE BMDPXX IS THE NAME OF THE BMDP
                     PROGRAM)

       FILE CONTAINING BMDP COMMANDS
       (ALWAYS ASKED)
       DEFAULT:  BMDPXX.INP

       FILE TO WHICH TO WRITE OUTPUT
       (ALWAYS ASKED)
       DEFAULT:  BMDPXX.OUT
       (USE "TYPE" TO HAVE THE OUTPUT SENT TO YOUR TERMINAL)
       (USE "PRINT" TO HAVE THE OUTPUT SENT TO THE SYSTEM PRINTER)

       FILE CONTAINING DATA TO ANALYZE
       (ALWAYS ASKED)
       DEFAULT:  BMDPXX.DAT

       FILE TO WHICH TO WRITE A SAVE FILE
       (ALWAYS ASKED)
       DEFAULT:  BMDPXX.SAV
       IF YOUR PROGRAM IS NOT WRITING A SAVE FILE, RESPOND WITH "NONE"

       FILE TO USE AS FOR010
       (ONLY ASKED WHEN BMDP WILL BE RUN IN BATCH MODE)
       DEFAULT:  BMDPXX.F10
       IF YOU DO NOT NEED SUCH A FILE, RESPOND WITH "NONE"

       FILE TO USE AS FOR020
       DEFAULT:  BMDPXX.F20

       FILE TO USE AS FOR030
       DEFAULT:  BMDPXX.F30

 YOU CAN RESPOND  TO  ANY  REQUEST  FOR  A  PARAMETER  WITH  EITHER  THE
 PARAMETER, A COMMAND, OR A SWITCH.

 
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                                COMMANDS

 BIMED RECOGNIZES 6 COMMANDS.  THE COMMANDS AND THEIR FUNCTIONS ARE:

       -FORMAT         DISPLAY THE FORMAT OF THE BIMED COMMAND
       -HELP           DISPLAY THIS HELP PACKAGE
       -SHOW-SWITCHES  DISPLAY THE STATUS OF ALL SWITCHES
       -QUIT           STOP RUNNING BIMED, AND RETURN TO THE CALLING 
                               LEVEL
       -INPUT:FILENAME READ INPUT FROM THE SUPPLIED FILE
       -Z              INDICATES THAT THERE ARE NO MORE PROBLEMS:
                           "-Z"  IS  USED  WHEN  YOU HAVE INDICATED THAT
                           THERE ARE  MULTIPLE  PROBLEMS  IN  YOUR  BMDP
                           CONTROL LANGUAGE  FILE.   BIMED WILL CONTINUE
                           TO  ASK  FOR  DATA  FILES  AND  SAVE   FILES,
                           CONTINUING  TO  ASSUME  THAT  THERE  ARE MORE
                           SUBPROBLEMS.  TO INDICATE THAT THERE  ARE  NO
                           MORE  SUBPROBLEMS,  TYPE "-Z" WHEN BIMED ASKS
                           FOR THE DATA FILE.

 ALL COMMAND NAMES CAN BE TRUNCATED DOWN  TO  AS  LITTLE  AS  THE  FIRST
 LETTER.   NOTICE  THAT  ONLY THE "-INPUT" COMMANDS ACCEPTS A PARAMETER.
 AFTER "-INPUT", YOU SHOULD TYPE A COLON  FOLLOWED  IMMEDIATELY  BY  THE
 NAME OF THE FILE FROM WHICH BIMED SHOULD READ INPUT.

 
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                                SWITCHES

 BIMED RECOGNIZES 5 SWITCHES.  THE SWITCHES AND THEIR FUNCTIONS ARE:

       #MULTIPLE       MULTIPLE PROBLEMS ARE CONTAINED IN YOUR CONTROL
                             LANGUAGE FILE
       #EXECUTE        BIMED SHOULD EDIT AND EXECUTE BMDP
       #BATCH          THE BMDP PROGRAM SHOULD BE RUN ON THE BATCH QUEUE
       #TRANSFORMS     USER-SUPPLIED FORTRAN TRANSFORMS WILL BE USED
       #DETAILED       DETAILED ERROR MESSAGES WILL BE ISSUED

 SWITCHES ARE TURNED ON BY MERELY TYPING THEIR NAMES, AND ARE TURNED OFF
 BY TYPING THEM WITH THE WORD "NO" IN FRONT.  FOR EXAMPLE

       #TRANSFORMS

 TURNS ON THE #TRANSFORMS  SWITCH  AND  INDICATES  TO  BIMED  THAT  YOUR
 FORTRAN TRANSFORMATIONS SHOULD BE LINKED WITH BMDP.  SIMILARLY,

       #NOEXECUTE

 INDICATES THAT THE BMDP PROGRAM SHOULD NOT BE EXECUTED, AND RATHER  THE
 COMMAND LANGUAGE FILE SHOULD ONLY BE EDITTED.

 ALL SWITCHES CAN BE TRUNCATED DOWN TO A SINGLE LETTER.  HENCE, YOU  CAN
 SET  ANY SWITCH BY TYPING THE CHARACTER "#" AND THE FIRST LETTER OF THE
 SWITCH NAME;  YOU CAN TURN OFF ANY SWITCH BY TYPING "#NO" AND THE FIRST
 LETTER  OF  THE SWITCH NAME.  AS MAY BE EXPECTED, YOU MUST ALSO SPECIFY
 THE SWITCH PRIOR TO THE TIME WHEN  THE  PROGRAM  ACTS  BASED  UPON  THE
 SWITCH.    FOR   EXAMPLE,   AS   THE  PROGRAM  ASKS  FOR  YOUR  FORTRAN
 TRANSFORMATIONS AS THE SECOND PARAMETER, YOU MUST SET THE "#TRANSFORMS"
 SWITCH  PRIOR  TO  THE  TIME THE PROGRAM ASKS FOR YOUR COMMAND LANGUAGE
 FILE.

 NOTICE ON THE "#MULTIPLE" SWITCH THAT "MULTIPLE  PROBLEMS"  MEANS  THAT
 YOU  HAVE  SEVERAL  "/PROBLEM"  AND  "/INPUT"  PARAGRAPHS  IN YOUR BMDP
 CONTROL LANGUAGE FILE.  IF YOU ONLY HAVE ONE "/PROBLEM" PARAGRAPH,  YOU
 ONLY HAVE ONE PROBLEM, ALTHOUGH YOU MAY HAVE NUMEROUS SUBPROBLEMS.

 
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                                 ERRORS

 BIMED  RECOGNIZES  NUMEROUS  ERRORS.   THESE   ARE   CHARACTERISTICALLY
 INAPPROPRIATE  RESPONSES  TO  PROMPTS, UNKNOWN SWITCHES OR COMMANDS, OR
 INCOMPATIBLE COMBINATIONS OF SWITCHES.  WHEN BIMED RECOGNIZES  SUCH  AN
 ERROR,  IT  WILL  ISSUE  AN  ERROR WARNING AND IGNORE THE INPUT STRING.
 THIS MEANS THAT IF YOU HAVE SUPPLIED A LONG STRING OF  PARAMETERS,  AND
 ONE  OF  YOUR SWITCHES OR COMMANDS IS INCORRECT AT THE BEGINNING, BIMED
 WILL CONTINUE TO READ ALL OF  YOUR  INPUTS  AS  THOUGH  THAT  ERRONEOUS
 INFORMATION  WERE NEVER THERE.  THIS MAY RESULT IN THE WRONG FILE BEING
 USED FOR SOME PURPOSE.  BE CAREFUL!

 ERROR MESSAGES CONSIST OF TWO PARTS.  THE FIRST PART  CONSISTS  OF  THE
 STANDARD  SYSTEM ERROR MESSAGE.  THE SECOND PART CONSISTS OF A DETAILED
 DESCRIPTION OF THE MISTAKE.  THE SYSTEM ERROR MESSAGE IS ALWAYS  GIVEN;
 THE  DETAILED  DESCRIPTION OF THE ERROR WILL BE GIVEN UNLESS THE SWITCH
 "#NODETAILED"   IS   GIVEN.    THE   DETAILED   ERROR   MESSAGES    ARE
 SELF-EXPLANATORY  AND ARE VERY USEFUL IN DETERMINING WHAT MISTAKES WERE
 MADE.

 
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                    RUNNING BMDP ON THE BATCH QUEUE

 BIMED WILL TAKE YOUR INPUT FROM YOU AND RUN BMDP ON  THE  BATCH  QUEUE.
 YOU  SHOULD  BE AWARE OF SEVERAL THINGS IN THESE CIRCUMSTANCES.  ONE IS
 THAT WHATEVER THE DEFAULT DIRECTORY IS WHEN YOU RUN BIMED WILL  BE  THE
 SAME  DEFAULT DIRECTORY FOR THE BMDP PROGRAM.  YOU SHOULD BE CAREFUL IN
 SPECIFYING FILES.  THE OTHER FACT IS THAT BIMED WILL ASSIGN THREE FILES
 FOR  USE  AS FOR010, FOR020, AND FOR030.  THESE FILES ARE FOR YOUR USE,
 AND CAN BE USED IN YOUR FORTRAN TRANSFORMATIONS IF DESIRED.

 IN GENERAL, ALTHOUGH YOU CAN SUBMIT BIMED TO THE  BATCH  QUEUE,  IT  IS
 MORE  EFFICIENT AND LESS ERROR-PRODUCING TO RUN BIMED INTERACTIVELY AND
 USE THE SWITCH "#BATCH" TO RUN BMDP ON THE BATCH QUEUE.

 
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                     USER-SUPPLIED TRANSFORMATIONS

 IF YOU WISH TO USE YOUR OWN FORTRAN TRANSFORMATIONS, THEY MUST  ALREADY
 BE  COMPILED  AND  IN  AN  OBJECT [FILE.OBJ] FORM.  THE PAGE DESCRIBING
 USER-SUPPLIED FORTRAN  TRANSFORMATIONS  IS  MISSING  FROM  THE  BMDP-79
 MANUAL, SO IT IS REPRODUCED HERE:

           SECTTON 6.4  FORTRAN TRANSFORMATIONS USING BIMEDT

 FORTRAN TRANSFORMATIONS  ARE  MORE  ECONOMICAL  THAN  CONTROL  LANGUAGE
 TRANSFORMATIONS   WHEN   YOU   HAVE  LARGE  QUANTITIES  OF  DATA,  WHEN
 COMPLICATED TRANSFORMATIONS ARE NECESSARY OR WHEN  THE  TRANSFORMATIONS
 ARE APPLIED TO MANY VARIABLES.  THE FORTRAN STATEMENTS ARE PROCESSED BY
 THE FORTRAN COMPILER AND TEMPORARILY BECOME PART OF THE  BMDP  PROGRAM.
 TRANSFORMATIONS   SPECIFIED  IN  FORTRAN  ARE  PROCESSED  BEFORE  THOSE
 SPECIFIED IN THE TRANSFORM PARAGRAPH  IF  BOTH  TYPES  ARE  USED.   ANY
 LEGITIMATE  FORTRAN  STATEMENTS,  SUCH AS READ, WRITE, DATA, DIMENSION,
 FUNCTION AND SUBROUTINE, CAN BE USED.  THE FORTRAN SUBROUTINE IN  WHICH
 THE   TRANSFORMATIONS  ARE  INCLUDED  STARTS  WITH  THE  FOLLOWING  TWO
 STATEMENTS:

            SUBROUTINE TRANSF(X,KASE,NPROB,USE,NVAR,XMIS)
            DIMENSION X(NVAR)

 [N.B.  IN USING BIMEDT ON THE VAX, THESE TWO  STATEMENTS  MUST  BE  THE
 FIRST  TWO  STATEMENTS  INCLUDED  IN  YOUR  OWN  SUBROUTINE  WHEN IT IS
 COMPILED.  SIMILARLY, RETURN AND END MUST BE THE LAST  TWO  STATEMENTS.
 THIS IS BECAUSE ON THE VAX, YOU MUST LINK WITH COMPILED SUBROUTINES.]

 WHERE THE FOLLOWING VALUES SHOULD NOT BE CHANGED:

     KASE:  IS THE SEQUENCE NUMBER OF THE CASE BEING PROCESSED

     NPROB:  IS THE SEQUENCE NUMBER OF THE PROBLEM  (PROBLEM  PARAGRAPH)
     BEING PROCESSED

     NVAR:  IS THE GREATER OF THE NUMBER OF THE VARIABLES  READ  OR  THE
     NUMBER  OF  VARIABLES  AFTER  TRANSFORMATIONS  (I.E., THE NUMBER OF
     VARIABLES  READ   PLUS   THE   NUMBER   OF   VARIABLES   ADDED   BY
     TRANSFORMATIONS, P.  99)

     XMIS:  IS THE MISSING  VALUE  CODE  USED  INTERNALLY  BY  THE  BMDP
     PROGRAM.  VALUES THAT ARE LESS THAN THE LOWER LIMIT OR GREATER THAN
     THE UPPER LIMIT SPECIFIED FOR A  VARIABLE  ARE  RECODED  TO  VALUES
     GREATER IN ABSOLUTE VALUE THAN XMIS.  THE VALUES ARE RECODED BEFORE
     THE TRANSFORMATIONS ARE PROCESSED, UNLESS AFTER IS SPECIFIED IN THE
     VARIABLE PARAGRAPH (P.  100)

 YOU CAN CHANGES THE VALUES OF X AND USE.

     X:  IS THE VECTOR CONTAINING THE DATA FOR THE CASE BEING PROCESSED.
     THE VALUES FOR ALL VARAIBLES READ IN THE DATA ARE PRESENT.  X(1) IS
     THE VALUE OF THE FIRST VARIABLE, X(2) THE SECOND, ETC.  THE  VALUES
     OF X CAN BE MODIFIED TO CONTAIN THE TRANSFORMED VALUES.
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     USE:   IS  A  FLAG  FOR  CASE  SELECTION.   ITS  INTERPRETATION  IS
     IDENTICAL  TO THAT OF USE IN THE TRANSFORM PARAGRAPH (P.  104).  IF
     USE IS POSITIVE (1), THE CASE IS USED IN  THE  ANALYSIS;   IF  ZERO
     (0),  THE CASE IS NOT USED BUT IS INCLUDED IN A BMDP FILE IF ONE IS
     CREATED;  IF NEGATIVE (-1) THE CASE IS NOT USED AND IS  NOT  COPIED
     INTO A BMDP FILE.
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