Installing and operating the Asian-Pacific American BrCa Absolute Risk Assessment Tool
version 1.0                                                     creation date 08/25/10
version 1.1                                                     creation date 12/05/13

This installation and operation module pertains to Windows 32-bit operating system
or Windows 64-bit operation system, depending of the user's requirements.


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@ Note that there are two versions of this software.  One version is for a 64-bit @
@ operating system.  The other for a 32-bit system.  Please select the version    @
@ which corresponds to the operating system on the computer which it will be used @
@ All needed components specifically for the 64-bit machine will have  "_64"  in  @
@ it's name.   Similarly, any needed componets for the 32-bit machine will have   @
@ "_32"  somewhere in it's name.  All shared components will not have show these  @
@ three characters.                                                               @
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@   NOTE WHEN UNSURE OF WHICH WINDOWS OPERATING SYSTEM, USE THE 32-BIT VERSION    @
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Contents of the Zip file  "APA_BrCa_AbsRsk_Ver1_1.zip":


(a) APA_BrCa_AbsRsk_32.gcg   pre-compiled gauss program which performs
                             Asian-American/Pacific Islander BrCa Risk Projection
                             for 32-bit Windows Operating System

(b) APA_BrCa_AbsRsk_64.gcg   pre-compiled gauss program which performs
                             Asian-American/Pacific Islander BrCa Risk Projection
                             for 64-bit Windows Operating System

(c) APA_RR.Fil               sample relative risk profile input file read by the
                             above either of the above  programs
                            "APA_BrCa_AbsRsk_32.gcg"   or   "APA_BrCa_AbsRsk_64.gcg"

(d) APA_RR.compare           projected risks by reading the above sample input file

(e) APA JNCI 12-18-2010.pdf  JNCI Asian American/Pacific Islander manuscript

(f) GRTM_11_Win_32.msi       installation file for the gauss run-time module GSRun
                             on a 32-bit computer

(g) GRTM_11_Win_64.msi       installation file for the gauss run-time module GSRun
                             on a 64-bit computer

(h) ReadMe.fil               this file you are reading
    ReadMe.pdf               pdf version of ReadMe.fil

After unzipping  "APA_BrCa_AbsRsk_Ver1_1.zip",  check to see that all files listed
above are included.  At this point, a cursory examination of  "APA_RR.Fil"  will
prove useful. This file can be veiwed using your favorite text editor or  Notepad
which is included with Windows.



Installation of the gauss run-time module GSRun:

The gauss run-time module GSRun will execute any pre-compiled gauss program.  It
is needed for the user to perform BrCa Absolute Risk Projections for Asian-
Pacific American Women by executing the provided pre-compiled gauss program
"APA_BrCa_AbsRsk_32.gcg"   or  "APA_BrCa_AbsRsk_64.gcg".  Depending on the
operating system.

For a 32 bit system, click on  "GRTM_11_Win_32.msi"  to start the installation
process.

For a 64 bit system, click on  "GRTM_11_Win_64.msi"  to start the installation
process.

(a) the installer will ask you to accept the standard license agreement. After
    you accept the agreement, it will ask you which folder you want to install
    the gauss run-time module GSRun.  If the default is acceptable click "next",
    otherwise click "browse".  If you clicked "browse", a box will appear where
    you can type in the destination of the installation process.  In the
    following, assume you chose to install in the the folder  "c:\APA_Risk".

(b) at the completion of the installation process, the installer will place a
    gauss run-time module icon on the desktop.  It is recommended leaving the
    icon on the desktop for ease of use.

(c) copy the three files  "APA_BrCa_AbsRsk_32.gcg" or "APA_BrCa_AbsRsk_32.gcg",
    "APA_RR.fil"   and   "APA_RR.fil.compare"  to where you installed the gauss
    run-time module GSRun, namely  "c:\APA_Risk".

(d) you may wish to copy this  "ReadMe.fil"  and the enclosed APA manuscript to
    the folder  "c:\APA_Risk"  as well.

(e) the installation process is now complete.



A step by step example using the Asian-Pacific American BrCa Risk Assessment Tool:

(a) after the installation process and assuming that you have copied the files
   "APA_BrCa_AbsRsk_32.gcg"   or "APA_BrCa_AbsRsk_32.gcg"  and  "APA_RR.Fil"  to
   "c:\APA_Risk",  click on the gauss run-time module icon which was placed on the
    desktop by the installer.

(b) gauss run-time module GSRun will open a window.  At the gauss prompt  ">>",
    type "run APA_BrCa_AbsRsk_32.gcg"  or "run APA_BrCa_AbsRsk_64.gcg".  The gauss
    run-time module GSRun will begin to execute the absolute risk projection
    program.

(c) the program will ask you to type the name of the input file.  For this instance
    you should type  "APA_RR.fil"  as your input file name.  Note that the output
    file will be named  "INPUT FILE NAME.out",  i.e. the output file will be named
    "APA_RR.Fil.out".

(d) the output file "APA_RR.Fil.out",  written to  "c:\APA_Risk",  containing
    the BrCa risk projections will be available for further perusal and
    analysis.  For peace of mind, you may want to compare the generated output
    file  "eXample_File.out"  with the file  "APA_RR.Fil.compare"  included with
    the installation module.  These two files can be viewed using  Notepad  or any
    other text editor.  Upon ascertainment of complete agreement between the two
    files, you can proceed to delete the file  "APA_RR.Fil.compare".


File name/structure for the input file to the Asian-Pacific American Risk program :

(a) since the program prompts for the input file name,  it may take on any arbitrary
    name.  The name of the input file is case insensitive.  For ease of use, the input
    file should be placed in the folder  "c:\APA_Risk".
    Again, note that the output file name will be  "input file name.out"  and will be
    created in the folder  "c:\APA_Risk".

    the input file structure includes 9 columns of data with the following column order.
    all columns/fields are format free with each column separated by at least one
    or more blank space(s).

    Col1   ID               : integers taking on the values in {1,2,3...}

    Col2   Current     age  : ages between the interval [20, T2)  e.g. 35.8
    Col3   Projection  age  : ages between the interval (T1, 90]  e.g. 58.9
                              constraint of 20 <= T1 < T2 <= 90

    Col4   # Biopsy         : 0,1,2 ...     99 (missing)       (non-negative integer)

    Col5   Age Menarche     : age in years  99 (missing)       (non-negative integer years)
    Col6   Age 1st Birth    : age in years  99 (missing)       (non-negative integer years)
                                            98 (nulliparous)

                              constraint of Age Menarche <= Age 1st Live Birth

    Col7   # Rel with BrCa  : 0,1,2 ...     99 (missing)       (non-negative integer)

    Col8   Atypical Hyprplsa: 0=No,    1=Yes ,   99=Not applicable or UNK
                              if # Biops=0 than Atypical Hyperplasia must be 99=Not applicable
                              if # Biops>0 than Atypical Hyperplasia= 0,1 or 99=UNK

    Col9   Race             : 1=Chinese   2=Japanese    3=Filipino
                              4=Hawaiian  5=otrPacific  6=otrAsian

    in the above {} denotes a collection/set of numbers
                 [) represents an interval closed on the left and   open on the right
                 (] represents an interval   open on the left and closed on the right


    this program will categorize the raw values of NBiops, AgeMen, Age1st, NumRel into
    risk categories level numbers according to the rules outlined in the APA manuscript.

    note that the program, being an analytical tool, will make the most rudimentary
    checks for logical consistency between the input variables.  It is the user's
    responsibility to make sure that all input covariate values are logically
    consistent and correct within each person.  As a final step, the program
    will generate a missing projected Absolute Risk for records which it deems to
    be in error.  The user should examine the output file for any records with a
    missing Absolute Risk and rectify the error(s) for these records.

       e.g.  if NBiops equals zero than atypical hyperplasia must be 99 (not applicable)
        or   Projection Age in years must be greater than Current Age


Contacts:
Dr. Mitchell Gail     gailm@exchange.nih.gov      Scientific/Medical issues
Mr. David    Pee      peed@imsweb.com             Technical/software problems



Terms & Conditions

Source Code for APA model: Asian-Pacific American Women Breast Cancer Risk Calculation Module

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