CCRAT Readme - Male Model
04/02/2012
Installing and operating the Men Colorectal Cancer Absolute Risk Assessment Tool
version 1.0 creation date 04/02/12
This installation and operation pertains to Windows 2000, Windows XP,
Windows Vista and Windows 7 32-bit operating systems for desktop/laptop PCs.
(1) Contents of the Zip file "M_CRCAbsRsk.zip":
(a) Men_CRC_Risk_Tool.gcg gauss program which performs the CRC Risk Projection
and 95% confidence interval calculations
(32-bit version)
(b) Men_CRC_Risk_Input.dat sample relative risk profile input file read by the
risk program "Men_CRC_Risk_Tool.gcg"
(c) Men_CRC_Risk_Tool.list projected risks by reading the above sample input file
(d) MenColnCaCovPat ancillary file used by the risk program
Men_CRC_Risk_Tool.gcg for data editing of the input
file Men_CRC_Risk_Input.dat. If it is not found,
data editing on the input file will not be performed
(e) Men_CRC_Risk_Tool.err input data editing error file listing
(f) MenCov_1_AR_RPD ancillary file used by the risk program
Men_CRC_Risk_Tool.gcg for 95% for confidence interval
calculations. If not found, confidence intervals will
not be produced.
(g) GRTM_11_Win_32.msi setup file for Gauss Run Time Module for Windows with
a 32 or 64 bit operating system
(h) MReadMe.fil this file you are reading
After unzipping the contents of "M_CRCAbsRsk.zip", check to see that all files
listed above are included.
Ref: "Colorectal Cancer Risk Prediction Tool for White Men and Women Without Known
Susceptibility". A Freedman et al. JCO 27:686-693 2008.
(2) Installing the Gauss Run Time Moduel:
Note: If you have previously installed the gauss run-time module using
GRTM_11_Win_32.msi, you can ignore this section.
The gauss run-time module will execute any pre-compiled gauss program. It is
needed for the user to perform CRC Absolute Risk Projections for men by executing
the provided pre-compiled Gauss program "Men_CRC_Risk_Tool.gcg".
click on "GRTM_11_Win_32.msi" to start the installation process and you are
using 32-bit Windows operating system.
(a) the installer will ask you to accept the standard license agreement. After
you accept the agreement, it will ask you where you want to install the
gauss run-time module. The default folder is "C:\gsrun11". 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 your installation
process. In the following discussion, the installation will be into the folder
"c:\CRC_AbsRisk"
(b) at the completion of the installation process, the installer will place a
gauss run time module icon on your desktop. It is recommended leaving the
icon on the desktop for ease of use.
(c) copy the six files:
"Men_CRC_Risk_Tool.gcg"
"Men_CRC_Risk_Input.dat"
"Men_CRC_Risk_Tool.list"
"MenColnCaCovPat"
"Men_CRC_Risk_Tool.err"
"MenCov_1_AR_RPD"
to where you installed the gauss run time module, i.e. in this example,
c:\CRC_AbsRisk.
(d) you may want to copy this "MReadMe.fil" to the folder c:\CRC_AbsRisk.
(e) the installation process is now complete.
(3) Input file desciription:
The men's colorectal cancer absolute risk projection Gauss program, Men_CRC_Risk_Tool.gcg,
needs the following information as input to project for absolute risk of colorectal cancer.
The ordering of each field MUST be in the indicated order given below. So Col 13 must
contain BMI Trend. Similarly for all of the columns.
Compare following with the header area of the sample input file Men_CRC_Risk_Input.dat:
Col 1 Race =1, white
=2, african-american
=3, hispanic
=4, asian-american
Col 2 Posi 0 =1, yes sigmoidoscopy and/or colonscopy last 10 years, no history of polyps
=0, otherwise
Col 3 Posi 1 =1. no sigmoidoscopy and/or colonscopy last 10 years
=0, otherwise
Col 4 Posi 2 =1, yes sigmoidoscopy and/or colonscopy last 10 years, yes history of polyps
=0, otherwise
Col 5 No IBupro =0, regular user of IBuprofin only
=1, non user of IBuprofin only
Col 6 Rel CRC >=1 =0, 0 relative with CRC (CRC=Colorectal Cancer)
=1, 1 or more relatives with CRC
Col 7 Hours Xrcise =0, greater than 4 hrs/wk
=1, greater than 2 and less than equal 4 hrs/wk
=2, greater than 0 and less than equal 2 hrs/wk
=3, 0 hrs/wk
Note: Hours Xrcise coding is "backward" i.e. 0 is most exercise, 3 is no exercise
Col 8 CigYrs 0 =1, # yrs cigarette smoking = 0
=0, otherwise
Col 9 CigYrs 2 =1, # yrs cigarette smoking >= 15 and < 35
=0, otherwise
Col 10 CigYrs 3 =1, # yrs cigarette smoking >= 35
=0, otherwise
Col 11 Veg <5 =1, less than five servings of vegetables per day
=0, greater equal to five servings of vegetables per day
Col 12 #Cigs Trend =0, # cigarettes smokes = 0
=1, # cigarettes smokes >= 1 and < 11
=2, # cigarettes smokes >= 11 and <= 20
=3, # cigarettes smokes >= 21
Col 13 BMI Trend =0, BMI <= 24.9
=1, BMI > 24.9 and BMI <= 29.9
=2, BMI > 29.9
Col 14 Posi 1 =1. no sigmoidoscopy and/or colonscopy last 10 years
=0, otherwise
Col 15 Posi 2 =1, yes sigmoidoscopy and/or colonscopy last 10 years, yes history of polyps
=0, otherwise
Col 16 Posi 3 =1, unk sigmoidoscopy and/or colonscopy last 10 years, unk history of polyps
=0, otherwise
Col 17 No NSaids =0, regular user of asprin/NSaids
=1, non user of asprin/NSaids
Col 18 #Rel Trend =0, 0 relative with CRC (CRC=Colorectal Cancer)
=1, 1 relative with CRC
=2, 2 or more relatives with CRC
Col 19 Age1 current age,
Col 20 Age2 projection age, ranges from: 50 <= Age1 < Age2 <=90
!!!!!!!!!!!! Warning Warning Warning Warning Warning Warning !!!!!!!!!!!!
!!!!!!!!!!!! Warning about an inadmissible error condition !!!!!!!!!!!!
Inadmissable condition of NoIBupro=0 and NoNSAIDS=1
i.e. individual uses IBuprofin but does not use NSaids.
This is contradictory since IBuprofin is a NSaid drug
projected absolute risk for records with this contradition will be missing
!!!!!!!!!!!! Warning about an inadmissible error condition !!!!!!!!!!!!
!!!!!!!!!!!! Warning Warning Warning Warning Warning Warning !!!!!!!!!!!!
Alogrithm used for calculating Risk Covariate Pattern ID for each input covariate pattern:
Pattrn_ID = 4*2*3*4*2*2*4*3*1* Hours Exercis (0,1,2,3) +
2*3*4*2*2*4*3*1* CigYr (0,1,2,3) +
3*4*2*2*4*3*1* VEGlt5 (0,1) +
4*2*2*4*3*1* BMItrnd (0,1,2) +
2*2*4*3*1* sigmod (0,1,2,3) +
2*4*3*1* NoNSaids (0,1) +
4*3*1* NoIBuprofen (0,1) +
3*1* #CigTrnd (0,1,2,3) +
1* NRel (0,1,2) +
1* 1
Pattrn_ID ranges in values from 1:18432
Pattrn_ID used for input Risk Covariate Pattern edit checking as well as
for 95% CI calculations. The numbers separated by commas in the parenthesis
is the number of levels and valid values for the levels for the associated
risk covariate. Note that "sigmod" is the trend variable created from
Posi 0, Posi 1, Posi 2 and Posi 3:
sigmod = 0 if Posi 0=1
1 if Posi 1=1
2 if Posi 2=1
3 if Posi 3=1
Similarly for CigYr:
CigYr = 0 if CigYrs 0=1
1 if CigYrs 0=0 and CigYrs 2=0 and CigYrs 3=0
2 if CigYrs 2=1
3 if CigYrs 3=1
Before exeucting the risk projection program, it should prove beneficial to
take a brief examination of the input file "Men_CRC_Risk_Input.dat"
included with this package.
(4) Executing Men's colorectal cancer (CRC) risk program "Men_CRC_Risk_Tool.gcg":
Method 1: Associate any file which ends with ".gcg" with the gauss run time module.
Once this has been performed, you can just click on "Men_CRC_Risk_Tool.gcg"
or any file ending with ".gcg" for that matter, and the gauss run time
moduele will execute the file and the absolute risk program will start to
execute.
Method 2: Click on the gauss run time module icon which has been placed on your desktop
by the installer. The gauss run time module window will open. On top of the
window, will be a white rectangular box, with the name of the folder which the
gauss run time module is pointing. If it is pointing at the folder which
contains "Men_CRC_Risk_Tool.gcg" then you don't have to navigate anywhere. If
it is not pointing at the folder which contains "Men_CRC_Risk_Tools.gcg", then
either use the browse buttom (the little gray rectangle with three dots on it)
to navigate to the correct folder, or just type in the name of the folder in the
white rectangle. In this discussion, you would type "c:\CRC_AbsRisk". Once
this is done, at the ">>" symbol, type "run Men_CRC_Risk_Tool.gcg" and the
absolute risk program will start to execute.
Once the absolute risk program "Men_CRC_Risk_Tool.gcg" completes execution, it will output
two files. One is the output file:
"Men_CRC_Risk_Tool.out" which contains absolute risk associated quantities.
the other is the edit error file :
"Men_CRC_Risk_Tool.err" which indicates input records with editing errors.
It would be beneficial to look at both files. If the error file only contains a table heading,
this means that no editing errors was discovered by the program. Please note that this does
not guarantee that unanticipated errors have not occured in the input file. Integrity of the
input data is still the user's responsibility.
The included error file lists errors for seven records.
1st error: Incorrect value 5 for race. Race takes on the values 1,2,3 and 4
2nd error: Incorrect value 49 for Age1. Age1 must be ge 50.
3rd error: Incorrect value 60 for Age1 and Age2. Age2 must be gt Age1.
4th error: Incorrect value 91 for Age2. Age2 must be le 90.
5th error: Incorrect value 9 for #Rel012. #Rel012 takes only values of 0,1,2.
6th error: Incorrect value 9 for Hours Xrcise Hours Xrcise takes only values of 0,1,2,3.
7th error: Incorrect value 0 for noIBup and 1 for noNSAD. This scenairo is inadmissable.
The above seven errors are but a sub-set of all possible errors and are not meant to be exhaustive
of all possible errors.
Note that if the Pattrn_ID obtained for an input covariateis pattern from the above formula, is
not within the range of 1:18432, the inputted covariate pattern is inadmissable and flagged.
Even when the Pattrn_ID is within this range, different covariate patterns may give rise to the
same Pattrn_ID. So if an input covariate pattern is flagged, the "correct" covariate pattern
associated with the Pattrn_ID is given below the "incorrect" input covariate pattern and a
covariate by covariate comparison might help in pinpointing the error.
Looking at the output file "Men_CRC_Risk_Tool.out", first note all the constants utilized by
this tool are listed. Next you will see all the inputed risk covariate information for each
person, as well the the projected absolute risk and 95% confidence interval. Note that for
covariate patterns which have editing errors (the first 7 records in this case), all the
absolute risk related output quantities are set to a missing value of ".". Compare the output
which you obtained with the file "Men_CRC_Risk_Tool.list". There should be complete agreement,
with the exception of the date when the program was executed.