* Read in the data;

PROC IMPORT DATAFILE = 'C:\Documents and Settings\richc\My Documents\CPH931F08\BMTdata.xls'
     OUT = BMT  DBMS = EXCEL REPLACE;
     SHEET =  BMTdata;
     GETNAMES = YES;
RUN;

PROC PRINT DATA = BMT;
RUN;


* Create indicator variables for second and
* third disease groups;

DATA BMT;
SET BMT;
Z1 = 0;
Z2 = 0;
IF DISEASEGROUP = 2 THEN Z1 = 1;
IF DISEASEGROUP = 3 THEN Z2 = 1;
RUN;


* Begin transcript;

ODS RTF FILE = 'C:\Documents and Settings\richc\My Documents\CPH931F08\BMTExamples.rtf';


* Perform proportional hazards regression 
* relating hazard of death or relapse, in
* the presence of right censoring, to the
* indicator variables for the second and
* third disease groups and to a time-dependent
* covariate indicating whether platelets 
* returned to normal levels;

PROC PHREG DATA = BMT;
MODEL TIMETODEATHORRELAPSE*DEATHORRELAPSE(0) = Z1 Z2 TDPLATEREC / RISKLIMITS;
IF (TIMETOPLATEREC < TIMETODEATHORRELAPSE) THEN TDPLATEREC = 1; 
ELSE TDPLATEREC = 0;
RUN;



* Perform proportional hazards regression
* relating hazard of death or relapse, in
* the presence of right censoring, to the
* indicator variables for the second and
* third disease groups and an indicator
* variable for methotrexate use.  Include
* artificial time-dependent covariates
* to assess the proportional hazards
* assumption;

PROC PHREG DATA = BMT;
MODEL TIMETODEATHORRELAPSE*DEATHORRELAPSE(0) = Z1 Z2 MTXUsed NPHZ1 NPHZ2 NPHMTXUsed / RISKLIMITS;
NPHZ1 = Z1*log(TIMETODEATHORRELAPSE);
NPHZ2 = Z2*log(TIMETODEATHORRELAPSE);
NPHMTXUsed = MTXUsed*log(TIMETODEATHORRELAPSE);
RUN;


* Perform proportional hazards regression
* relating hazard of death or relapse, in
* the presence of right censoring, to the
* indicator variables for the second and
* third disease groups, within each stratum
* defined by the indicator variable for
* methotrexate use, enforcing the same 
* partial slope coefficient estimates
* for each stratum;

PROC PHREG DATA = BMT;
MODEL TIMETODEATHORRELAPSE*DEATHORRELAPSE(0) = Z1 Z2 / RISKLIMITS;
STRATA MTXUsed;
RUN;



* Perform proportional hazards regression
* relating hazard of death or relapse, in
* the presence of right censoring, to the
* indicator variables for the second and
* third disease groups, within each stratum
* defined by the indicator variable for
* methotrexate use, not enforcing the same 
* partial slope coefficient estimates
* for each stratum;

PROC SORT DATA = BMT;
BY MTXUsed;
RUN;

PROC PHREG DATA = BMT;
BY MTXUsed;
MODEL TIMETODEATHORRELAPSE*DEATHORRELAPSE(0) = Z1 Z2 / RISKLIMITS;
RUN;
 


* End transcript;

ODS RTF CLOSE;
RUN;