/* Data Input and Summary */

LIBNAME REF 'C:\';
PROC CONTENTS DATA=REF.ADDICTS;RUN;
PROC PRINT DATA=REF.ADDICTS;RUN;
PROC UNIVARIATE DATA=REF.ADDICTS;VAR SURVT;RUN;
PROC FREQ DATA=REF.ADDICTS;TABLES CLINIC PRISON;RUN;
PROC MEANS DATA=REF.ADDICTS;VAR SURVT;CLAS CLINIC;RUN;

/* KM estimate, log rank test, graphic checking */

PROC LIFETEST DATA=REF.ADDICTS METHOD=KM PLOTS=(S);
TIME SURVT*STATUS(0);
RUN;

PROC LIFETEST DATA=REF.ADDICTS METHOD=KM PLOTS=(S,LLS);
TIME SURVT*STATUS(0);
STRATA CLINIC;
RUN;


/*The Cox model*/
PROC PHREG DATA=REF.ADDICTS;
MODEL SURVT*STATUS(0)= PRISON DOSE CLINIC;
RUN;

PROC PHREG DATA=REF.ADDICTS;
MODEL SURVT*STATUS(0)= PRISON DOSE CLINIC/TIES=EXACT RL;
RUN;

/*ADDING INTERACTION TERMS*/
DATA ADDICTS2;
SET REF.ADDICTS;
CLIN_PR=CLINIC*PRISON;
CLIN_DO=CLINIC*DOSE;
RUN;

PROC PHREG DATA=ADDICTS2;
MODEL SURVT*STATUS(0)= PRISON DOSE CLINIC CLIN_PR CLIN_DO;
CONTRAST "TEST INTERACTION" CLIN_PR 1 CLIN_DO  1;
RUN;

/*RUNNING STRATIFIED COX MODEL*/

PROC PHREG DATA=REF.ADDICTS;
MODEL SURVT*STATUS(0)=PRISON DOSE/RL;
STRATA CLINIC;
RUN;

DATA ADDICTS2;
SET REF.ADDICTS;
CLIN_PR=CLINIC*PRISON;
CLIN_DO=CLINIC*DOSE;
RUN;

PROC PHREG DATA=ADDICTS2;
MODEL SURVT*STATUS(0)=PRISON DOSE CLIN_PR CLIN_DO;
STRATA CLINIC;
CONTRAST 'HR FOR PRISON AMONG CLINIC=1' PRISON 1 CLIN_PR 1/ESTIMATE=EXP;
CONTRAST 'HR FOR PRISON AMONG CLINIC=2' PRISON 1 CLIN_PR 2/ESTIMATE=EXP;
CONTRAST "TEST INTERACTION" CLIN_PR 1 CLIN_DO  1;
RUN;

/*COX MODEL RUN ONLY ON DATA WHERE CLINIC=1*/
PROC PHREG DATA=ADDICTS2;
MODEL SURVT*STATUS(0)=PRISON DOSE;
WHERE CLINIC=1;
TITLE COX MODEL RUN ONLY ON DATA WHERE CLINIC=1;
RUN;

PROC PHREG DATA=ADDICTS2;
MODEL SURVT*STATUS(0)=PRISON DOSE;
WHERE CLINIC=2;
TITLE COX MODEL RUN ONLY ON DATA WHERE CLINIC=2;
RUN;


/*RUNNING AFT PARAMETRIC MODELS WITH PROC LIFEREG*/
PROC LIFETEST DATA=REF.ADDICTS METHOD=KM PLOTS=(LLS);
TIME SURVT*STATUS(0);
STRATA CLINIC PRISON;
RUN;

PROC LIFEREG DATA=REF.ADDICTS;
MODEL SURVT*STATUS(0)=PRISON DOSE CLINIC/DIST=EXPONENTIAL;
RUN;

PROC LIFEREG DATA=REF.ADDICTS;
MODEL SURVT*STATUS(0)=PRISON DOSE CLINIC/DIST=WEIBULL;
RUN;

PROC LIFEREG DATA=REF.ADDICTS;
MODEL SURVT*STATUS(0)=PRISON DOSE CLINIC/DIST=LLOGISTIC NOLOG;
RUN;

PROC LIFEREG DATA=REF.ADDICTS;
MODEL SURVT*STATUS(0)=PRISON DOSE CLINIC/DIST=LNORMAL;
RUN;

PROC LIFEREG DATA=REF.ADDICTS;
MODEL SURVT*STATUS(0)=PRISON DOSE CLINIC/DIST=GAMMA;
RUN;


/*MODELING RECURRENT EVENTS*/
LIBNAME REF 'C:\';

PROC PRINT DATA=REF.BLADDER (FIRSTOBS=12 OBS=20);
RUN;

PROC PHREG DATA=REF.BLADDER COVS(AGGREGATE);
MODEL (START, STOP)*EVENT(0)= TX NUM SIZE;
ID ID;
RUN;

/*STRATIFIED ON INTERVAL (AG & PWP*/
PROC PHREG DATA=REF.BLADDER COVS(AGGREGATE);
MODEL (START, STOP)*EVENT(0)= TX NUM SIZE;
STRATA INTERVAL;
ID ID;
RUN;

/*GAP TIME STRATIFIED (WLW*/
DATA BLADDER2;
SET REF.BLADDER;
START2=0;
STOP2=STOP-START;
RUN;

PROC PHREG DATA=BLADDER2 COVS(AGGREGATE);
MODEL (START2, STOP2)*EVENT(0)= TX NUM SIZE;
STRATA INTERVAL;
ID ID;
RUN;