Regression Analysis for Cometing-Risks Data
/****************************************************************/
/* S A S S A M P L E L I B R A R Y */
/* */
/* NAME: PHRCRSK */
/* TITLE: Regression Analysis for Cometing-Risks Data */
/* PRODUCT: STAT */
/* SYSTEM: ALL */
/* KEYS: Competing Risks, Cause-Specific Hazard, Sub- */
/* distribution Hazard */
/* PROCS: PHREG */
/* DATA: Pintilie, M. (2006): Competing Risks -- A Practical */
/* Perspective */
/* SUPPORT: sasycs */
/* MISC: */
/****************************************************************/
proc format;
value $ node
'N' = 0
'E'= 0
'Y' = 1;
data hypoxia;
input pelvicln $ pelrec$ disrec $ tumsize hgb ifp age hp5 survtime
stat dftime dfcens resp $ stnum;
if pelrec='Y' then cens=1;
else if disrec='Y' then cens=2;
else cens=0;
if disrec='Y' then cens2=1;
else if pelrec='Y' then cens2=2;
else cens2=0;
format pelvicln $node.;
datalines;
N N N 7.0 119 8.0 78 32.1428571 6.152 0 6.152 0 CR 1
N N N 2.0 131 8.2 69 2.1739130 8.008 0 8.008 0 CR 2
N Y N 10.0 126 8.6 55 52.3255814 0.621 1 0.003 1 NR 3
N Y Y 8.0 141 3.3 55 3.2608696 1.120 1 1.073 1 CR 4
Y Y N 8.0 95 18.5 50 85.4304636 1.292 1 0.003 1 NR 5
N N N 8.0 132 20.0 57 19.3548387 7.929 0 7.929 0 CR 6
E N N 4.0 127 21.8 53 44.5783133 8.454 0 8.454 0 CR 7
N Y Y 5.0 142 31.6 62 59.6774194 7.116 0 7.107 1 CR 8
N N N 5.0 145 16.5 23 29.1666667 8.378 0 8.378 0 CR 9
N N N 3.0 142 31.5 57 85.7142857 8.178 0 8.178 0 CR 10
N N N 4.0 124 18.5 74 8.0645161 3.395 0 3.395 0 CR 11
Y Y Y 5.0 133 12.8 67 77.6315789 1.016 1 0.003 1 NR 12
N Y N 4.0 133 18.4 72 33.3333333 3.699 1 1.350 1 CR 13
E Y Y 8.0 116 18.5 66 99.2187500 0.630 1 0.003 1 NR 14
Y N Y 10.0 82 21.0 47 66.2921348 8.194 0 0.512 1 CR 15
N N Y 5.0 118 23.6 61 55.0000000 4.764 1 1.714 1 CR 16
N Y N 7.0 95 21.0 78 81.6000000 2.590 1 0.003 1 NR 17
N N N 6.0 150 11.1 52 56.7567568 7.707 0 7.707 0 CR 18
N Y Y 7.0 119 14.6 33 52.0408163 1.478 1 0.939 1 CR 19
N N N 5.0 125 30.9 45 46.7741935 7.316 0 7.316 0 CR 20
E N N 9.0 127 19.6 38 43.7500000 7.841 0 7.841 0 CR 21
N N Y 10.0 143 24.0 55 91.7293233 1.133 1 0.589 1 CR 22
Y Y N 5.0 105 15.8 31 12.7450980 1.268 1 0.003 1 NR 23
N N N 6.0 125 15.0 70 32.5000000 7.543 0 7.543 0 CR 24
Y N N 3.0 151 13.2 75 82.5000000 6.300 0 6.300 0 CR 25
N N N 5.0 142 16.8 71 57.7777778 7.587 0 7.587 0 CR 26
E Y Y 5.0 114 16.8 47 70.6293706 3.121 1 1.123 1 CR 27
N N N 4.0 145 6.6 67 12.2807018 6.957 0 6.957 0 CR 28
Y Y N 8.0 120 24.8 60 47.0198676 0.841 1 0.003 1 NR 29
Y N Y 5.0 132 12.0 41 17.1641791 1.766 1 0.460 1 CR 30
N Y Y 5.0 133 37.4 27 34.3750000 1.344 1 0.003 1 NR 31
N N N 4.0 123 10.3 55 64.8648649 6.114 0 6.114 0 CR 32
E N N 5.0 100 19.4 38 35.7142857 6.374 0 6.374 0 CR 33
Y Y N 4.0 137 14.2 30 58.8888889 7.277 0 2.519 1 CR 34
N N N 5.0 112 16.6 43 12.5984252 5.714 0 5.714 0 CR 35
N N Y 4.0 124 13.9 48 30.2325581 2.779 1 1.514 1 CR 36
N Y Y 8.0 115 47.9 36 54.8872180 1.098 1 0.003 1 NR 37
N N N 6.0 116 14.5 35 63.4782609 6.812 0 6.812 0 CR 38
N N N 7.0 99 29.9 66 87.3873874 1.689 0 1.689 0 CR 39
N N N 6.0 124 17.5 72 26.0162602 6.097 0 6.097 0 CR 40
N N N 3.5 129 23.6 63 24.8000000 5.421 0 5.421 0 CR 41
N Y N 6.0 135 18.5 68 63.0136986 2.938 1 1.246 1 CR 42
E N N 5.0 136 24.8 66 67.5000000 6.108 0 6.108 0 CR 43
E Y Y 8.0 147 34.6 54 27.6315789 2.294 1 1.084 1 CR 44
N N N 5.0 124 7.1 59 44.8275862 5.988 0 5.988 0 CR 45
E Y N 6.0 123 6.5 72 28.1609195 2.278 1 1.530 1 CR 46
Y Y N 3.0 143 19.6 32 51.8750000 1.949 1 1.029 1 CR 47
N N Y 6.0 117 32.0 43 78.8079470 3.784 0 1.068 1 CR 48
N N N 4.5 130 12.9 74 11.2500000 2.779 0 2.779 0 CR 49
E N N 6.0 109 16.3 35 11.8750000 6.442 0 6.442 0 CR 50
E N N 4.5 109 13.8 41 50.0000000 2.100 0 2.100 0 CR 51
N Y Y 8.0 126 22.3 46 88.7500000 1.287 1 0.003 1 NR 52
N N N 5.0 139 12.0 65 27.3437500 6.360 0 6.360 0 CR 53
N N N 4.0 129 9.8 46 31.5436242 0.901 0 0.901 0 CR 54
N N N 3.0 152 19.4 57 64.9253731 6.272 0 6.272 0 CR 55
E N N 5.0 124 18.7 27 29.0502793 3.316 0 3.316 0 CR 56
N Y Y 3.0 129 23.1 45 43.6241611 2.839 1 2.606 1 CR 57
N N N 5.0 122 12.1 33 30.6250000 5.938 0 5.938 0 CR 58
N N Y 6.0 139 23.4 49 80.8917197 1.514 1 1.013 1 CR 59
N N N 3.0 139 12.5 61 58.0246914 5.199 0 5.199 0 CR 60
N N N 5.0 151 11.7 33 58.7500000 5.306 0 5.306 0 CR 61
N N Y 4.0 123 12.9 67 19.5652174 4.331 0 3.814 1 CR 62
N N N 4.0 121 11.2 66 19.5652174 3.127 0 3.127 0 CR 63
N N Y 4.0 119 23.6 55 77.2972973 2.196 1 0.709 1 CR 64
E N Y 5.0 105 26.7 43 60.7142857 2.628 1 1.610 1 CR 65
N N N 4.0 140 21.5 77 35.5555556 5.153 0 5.153 0 CR 66
E N Y 6.0 132 28.9 53 81.7610063 2.313 1 1.391 1 CR 67
Y Y Y 8.0 122 21.1 44 65.6250000 1.210 1 0.003 1 NR 68
Y N N 6.0 128 23.2 68 87.7906977 1.076 0 1.076 0 CR 69
Y Y N 8.0 114 43.5 51 53.1645570 5.791 0 0.003 1 NR 70
E N Y 5.0 123 33.3 49 78.2608696 4.482 0 1.785 1 CR 71
E N N 4.0 136 10.0 23 62.7329193 4.446 0 4.446 0 CR 72
E Y N 7.5 95 11.0 32 93.0817610 0.980 1 0.003 1 NR 73
E N Y 4.0 129 42.1 64 58.7500000 1.106 1 0.690 1 CR 74
N N N 3.5 138 14.0 71 41.3043478 3.348 0 3.348 0 CR 75
Y N N 8.0 137 18.5 41 66.1870504 5.380 0 5.380 0 CR 76
N Y N 5.0 124 18.5 54 83.0357143 5.350 0 0.991 1 CR 77
E N N 5.0 144 28.5 46 73.7500000 4.786 0 4.786 0 CR 78
Y Y Y 10.0 106 20.2 62 71.8750000 2.593 1 1.541 1 CR 79
N N N 8.0 124 20.6 42 59.1397849 5.021 0 5.021 0 CR 80
Y Y Y 10.0 84 22.7 49 18.7500000 0.775 1 0.003 1 NR 81
N N Y 4.0 123 38.0 61 17.8947368 5.276 0 4.988 1 CR 82
Y Y Y 7.0 109 20.9 48 55.6250000 2.094 1 0.003 1 NR 83
Y N N 7.0 138 2.8 68 4.3478261 4.405 0 4.405 0 CR 84
Y N N 7.0 107 27.6 74 92.5000000 2.875 0 2.875 0 CR 85
N Y N 5.0 130 25.6 40 0.6622517 5.005 0 1.741 1 CR 86
E N N 5.0 124 38.4 65 0.0000000 4.433 0 4.433 0 CR 87
Y N Y 5.0 123 9.5 51 69.3333333 2.108 1 0.868 1 CR 88
N N N 5.0 132 18.1 58 9.8360656 4.526 0 4.526 0 CR 89
N N N 7.0 117 28.7 43 59.0551181 4.057 0 4.057 0 CR 90
E N Y 3.0 134 19.8 53 14.9532710 2.886 1 1.941 1 CR 91
N N N 4.0 137 23.2 47 0.0000000 2.916 0 2.916 0 CR 92
N N N 5.0 122 19.5 74 7.6271186 3.559 0 3.559 0 CR 93
N Y N 8.0 121 46.2 49 44.9367089 0.663 1 0.003 1 NR 94
N Y N 7.0 136 39.7 46 2.3121387 2.168 1 1.112 1 CR 95
N N Y 5.0 140 18.9 51 12.3287671 2.812 1 1.873 1 CR 96
E N N 4.0 141 8.5 47 28.8461538 4.183 0 4.183 0 CR 97
Y Y N 8.0 130 22.3 42 20.6896552 1.684 0 0.003 1 NR 98
N N N 7.0 124 26.5 44 11.8055556 4.408 0 4.408 0 CR 99
N N N 8.0 124 14.3 54 88.6792453 4.016 0 4.016 0 CR 100
E Y N 5.0 103 16.9 28 44.6540880 1.927 1 0.706 1 CR 101
Y N N 4.0 128 9.6 45 82.7160494 4.112 0 4.112 0 CR 102
N N N 4.0 128 9.4 61 28.1481481 3.833 0 3.833 0 CR 103
N N N 3.0 132 23.6 66 1.8750000 4.153 0 4.153 0 CR 104
N N N 5.0 133 21.2 65 51.3043478 3.775 0 3.775 0 CR 105
N N N 6.0 107 14.6 43 49.1891892 3.784 0 3.784 0 CR 106
Y N N 5.0 136 12.2 47 89.3939394 3.901 0 3.901 0 CR 107
E N N 4.0 127 12.9 46 51.8181818 3.606 0 3.606 0 CR 108
N N N 5.0 121 16.7 77 26.8292683 3.288 0 3.288 0 CR 109
;
data x;
input ifp tumsize pelvicln $ Covariates$ 8-53;
format pelvicln $node.;
datalines;
5 5 N IFP=5, Tumor size=5, Negative/Equivocal nodes
5 5 Y IFP=5, Tumor size=5, Positive nodes
20 5 N IFP=20, Tumor size=5, Negative/Equivocal nodes
20 5 Y IFP=20, Tumor size=5, Positive nodes
;
***********************************************************
********* Fine and Gray's (1999) Regression Model *********
***********************************************************;
title "Modeling Subdistribution Hazards (Pintilie, 2006, pp 93-98)";
title2 "Failure of Interest: Local Relapse Only";
proc phreg data=hypoxia;
model dftime*cens(0)=ifp / eventcode=1;
run;
ods graphics on;
proc phreg data=hypoxia(keep=dftime cens ifp tumsize pelvicln)
plot(overlay=stratum)=cif;
class pelvicln;
model dftime*cens(0)=ifp tumsize pelvicln / eventcode=1;
baseline covariates=x out=base1 cif / row=Covariates seed=191;
run;
title3 "Predicted Cumulative Incidence Functions";
proc print data=base1;
run;
title3;
title2 "Failure of Interest: Distance Relapse without Local Relapse";
proc phreg data=hypoxia;
model dftime*cens(0)=ifp / eventcode=2;
run;
proc phreg data=hypoxia;
class pelvicln;
model dftime*cens(0)=ifp tumsize pelvicln / eventcode=2 covb;
output out=out1 ressch=r_ifp r_tumsize r_pelnode;
run;
data schoen;
set out1;
if (cens=2);
keep dftime r_ifp r_tumsize r_pelnode;
run;
proc sort data=schoen; by dftime;run;
data res(drop=r_ifp r_tumsize r_pelnode);
retain s_ifp s_tumsize s_pelnode;
set schoen;
by dftime;
if first.dftime then do;
s_ifp= r_ifp;
s_tumsize= r_tumsize;
s_pelnode= r_pelnode;
end;
else do;
s_ifp= s_ifp + r_ifp;
s_tumsize= s_tumsize + r_tumsize;
s_pelnode= s_pelnode + r_pelnode;
end;
if last.dftime then output;
run;
title3 "Schoenfeld Residuals";
proc print data=res;
id dftime;
run;
title3;
title2 "Failure of Interest: Distance Relapse";
proc phreg data=hypoxia(keep=dftime cens2 ifp tumsize pelvicln) ;
class pelvicln;
model dftime*cens2(0)=ifp tumsize pelvicln / eventcode=1;
run;
***********************************************************
****************** Cox's Regression Model *****************
***********************************************************;
title1 "Modeling Cause-Specific Hazards (Pintilie, 2006, pp 102-103)";
title2 "Failure of Interest: Local Lapse";
proc phreg data=hypoxia;
class pelvicln;
model dftime*cens(0,2)=ifp/ ties=efron;
run;
proc phreg data=hypoxia;
class pelvicln;
model dftime*cens(0,2)=ifp tumsize pelvicln / ties=efron;
run;
title2 "Failure of Interest: Distance Lapse";
proc phreg data=hypoxia;
class pelvicln;
model dftime*cens2(0,2)=ifp/ ties=efron;
run;
proc phreg data=hypoxia;
class pelvicln;
model dftime*cens2(0,2)=ifp tumsize pelvicln / ties=efron;
run;