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Paul Miller
2011-Jun-13 19:45 UTC
[R] Setting up counting process data for survival analysis

Hello Everyone,

I'm learning to do survival analysis in R using a time-varying covariate.
I've managed to set up my data correctly using SAS and then to get the
correct result using R.

What I'd like help with is getting the data set up correctly in R without
having to resort to using SAS. Below are two datasets. The first is the raw data
I'm starting out with. The second is set up so that the survival analysis
can be conducted using R.

Can anyone show me an elegant way of getting from the first dataset to the
second? I think I could probably find an ugly way. But I'm anticipating
doing this sort of analysis repeatedly. And so I'd like to have an elegant
way of setting up the data if possible.

Thanks,

Paul
 

connection <- textConnection("
101  32 1 A 3  .   102  20 1 A 4 10   103 -52 0 A 3  .
104   4 0 A 4  .   105  24 1 A 4 52   106  41 1 A 3  .
107  32 0 A 4 12   108  32 1 A 4  .   109  25 0 A 3  .
110 -10 1 A 3  .   111   8 0 A 3  .   112  32 1 A 4  .
113 -52 0 A 4 38   114  45 1 A 3 36   115 -14 0 A 4  .
116   6 1 A 3  .   117 -52 1 A 4  .   118   9 0 A 4 28
119  13 1 A 3  .   120  36 0 A 4  .   121   6 1 A 4  .
122 -42 0 A 4  .   123  44 1 A 3 28   124 -52 0 A 3  .
125  23 1 A 4  .   126  30 1 A 3  .   127  16 0 A 3  .
128   2 1 A 3  .   129  21 0 A 3  6   130  26 1 A 4  .
131   8 0 A 3  .   132  46 1 A 4 18   133  21 1 A 4  .
134  14 1 A 3  .   135 -52 0 A 3  .   136 -24 1 A 3  .
137 -22 0 A 3  .   138 -35 0 A 3  .   139  19 1 A 3  .
140  24 1 A 4 20   141  31 1 A 3 12   142  28 0 A 4  .
143 -52 0 A 4 34   144 -52 1 A 3  .   145  35 0 A 3  .
146  40 1 A 4  .   147   4 0 A 3  .   148   7 1 A 4 24
149  -2 0 A 4  .   150  16 1 A 4  .   151  36 1 A 3  4
152  12 0 A 3  .   153  28 1 A 3  .   154  48 0 A 3 42
155 -38 1 A 3  .   156   9 1 A 3  .   157  11 0 A 3  .
158  20 0 A 4  .   159  30 1 A 4  .   160   6 1 A 4  .
201 -15 0 B 3  .   202  -4 1 B 3  .   203  10 1 B 4  .
204  10 0 B 4  .   205   8 0 B 3  .   206  11 1 B 3  .
207 -52 1 B 4  .   208  12 1 B 3  .   209  20 0 B 3  .
210  46 1 B 4  .   211  32 0 B 4 44   212  10 1 B 3  .
213  42 0 B 3  .   214  31 1 B 4 20   215   4 1 B 4  .
216 -24 0 B 3  .   217  20 1 B 3 33   218  16 0 B 3  .
219   2 1 B 3  .   220  25 1 B 4  .   221  11 0 B 4  .
222 -52 0 B 4  .   223  20 1 B 4  .   224   9 1 B 3  .
225  22 1 B 3  .   226  23 1 B 3  .   227  11 0 B 3  .
228  13 1 B 3  .   229  -7 0 B 4  .   230   8 1 B 4  .
231  37 1 B 4  .   232  32 0 B 4 26   233  24 1 B 3 10
234 -52 1 B 4  .   235  20 0 B 4  .   236  34 0 B 4  .
237  27 1 B 3  .   301  10 1 C 3  .   302 -10 0 C 4  8
303  32 1 C 4  .   304  14 1 C 4 20   305  24 0 C 3  .
306  14 1 C 4  .   307  36 0 C 3  .   308 -52 0 C 3  .
309   7 1 C 3  .   310   6 0 C 4  .   311   5 1 C 3  .
312   9 1 C 3  .   313  12 1 C 4  .   314  21 0 C 3  .
315  10 1 C 3  .   316  26 0 C 4 36   317 -52 1 C 4  .
318  10 1 C 3  .   319  27 0 C 4 12   320   5 1 C 3  .
321  34 1 C 3 16   322  14 0 C 4  .   323   6 1 C 3  .
324  22 1 C 4  .   325  45 0 C 4 12   326  16 0 C 3  .
327  15 1 C 3 30   328  33 0 C 4 22   329  20 1 C 3  .
330 -52 1 C 3 30   331   5 0 C 4  .   332  10 1 C 3  .
333  16 0 C 3  .   334  -2 1 C 4  .   335  17 0 C 4  .
336  16 0 C 4  .   337  16 1 C 3  .   338  33 1 C 3 20
339  24 0 C 3 11   340  12 1 C 3  .   341  27 1 C 4 18
342   2 1 C 4  .   343  -6 0 C 4  .   344 -20 1 C 4  .
345  14 0 C 3  .   346   3 1 C 3  .
")
 
vitclear <- data.frame(scan(connection, na.strings=".",
  list(PAT=0, RSPTIM=0, TRT=0, CENTER="", DENS=0, INFTIM=0)))

head(vitclear)

connection <- textConnection("
PAT RSPTIM CENS TRT DENS CENTER T1 T2 INFCTN
101 2 0 1 3 A 0 2 0
101 4 0 1 3 A 2 4 0
101 6 0 1 3 A 4 6 0
101 7 0 1 3 A 6 7 0
101 8 0 1 3 A 7 8 0
101 9 0 1 3 A 8 9 0
101 11 0 1 3 A 9 11 0
101 12 0 1 3 A 11 12 0
101 13 0 1 3 A 12 13 0
101 14 0 1 3 A 13 14 0
101 16 0 1 3 A 14 16 0
101 19 0 1 3 A 16 19 0
101 20 0 1 3 A 19 20 0
101 21 0 1 3 A 20 21 0
101 23 0 1 3 A 21 23 0
101 24 0 1 3 A 23 24 0
101 25 0 1 3 A 24 25 0
101 26 0 1 3 A 25 26 0
101 28 0 1 3 A 26 28 0
101 30 0 1 3 A 28 30 0
101 31 0 1 3 A 30 31 0
101 32 1 1 3 A 31 32 0
102 2 0 1 4 A 0 2 0
102 4 0 1 4 A 2 4 0
102 6 0 1 4 A 4 6 0
102 7 0 1 4 A 6 7 0
102 8 0 1 4 A 7 8 0
102 9 0 1 4 A 8 9 0
102 11 0 1 4 A 9 11 1
102 12 0 1 4 A 11 12 1
102 13 0 1 4 A 12 13 1
102 14 0 1 4 A 13 14 1
102 16 0 1 4 A 14 16 1
102 19 0 1 4 A 16 19 1
102 20 1 1 4 A 19 20 1
103 2 0 0 3 A 0 2 0
103 4 0 0 3 A 2 4 0
103 6 0 0 3 A 4 6 0
103 7 0 0 3 A 6 7 0
103 8 0 0 3 A 7 8 0
103 9 0 0 3 A 8 9 0
103 11 0 0 3 A 9 11 0
103 12 0 0 3 A 11 12 0
103 13 0 0 3 A 12 13 0
103 14 0 0 3 A 13 14 0
103 16 0 0 3 A 14 16 0
103 19 0 0 3 A 16 19 0
103 20 0 0 3 A 19 20 0
103 21 0 0 3 A 20 21 0
103 23 0 0 3 A 21 23 0
103 24 0 0 3 A 23 24 0
103 25 0 0 3 A 24 25 0
103 26 0 0 3 A 25 26 0
103 28 0 0 3 A 26 28 0
103 30 0 0 3 A 28 30 0
103 31 0 0 3 A 30 31 0
103 32 0 0 3 A 31 32 0
103 35 0 0 3 A 32 35 0
103 36 0 0 3 A 35 36 0
103 40 0 0 3 A 36 40 0
103 41 0 0 3 A 40 41 0
103 44 0 0 3 A 41 44 0
103 45 0 0 3 A 44 45 0
103 46 0 0 3 A 45 46 0
103 48 0 0 3 A 46 48 0
103 52 0 0 3 A 48 52 0
104 2 0 0 4 A 0 2 0
104 4 1 0 4 A 2 4 0
105 2 0 1 4 A 0 2 0
105 4 0 1 4 A 2 4 0
105 6 0 1 4 A 4 6 0
105 7 0 1 4 A 6 7 0
105 8 0 1 4 A 7 8 0
105 9 0 1 4 A 8 9 0
105 11 0 1 4 A 9 11 0
105 12 0 1 4 A 11 12 0
105 13 0 1 4 A 12 13 0
105 14 0 1 4 A 13 14 0
105 16 0 1 4 A 14 16 0
105 19 0 1 4 A 16 19 0
105 20 0 1 4 A 19 20 0
105 21 0 1 4 A 20 21 0
105 23 0 1 4 A 21 23 0
105 24 1 1 4 A 23 24 0
106 2 0 1 3 A 0 2 0
106 4 0 1 3 A 2 4 0
106 6 0 1 3 A 4 6 0
106 7 0 1 3 A 6 7 0
106 8 0 1 3 A 7 8 0
106 9 0 1 3 A 8 9 0
106 11 0 1 3 A 9 11 0
106 12 0 1 3 A 11 12 0
106 13 0 1 3 A 12 13 0
106 14 0 1 3 A 13 14 0
106 16 0 1 3 A 14 16 0
106 19 0 1 3 A 16 19 0
106 20 0 1 3 A 19 20 0
106 21 0 1 3 A 20 21 0
106 23 0 1 3 A 21 23 0
106 24 0 1 3 A 23 24 0
106 25 0 1 3 A 24 25 0
106 26 0 1 3 A 25 26 0
106 28 0 1 3 A 26 28 0
106 30 0 1 3 A 28 30 0
106 31 0 1 3 A 30 31 0
106 32 0 1 3 A 31 32 0
106 35 0 1 3 A 32 35 0
106 36 0 1 3 A 35 36 0
106 40 0 1 3 A 36 40 0
106 41 1 1 3 A 40 41 0
107 2 0 0 4 A 0 2 0
107 4 0 0 4 A 2 4 0
107 6 0 0 4 A 4 6 0
107 7 0 0 4 A 6 7 0
107 8 0 0 4 A 7 8 0
107 9 0 0 4 A 8 9 0
107 11 0 0 4 A 9 11 0
107 12 0 0 4 A 11 12 1
107 13 0 0 4 A 12 13 1
107 14 0 0 4 A 13 14 1
107 16 0 0 4 A 14 16 1
107 19 0 0 4 A 16 19 1
107 20 0 0 4 A 19 20 1
107 21 0 0 4 A 20 21 1
107 23 0 0 4 A 21 23 1
107 24 0 0 4 A 23 24 1
107 25 0 0 4 A 24 25 1
107 26 0 0 4 A 25 26 1
107 28 0 0 4 A 26 28 1
107 30 0 0 4 A 28 30 1
107 31 0 0 4 A 30 31 1
107 32 1 0 4 A 31 32 1
108 2 0 1 4 A 0 2 0
108 4 0 1 4 A 2 4 0
108 6 0 1 4 A 4 6 0
108 7 0 1 4 A 6 7 0
108 8 0 1 4 A 7 8 0
108 9 0 1 4 A 8 9 0
108 11 0 1 4 A 9 11 0
108 12 0 1 4 A 11 12 0
108 13 0 1 4 A 12 13 0
108 14 0 1 4 A 13 14 0
108 16 0 1 4 A 14 16 0
108 19 0 1 4 A 16 19 0
108 20 0 1 4 A 19 20 0
108 21 0 1 4 A 20 21 0
108 23 0 1 4 A 21 23 0
108 24 0 1 4 A 23 24 0
108 25 0 1 4 A 24 25 0
108 26 0 1 4 A 25 26 0
108 28 0 1 4 A 26 28 0
108 30 0 1 4 A 28 30 0
108 31 0 1 4 A 30 31 0
108 32 1 1 4 A 31 32 0
109 2 0 0 3 A 0 2 0
109 4 0 0 3 A 2 4 0
109 6 0 0 3 A 4 6 0
109 7 0 0 3 A 6 7 0
109 8 0 0 3 A 7 8 0
109 9 0 0 3 A 8 9 0
109 11 0 0 3 A 9 11 0
109 12 0 0 3 A 11 12 0
109 13 0 0 3 A 12 13 0
109 14 0 0 3 A 13 14 0
109 16 0 0 3 A 14 16 0
109 19 0 0 3 A 16 19 0
109 20 0 0 3 A 19 20 0
109 21 0 0 3 A 20 21 0
109 23 0 0 3 A 21 23 0
109 24 0 0 3 A 23 24 0
109 25 1 0 3 A 24 25 0
110 2 0 1 3 A 0 2 0
110 4 0 1 3 A 2 4 0
110 6 0 1 3 A 4 6 0
110 7 0 1 3 A 6 7 0
110 8 0 1 3 A 7 8 0
110 9 0 1 3 A 8 9 0
110 10 0 1 3 A 9 10 0
111 2 0 0 3 A 0 2 0
111 4 0 0 3 A 2 4 0
111 6 0 0 3 A 4 6 0
111 7 0 0 3 A 6 7 0
111 8 1 0 3 A 7 8 0
112 2 0 1 4 A 0 2 0
112 4 0 1 4 A 2 4 0
112 6 0 1 4 A 4 6 0
112 7 0 1 4 A 6 7 0
112 8 0 1 4 A 7 8 0
112 9 0 1 4 A 8 9 0
112 11 0 1 4 A 9 11 0
112 12 0 1 4 A 11 12 0
112 13 0 1 4 A 12 13 0
112 14 0 1 4 A 13 14 0
112 16 0 1 4 A 14 16 0
112 19 0 1 4 A 16 19 0
112 20 0 1 4 A 19 20 0
112 21 0 1 4 A 20 21 0
112 23 0 1 4 A 21 23 0
112 24 0 1 4 A 23 24 0
112 25 0 1 4 A 24 25 0
112 26 0 1 4 A 25 26 0
112 28 0 1 4 A 26 28 0
112 30 0 1 4 A 28 30 0
112 31 0 1 4 A 30 31 0
112 32 1 1 4 A 31 32 0
113 2 0 0 4 A 0 2 0
113 4 0 0 4 A 2 4 0
113 6 0 0 4 A 4 6 0
113 7 0 0 4 A 6 7 0
113 8 0 0 4 A 7 8 0
113 9 0 0 4 A 8 9 0
113 11 0 0 4 A 9 11 0
113 12 0 0 4 A 11 12 0
113 13 0 0 4 A 12 13 0
113 14 0 0 4 A 13 14 0
113 16 0 0 4 A 14 16 0
113 19 0 0 4 A 16 19 0
113 20 0 0 4 A 19 20 0
113 21 0 0 4 A 20 21 0
113 23 0 0 4 A 21 23 0
113 24 0 0 4 A 23 24 0
113 25 0 0 4 A 24 25 0
113 26 0 0 4 A 25 26 0
113 28 0 0 4 A 26 28 0
113 30 0 0 4 A 28 30 0
113 31 0 0 4 A 30 31 0
113 32 0 0 4 A 31 32 0
113 35 0 0 4 A 32 35 0
113 36 0 0 4 A 35 36 0
113 40 0 0 4 A 36 40 1
113 41 0 0 4 A 40 41 1
113 44 0 0 4 A 41 44 1
113 45 0 0 4 A 44 45 1
113 46 0 0 4 A 45 46 1
113 48 0 0 4 A 46 48 1
113 52 0 0 4 A 48 52 1
114 2 0 1 3 A 0 2 0
114 4 0 1 3 A 2 4 0
114 6 0 1 3 A 4 6 0
114 7 0 1 3 A 6 7 0
114 8 0 1 3 A 7 8 0
114 9 0 1 3 A 8 9 0
114 11 0 1 3 A 9 11 0
114 12 0 1 3 A 11 12 0
114 13 0 1 3 A 12 13 0
114 14 0 1 3 A 13 14 0
114 16 0 1 3 A 14 16 0
114 19 0 1 3 A 16 19 0
114 20 0 1 3 A 19 20 0
114 21 0 1 3 A 20 21 0
114 23 0 1 3 A 21 23 0
114 24 0 1 3 A 23 24 0
114 25 0 1 3 A 24 25 0
114 26 0 1 3 A 25 26 0
114 28 0 1 3 A 26 28 0
114 30 0 1 3 A 28 30 0
114 31 0 1 3 A 30 31 0
114 32 0 1 3 A 31 32 0
114 35 0 1 3 A 32 35 0
114 36 0 1 3 A 35 36 1
114 40 0 1 3 A 36 40 1
114 41 0 1 3 A 40 41 1
114 44 0 1 3 A 41 44 1
114 45 1 1 3 A 44 45 1
115 2 0 0 4 A 0 2 0
115 4 0 0 4 A 2 4 0
115 6 0 0 4 A 4 6 0
115 7 0 0 4 A 6 7 0
115 8 0 0 4 A 7 8 0
115 9 0 0 4 A 8 9 0
115 11 0 0 4 A 9 11 0
115 12 0 0 4 A 11 12 0
115 13 0 0 4 A 12 13 0
115 14 0 0 4 A 13 14 0
116 2 0 1 3 A 0 2 0
116 4 0 1 3 A 2 4 0
116 6 1 1 3 A 4 6 0
117 2 0 1 4 A 0 2 0
117 4 0 1 4 A 2 4 0
117 6 0 1 4 A 4 6 0
117 7 0 1 4 A 6 7 0
117 8 0 1 4 A 7 8 0
117 9 0 1 4 A 8 9 0
117 11 0 1 4 A 9 11 0
117 12 0 1 4 A 11 12 0
117 13 0 1 4 A 12 13 0
117 14 0 1 4 A 13 14 0
117 16 0 1 4 A 14 16 0
117 19 0 1 4 A 16 19 0
117 20 0 1 4 A 19 20 0
117 21 0 1 4 A 20 21 0
117 23 0 1 4 A 21 23 0
117 24 0 1 4 A 23 24 0
117 25 0 1 4 A 24 25 0
117 26 0 1 4 A 25 26 0
117 28 0 1 4 A 26 28 0
117 30 0 1 4 A 28 30 0
117 31 0 1 4 A 30 31 0
117 32 0 1 4 A 31 32 0
117 35 0 1 4 A 32 35 0
117 36 0 1 4 A 35 36 0
117 40 0 1 4 A 36 40 0
117 41 0 1 4 A 40 41 0
117 44 0 1 4 A 41 44 0
117 45 0 1 4 A 44 45 0
117 46 0 1 4 A 45 46 0
117 48 0 1 4 A 46 48 0
117 52 0 1 4 A 48 52 0
118 2 0 0 4 A 0 2 0
118 4 0 0 4 A 2 4 0
118 6 0 0 4 A 4 6 0
118 7 0 0 4 A 6 7 0
118 8 0 0 4 A 7 8 0
118 9 1 0 4 A 8 9 0
119 2 0 1 3 A 0 2 0
119 4 0 1 3 A 2 4 0
119 6 0 1 3 A 4 6 0
119 7 0 1 3 A 6 7 0
119 8 0 1 3 A 7 8 0
119 9 0 1 3 A 8 9 0
119 11 0 1 3 A 9 11 0
119 12 0 1 3 A 11 12 0
119 13 1 1 3 A 12 13 0
120 2 0 0 4 A 0 2 0
120 4 0 0 4 A 2 4 0
120 6 0 0 4 A 4 6 0
120 7 0 0 4 A 6 7 0
120 8 0 0 4 A 7 8 0
120 9 0 0 4 A 8 9 0
120 11 0 0 4 A 9 11 0
120 12 0 0 4 A 11 12 0
120 13 0 0 4 A 12 13 0
120 14 0 0 4 A 13 14 0
120 16 0 0 4 A 14 16 0
120 19 0 0 4 A 16 19 0
120 20 0 0 4 A 19 20 0
120 21 0 0 4 A 20 21 0
120 23 0 0 4 A 21 23 0
120 24 0 0 4 A 23 24 0
120 25 0 0 4 A 24 25 0
120 26 0 0 4 A 25 26 0
120 28 0 0 4 A 26 28 0
120 30 0 0 4 A 28 30 0
120 31 0 0 4 A 30 31 0
120 32 0 0 4 A 31 32 0
120 35 0 0 4 A 32 35 0
120 36 1 0 4 A 35 36 0
121 2 0 1 4 A 0 2 0
121 4 0 1 4 A 2 4 0
121 6 1 1 4 A 4 6 0
122 2 0 0 4 A 0 2 0
122 4 0 0 4 A 2 4 0
122 6 0 0 4 A 4 6 0
122 7 0 0 4 A 6 7 0
122 8 0 0 4 A 7 8 0
122 9 0 0 4 A 8 9 0
122 11 0 0 4 A 9 11 0
122 12 0 0 4 A 11 12 0
122 13 0 0 4 A 12 13 0
122 14 0 0 4 A 13 14 0
122 16 0 0 4 A 14 16 0
122 19 0 0 4 A 16 19 0
122 20 0 0 4 A 19 20 0
122 21 0 0 4 A 20 21 0
122 23 0 0 4 A 21 23 0
122 24 0 0 4 A 23 24 0
122 25 0 0 4 A 24 25 0
122 26 0 0 4 A 25 26 0
122 28 0 0 4 A 26 28 0
122 30 0 0 4 A 28 30 0
122 31 0 0 4 A 30 31 0
122 32 0 0 4 A 31 32 0
122 35 0 0 4 A 32 35 0
122 36 0 0 4 A 35 36 0
122 40 0 0 4 A 36 40 0
122 41 0 0 4 A 40 41 0
122 42 0 0 4 A 41 42 0
123 2 0 1 3 A 0 2 0
123 4 0 1 3 A 2 4 0
123 6 0 1 3 A 4 6 0
123 7 0 1 3 A 6 7 0
123 8 0 1 3 A 7 8 0
123 9 0 1 3 A 8 9 0
123 11 0 1 3 A 9 11 0
123 12 0 1 3 A 11 12 0
123 13 0 1 3 A 12 13 0
123 14 0 1 3 A 13 14 0
123 16 0 1 3 A 14 16 0
123 19 0 1 3 A 16 19 0
123 20 0 1 3 A 19 20 0
123 21 0 1 3 A 20 21 0
123 23 0 1 3 A 21 23 0
123 24 0 1 3 A 23 24 0
123 25 0 1 3 A 24 25 0
123 26 0 1 3 A 25 26 0
123 28 0 1 3 A 26 28 1
123 30 0 1 3 A 28 30 1
123 31 0 1 3 A 30 31 1
123 32 0 1 3 A 31 32 1
123 35 0 1 3 A 32 35 1
123 36 0 1 3 A 35 36 1
123 40 0 1 3 A 36 40 1
123 41 0 1 3 A 40 41 1
123 44 1 1 3 A 41 44 1
124 2 0 0 3 A 0 2 0
124 4 0 0 3 A 2 4 0
124 6 0 0 3 A 4 6 0
124 7 0 0 3 A 6 7 0
124 8 0 0 3 A 7 8 0
124 9 0 0 3 A 8 9 0
124 11 0 0 3 A 9 11 0
124 12 0 0 3 A 11 12 0
124 13 0 0 3 A 12 13 0
124 14 0 0 3 A 13 14 0
124 16 0 0 3 A 14 16 0
124 19 0 0 3 A 16 19 0
124 20 0 0 3 A 19 20 0
124 21 0 0 3 A 20 21 0
124 23 0 0 3 A 21 23 0
124 24 0 0 3 A 23 24 0
124 25 0 0 3 A 24 25 0
124 26 0 0 3 A 25 26 0
124 28 0 0 3 A 26 28 0
124 30 0 0 3 A 28 30 0
124 31 0 0 3 A 30 31 0
124 32 0 0 3 A 31 32 0
124 35 0 0 3 A 32 35 0
124 36 0 0 3 A 35 36 0
124 40 0 0 3 A 36 40 0
124 41 0 0 3 A 40 41 0
124 44 0 0 3 A 41 44 0
124 45 0 0 3 A 44 45 0
124 46 0 0 3 A 45 46 0
124 48 0 0 3 A 46 48 0
124 52 0 0 3 A 48 52 0
125 2 0 1 4 A 0 2 0
125 4 0 1 4 A 2 4 0
125 6 0 1 4 A 4 6 0
125 7 0 1 4 A 6 7 0
125 8 0 1 4 A 7 8 0
125 9 0 1 4 A 8 9 0
125 11 0 1 4 A 9 11 0
125 12 0 1 4 A 11 12 0
125 13 0 1 4 A 12 13 0
125 14 0 1 4 A 13 14 0
125 16 0 1 4 A 14 16 0
125 19 0 1 4 A 16 19 0
125 20 0 1 4 A 19 20 0
125 21 0 1 4 A 20 21 0
125 23 1 1 4 A 21 23 0
126 2 0 1 3 A 0 2 0
126 4 0 1 3 A 2 4 0
126 6 0 1 3 A 4 6 0
126 7 0 1 3 A 6 7 0
126 8 0 1 3 A 7 8 0
126 9 0 1 3 A 8 9 0
126 11 0 1 3 A 9 11 0
126 12 0 1 3 A 11 12 0
126 13 0 1 3 A 12 13 0
126 14 0 1 3 A 13 14 0
126 16 0 1 3 A 14 16 0
126 19 0 1 3 A 16 19 0
126 20 0 1 3 A 19 20 0
126 21 0 1 3 A 20 21 0
126 23 0 1 3 A 21 23 0
126 24 0 1 3 A 23 24 0
126 25 0 1 3 A 24 25 0
126 26 0 1 3 A 25 26 0
126 28 0 1 3 A 26 28 0
126 30 1 1 3 A 28 30 0
127 2 0 0 3 A 0 2 0
127 4 0 0 3 A 2 4 0
127 6 0 0 3 A 4 6 0
127 7 0 0 3 A 6 7 0
127 8 0 0 3 A 7 8 0
127 9 0 0 3 A 8 9 0
127 11 0 0 3 A 9 11 0
127 12 0 0 3 A 11 12 0
127 13 0 0 3 A 12 13 0
127 14 0 0 3 A 13 14 0
127 16 1 0 3 A 14 16 0
128 2 1 1 3 A 0 2 0
129 2 0 0 3 A 0 2 0
129 4 0 0 3 A 2 4 0
129 6 0 0 3 A 4 6 1
129 7 0 0 3 A 6 7 1
129 8 0 0 3 A 7 8 1
129 9 0 0 3 A 8 9 1
129 11 0 0 3 A 9 11 1
129 12 0 0 3 A 11 12 1
129 13 0 0 3 A 12 13 1
129 14 0 0 3 A 13 14 1
129 16 0 0 3 A 14 16 1
129 19 0 0 3 A 16 19 1
129 20 0 0 3 A 19 20 1
129 21 1 0 3 A 20 21 1
130 2 0 1 4 A 0 2 0
130 4 0 1 4 A 2 4 0
130 6 0 1 4 A 4 6 0
130 7 0 1 4 A 6 7 0
130 8 0 1 4 A 7 8 0
130 9 0 1 4 A 8 9 0
130 11 0 1 4 A 9 11 0
130 12 0 1 4 A 11 12 0
130 13 0 1 4 A 12 13 0
130 14 0 1 4 A 13 14 0
130 16 0 1 4 A 14 16 0
130 19 0 1 4 A 16 19 0
130 20 0 1 4 A 19 20 0
130 21 0 1 4 A 20 21 0
130 23 0 1 4 A 21 23 0
130 24 0 1 4 A 23 24 0
130 25 0 1 4 A 24 25 0
130 26 1 1 4 A 25 26 0
131 2 0 0 3 A 0 2 0
131 4 0 0 3 A 2 4 0
131 6 0 0 3 A 4 6 0
131 7 0 0 3 A 6 7 0
131 8 1 0 3 A 7 8 0
132 2 0 1 4 A 0 2 0
132 4 0 1 4 A 2 4 0
132 6 0 1 4 A 4 6 0
132 7 0 1 4 A 6 7 0
132 8 0 1 4 A 7 8 0
132 9 0 1 4 A 8 9 0
132 11 0 1 4 A 9 11 0
132 12 0 1 4 A 11 12 0
132 13 0 1 4 A 12 13 0
132 14 0 1 4 A 13 14 0
132 16 0 1 4 A 14 16 0
132 19 0 1 4 A 16 19 1
132 20 0 1 4 A 19 20 1
132 21 0 1 4 A 20 21 1
132 23 0 1 4 A 21 23 1
132 24 0 1 4 A 23 24 1
132 25 0 1 4 A 24 25 1
132 26 0 1 4 A 25 26 1
132 28 0 1 4 A 26 28 1
132 30 0 1 4 A 28 30 1
132 31 0 1 4 A 30 31 1
132 32 0 1 4 A 31 32 1
132 35 0 1 4 A 32 35 1
132 36 0 1 4 A 35 36 1
132 40 0 1 4 A 36 40 1
132 41 0 1 4 A 40 41 1
132 44 0 1 4 A 41 44 1
132 45 0 1 4 A 44 45 1
132 46 1 1 4 A 45 46 1
133 2 0 1 4 A 0 2 0
133 4 0 1 4 A 2 4 0
133 6 0 1 4 A 4 6 0
133 7 0 1 4 A 6 7 0
133 8 0 1 4 A 7 8 0
133 9 0 1 4 A 8 9 0
133 11 0 1 4 A 9 11 0
133 12 0 1 4 A 11 12 0
133 13 0 1 4 A 12 13 0
133 14 0 1 4 A 13 14 0
133 16 0 1 4 A 14 16 0
133 19 0 1 4 A 16 19 0
133 20 0 1 4 A 19 20 0
133 21 1 1 4 A 20 21 0
134 2 0 1 3 A 0 2 0
134 4 0 1 3 A 2 4 0
134 6 0 1 3 A 4 6 0
134 7 0 1 3 A 6 7 0
134 8 0 1 3 A 7 8 0
134 9 0 1 3 A 8 9 0
134 11 0 1 3 A 9 11 0
134 12 0 1 3 A 11 12 0
134 13 0 1 3 A 12 13 0
134 14 1 1 3 A 13 14 0
135 2 0 0 3 A 0 2 0
135 4 0 0 3 A 2 4 0
135 6 0 0 3 A 4 6 0
135 7 0 0 3 A 6 7 0
135 8 0 0 3 A 7 8 0
135 9 0 0 3 A 8 9 0
135 11 0 0 3 A 9 11 0
135 12 0 0 3 A 11 12 0
135 13 0 0 3 A 12 13 0
135 14 0 0 3 A 13 14 0
135 16 0 0 3 A 14 16 0
135 19 0 0 3 A 16 19 0
135 20 0 0 3 A 19 20 0
135 21 0 0 3 A 20 21 0
135 23 0 0 3 A 21 23 0
135 24 0 0 3 A 23 24 0
135 25 0 0 3 A 24 25 0
135 26 0 0 3 A 25 26 0
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233 24 1 1 3 B 23 24 1
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235 2 0 0 4 B 0 2 0
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235 20 1 0 4 B 16 20 0
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236 20 0 0 4 B 16 20 0
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236 25 0 0 4 B 24 25 0
236 27 0 0 4 B 25 27 0
236 31 0 0 4 B 27 31 0
236 32 0 0 4 B 31 32 0
236 34 1 0 4 B 32 34 0
237 2 0 1 3 B 0 2 0
237 4 0 1 3 B 2 4 0
237 8 0 1 3 B 4 8 0
237 9 0 1 3 B 8 9 0
237 10 0 1 3 B 9 10 0
237 11 0 1 3 B 10 11 0
237 12 0 1 3 B 11 12 0
237 13 0 1 3 B 12 13 0
237 16 0 1 3 B 13 16 0
237 20 0 1 3 B 16 20 0
237 22 0 1 3 B 20 22 0
237 23 0 1 3 B 22 23 0
237 24 0 1 3 B 23 24 0
237 25 0 1 3 B 24 25 0
237 27 1 1 3 B 25 27 0
301 2 0 1 3 C 0 2 0
301 3 0 1 3 C 2 3 0
301 5 0 1 3 C 3 5 0
301 6 0 1 3 C 5 6 0
301 7 0 1 3 C 6 7 0
301 9 0 1 3 C 7 9 0
301 10 1 1 3 C 9 10 0
302 2 0 0 4 C 0 2 0
302 3 0 0 4 C 2 3 0
302 5 0 0 4 C 3 5 0
302 6 0 0 4 C 5 6 0
302 7 0 0 4 C 6 7 0
302 9 0 0 4 C 7 9 1
302 10 0 0 4 C 9 10 1
303 2 0 1 4 C 0 2 0
303 3 0 1 4 C 2 3 0
303 5 0 1 4 C 3 5 0
303 6 0 1 4 C 5 6 0
303 7 0 1 4 C 6 7 0
303 9 0 1 4 C 7 9 0
303 10 0 1 4 C 9 10 0
303 12 0 1 4 C 10 12 0
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303 16 0 1 4 C 15 16 0
303 17 0 1 4 C 16 17 0
303 20 0 1 4 C 17 20 0
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303 22 0 1 4 C 21 22 0
303 24 0 1 4 C 22 24 0
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303 32 1 1 4 C 27 32 0
304 2 0 1 4 C 0 2 0
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314 20 0 0 3 C 17 20 0
314 21 1 0 3 C 20 21 0
315 2 0 1 3 C 0 2 0
315 3 0 1 3 C 2 3 0
315 5 0 1 3 C 3 5 0
315 6 0 1 3 C 5 6 0
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316 26 1 0 4 C 24 26 0
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317 33 0 1 4 C 32 33 0
317 34 0 1 4 C 33 34 0
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317 45 0 1 4 C 36 45 0
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318 2 0 1 3 C 0 2 0
318 3 0 1 3 C 2 3 0
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319 20 0 0 4 C 17 20 1
319 21 0 0 4 C 20 21 1
319 22 0 0 4 C 21 22 1
319 24 0 0 4 C 22 24 1
319 26 0 0 4 C 24 26 1
319 27 1 0 4 C 26 27 1
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321 17 0 1 3 C 16 17 1
321 20 0 1 3 C 17 20 1
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321 22 0 1 3 C 21 22 1
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321 26 0 1 3 C 24 26 1
321 27 0 1 3 C 26 27 1
321 32 0 1 3 C 27 32 1
321 33 0 1 3 C 32 33 1
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324 14 0 1 4 C 12 14 0
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324 16 0 1 4 C 15 16 0
324 17 0 1 4 C 16 17 0
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324 21 0 1 4 C 20 21 0
324 22 1 1 4 C 21 22 0
325 2 0 0 4 C 0 2 0
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325 16 0 0 4 C 15 16 1
325 17 0 0 4 C 16 17 1
325 20 0 0 4 C 17 20 1
325 21 0 0 4 C 20 21 1
325 22 0 0 4 C 21 22 1
325 24 0 0 4 C 22 24 1
325 26 0 0 4 C 24 26 1
325 27 0 0 4 C 26 27 1
325 32 0 0 4 C 27 32 1
325 33 0 0 4 C 32 33 1
325 34 0 0 4 C 33 34 1
325 36 0 0 4 C 34 36 1
325 45 1 0 4 C 36 45 1
326 2 0 0 3 C 0 2 0
326 3 0 0 3 C 2 3 0
326 5 0 0 3 C 3 5 0
326 6 0 0 3 C 5 6 0
326 7 0 0 3 C 6 7 0
326 9 0 0 3 C 7 9 0
326 10 0 0 3 C 9 10 0
326 12 0 0 3 C 10 12 0
326 14 0 0 3 C 12 14 0
326 15 0 0 3 C 14 15 0
326 16 1 0 3 C 15 16 0
327 2 0 1 3 C 0 2 0
327 3 0 1 3 C 2 3 0
327 5 0 1 3 C 3 5 0
327 6 0 1 3 C 5 6 0
327 7 0 1 3 C 6 7 0
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327 10 0 1 3 C 9 10 0
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327 14 0 1 3 C 12 14 0
327 15 1 1 3 C 14 15 0
328 2 0 0 4 C 0 2 0
328 3 0 0 4 C 2 3 0
328 5 0 0 4 C 3 5 0
328 6 0 0 4 C 5 6 0
328 7 0 0 4 C 6 7 0
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328 14 0 0 4 C 12 14 0
328 15 0 0 4 C 14 15 0
328 16 0 0 4 C 15 16 0
328 17 0 0 4 C 16 17 0
328 20 0 0 4 C 17 20 0
328 21 0 0 4 C 20 21 0
328 22 0 0 4 C 21 22 1
328 24 0 0 4 C 22 24 1
328 26 0 0 4 C 24 26 1
328 27 0 0 4 C 26 27 1
328 32 0 0 4 C 27 32 1
328 33 1 0 4 C 32 33 1
329 2 0 1 3 C 0 2 0
329 3 0 1 3 C 2 3 0
329 5 0 1 3 C 3 5 0
329 6 0 1 3 C 5 6 0
329 7 0 1 3 C 6 7 0
329 9 0 1 3 C 7 9 0
329 10 0 1 3 C 9 10 0
329 12 0 1 3 C 10 12 0
329 14 0 1 3 C 12 14 0
329 15 0 1 3 C 14 15 0
329 16 0 1 3 C 15 16 0
329 17 0 1 3 C 16 17 0
329 20 1 1 3 C 17 20 0
330 2 0 1 3 C 0 2 0
330 3 0 1 3 C 2 3 0
330 5 0 1 3 C 3 5 0
330 6 0 1 3 C 5 6 0
330 7 0 1 3 C 6 7 0
330 9 0 1 3 C 7 9 0
330 10 0 1 3 C 9 10 0
330 12 0 1 3 C 10 12 0
330 14 0 1 3 C 12 14 0
330 15 0 1 3 C 14 15 0
330 16 0 1 3 C 15 16 0
330 17 0 1 3 C 16 17 0
330 20 0 1 3 C 17 20 0
330 21 0 1 3 C 20 21 0
330 22 0 1 3 C 21 22 0
330 24 0 1 3 C 22 24 0
330 26 0 1 3 C 24 26 0
330 27 0 1 3 C 26 27 0
330 32 0 1 3 C 27 32 1
330 33 0 1 3 C 32 33 1
330 34 0 1 3 C 33 34 1
330 36 0 1 3 C 34 36 1
330 45 0 1 3 C 36 45 1
330 52 0 1 3 C 45 52 1
331 2 0 0 4 C 0 2 0
331 3 0 0 4 C 2 3 0
331 5 1 0 4 C 3 5 0
332 2 0 1 3 C 0 2 0
332 3 0 1 3 C 2 3 0
332 5 0 1 3 C 3 5 0
332 6 0 1 3 C 5 6 0
332 7 0 1 3 C 6 7 0
332 9 0 1 3 C 7 9 0
332 10 1 1 3 C 9 10 0
333 2 0 0 3 C 0 2 0
333 3 0 0 3 C 2 3 0
333 5 0 0 3 C 3 5 0
333 6 0 0 3 C 5 6 0
333 7 0 0 3 C 6 7 0
333 9 0 0 3 C 7 9 0
333 10 0 0 3 C 9 10 0
333 12 0 0 3 C 10 12 0
333 14 0 0 3 C 12 14 0
333 15 0 0 3 C 14 15 0
333 16 1 0 3 C 15 16 0
334 2 0 1 4 C 0 2 0
335 2 0 0 4 C 0 2 0
335 3 0 0 4 C 2 3 0
335 5 0 0 4 C 3 5 0
335 6 0 0 4 C 5 6 0
335 7 0 0 4 C 6 7 0
335 9 0 0 4 C 7 9 0
335 10 0 0 4 C 9 10 0
335 12 0 0 4 C 10 12 0
335 14 0 0 4 C 12 14 0
335 15 0 0 4 C 14 15 0
335 16 0 0 4 C 15 16 0
335 17 1 0 4 C 16 17 0
336 2 0 0 4 C 0 2 0
336 3 0 0 4 C 2 3 0
336 5 0 0 4 C 3 5 0
336 6 0 0 4 C 5 6 0
336 7 0 0 4 C 6 7 0
336 9 0 0 4 C 7 9 0
336 10 0 0 4 C 9 10 0
336 12 0 0 4 C 10 12 0
336 14 0 0 4 C 12 14 0
336 15 0 0 4 C 14 15 0
336 16 1 0 4 C 15 16 0
337 2 0 1 3 C 0 2 0
337 3 0 1 3 C 2 3 0
337 5 0 1 3 C 3 5 0
337 6 0 1 3 C 5 6 0
337 7 0 1 3 C 6 7 0
337 9 0 1 3 C 7 9 0
337 10 0 1 3 C 9 10 0
337 12 0 1 3 C 10 12 0
337 14 0 1 3 C 12 14 0
337 15 0 1 3 C 14 15 0
337 16 1 1 3 C 15 16 0
338 2 0 1 3 C 0 2 0
338 3 0 1 3 C 2 3 0
338 5 0 1 3 C 3 5 0
338 6 0 1 3 C 5 6 0
338 7 0 1 3 C 6 7 0
338 9 0 1 3 C 7 9 0
338 10 0 1 3 C 9 10 0
338 12 0 1 3 C 10 12 0
338 14 0 1 3 C 12 14 0
338 15 0 1 3 C 14 15 0
338 16 0 1 3 C 15 16 0
338 17 0 1 3 C 16 17 0
338 20 0 1 3 C 17 20 1
338 21 0 1 3 C 20 21 1
338 22 0 1 3 C 21 22 1
338 24 0 1 3 C 22 24 1
338 26 0 1 3 C 24 26 1
338 27 0 1 3 C 26 27 1
338 32 0 1 3 C 27 32 1
338 33 1 1 3 C 32 33 1
339 2 0 0 3 C 0 2 0
339 3 0 0 3 C 2 3 0
339 5 0 0 3 C 3 5 0
339 6 0 0 3 C 5 6 0
339 7 0 0 3 C 6 7 0
339 9 0 0 3 C 7 9 0
339 10 0 0 3 C 9 10 0
339 12 0 0 3 C 10 12 1
339 14 0 0 3 C 12 14 1
339 15 0 0 3 C 14 15 1
339 16 0 0 3 C 15 16 1
339 17 0 0 3 C 16 17 1
339 20 0 0 3 C 17 20 1
339 21 0 0 3 C 20 21 1
339 22 0 0 3 C 21 22 1
339 24 1 0 3 C 22 24 1
340 2 0 1 3 C 0 2 0
340 3 0 1 3 C 2 3 0
340 5 0 1 3 C 3 5 0
340 6 0 1 3 C 5 6 0
340 7 0 1 3 C 6 7 0
340 9 0 1 3 C 7 9 0
340 10 0 1 3 C 9 10 0
340 12 1 1 3 C 10 12 0
341 2 0 1 4 C 0 2 0
341 3 0 1 4 C 2 3 0
341 5 0 1 4 C 3 5 0
341 6 0 1 4 C 5 6 0
341 7 0 1 4 C 6 7 0
341 9 0 1 4 C 7 9 0
341 10 0 1 4 C 9 10 0
341 12 0 1 4 C 10 12 0
341 14 0 1 4 C 12 14 0
341 15 0 1 4 C 14 15 0
341 16 0 1 4 C 15 16 0
341 17 0 1 4 C 16 17 0
341 20 0 1 4 C 17 20 1
341 21 0 1 4 C 20 21 1
341 22 0 1 4 C 21 22 1
341 24 0 1 4 C 22 24 1
341 26 0 1 4 C 24 26 1
341 27 1 1 4 C 26 27 1
342 2 1 1 4 C 0 2 0
343 2 0 0 4 C 0 2 0
343 3 0 0 4 C 2 3 0
343 5 0 0 4 C 3 5 0
343 6 0 0 4 C 5 6 0
344 2 0 1 4 C 0 2 0
344 3 0 1 4 C 2 3 0
344 5 0 1 4 C 3 5 0
344 6 0 1 4 C 5 6 0
344 7 0 1 4 C 6 7 0
344 9 0 1 4 C 7 9 0
344 10 0 1 4 C 9 10 0
344 12 0 1 4 C 10 12 0
344 14 0 1 4 C 12 14 0
344 15 0 1 4 C 14 15 0
344 16 0 1 4 C 15 16 0
344 17 0 1 4 C 16 17 0
344 20 0 1 4 C 17 20 0
345 2 0 0 3 C 0 2 0
345 3 0 0 3 C 2 3 0
345 5 0 0 3 C 3 5 0
345 6 0 0 3 C 5 6 0
345 7 0 0 3 C 6 7 0
345 9 0 0 3 C 7 9 0
345 10 0 0 3 C 9 10 0
345 12 0 0 3 C 10 12 0
345 14 1 0 3 C 12 14 0
346 2 0 1 3 C 0 2 0
346 3 1 1 3 C 2 3 0
")

vitclear2 <- read.table(connection, header=TRUE)

head(vitclear2)

library("survival")
model <- coxph(Surv(t1, t2, cens) ~ 
	   TRT + DENS + INFCTN + strata(CENTER), data=vitclear2,
method="breslow")
summary(model)
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