relapse: Drug-relapse of patients with time-varying covariates

Description Usage Format Details Source References Examples

Description

Drug-relapse of patients with time-varying covariates. This data set is simulated.

Usage

1

Format

A data frame with 300 observations on the following 4 variables.

event

a numeric vector

delta

a logical vector

gender

a numeric vector

inter

a numeric vector

Details

This data is simulated under the following pretense. Patient records were obtained for 150 days after they joined a rehabilitation program. The event of interest was drug-relapse and two covariates were recorded. The event variable describes the observed or censored time; the delta variable describes whether the time denotes an observed relapse (TRUE) or a censored time; the gender variable is a time-independent covariate; and inter is a time-dependent covariate indicating whether the patient had was (randomly) assigned a second intervention: working 10 hours a week for a nonprofit. Each of these special interventions were assigned after the patients entered the clinic, meaning the intervention covariate changes for those patients who had an intervention before relapse.

Source

Simulated (David M Diez)

References

Fox J (2002). "Cox Proportional-Hazards Regression for Survival Data. Appendix to An R and S-PLUS Companion to Applied Regression." Comprehensive R Archive Network. http://cran.r-project.org/doc/contrib/Fox-Companion/appendix-cox-regression.pdf

Examples

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#=====> 10. Cox PH model, time-dependent covariates <=====#
data(relapse)
relapse

attach(relapse)
N  <- dim(relapse)[1]
t1 <- rep(0, N+sum(!is.na(inter)))  # Initialize start times at 0
t2 <- rep(NA, length(t1))           # The end times for each record
e  <- rep(NA, length(t1))           # Was the event censored?
g  <- rep(NA, length(t1))           # Gender
PI <- rep(FALSE, length(t1))        # Initialize intervention at FALSE

R  <- 1                         # Row of new record
for(ii in 1:dim(relapse)[1]){
  if(is.na(inter[ii])){         # no intervention, copy survival record
    t2[R] <- event[ii]
    e[R]  <- delta[ii]
    g[R]  <- gender[ii]
    R <- R+1
  } else {                  # intervention, split records
    g[R+0:1] <- gender[ii]  # gender is same for each time
    e[R]     <- 0           # no relapse observed pre-intervention
    e[R+1]   <- delta[ii]   # relapse occur post-intervention?
    PI[R+1]  <- TRUE        # Intervention covariate, post-intervention
    t2[R]    <- inter[ii]-1 # End of pre-intervention
    t1[R+1]  <- inter[ii]-1 # Start of post-intervention
    t2[R+1]  <- event[ii]   # End of post-intervention
    R <- R+2                # Two records added
  }
}

mySurv   <- Surv(t1, t2, e)
coxphFit <- coxph(mySurv ~ g + PI)

detach(relapse)

Example output

Loading required package: survival
Loading required package: KMsurv
    event delta gender inter
1     150 FALSE      0    84
2      53  TRUE      1    50
3      12  TRUE      1    NA
4     150 FALSE      0    89
5     150 FALSE      1    77
6     135  TRUE      1     7
7     150 FALSE      0    21
8      57  TRUE      1    NA
9      65  TRUE      0    NA
10     92  TRUE      1     6
11     16  TRUE      1    10
12     42  TRUE      0    NA
13     76  TRUE      1    NA
14    123  TRUE      0    15
15    150 FALSE      0    69
16    150 FALSE      1     6
17    120  TRUE      1    61
18    111  TRUE      0    46
19     58  TRUE      0    NA
20    150 FALSE      0    19
21    121  TRUE      1    66
22    150 FALSE      0    18
23    150 FALSE      1    27
24     62  TRUE      0    11
25    150 FALSE      0    41
26    150 FALSE      0    23
27     76  TRUE      0    65
28      2  TRUE      0    NA
29    141  TRUE      1    11
30    150 FALSE      0     8
31    150 FALSE      0    20
32     30  TRUE      0    NA
33     15  TRUE      1    NA
34    103  TRUE      1    40
35     37  TRUE      1     3
36    150 FALSE      1     6
37     30  TRUE      1    12
38     33  TRUE      0    NA
39    150 FALSE      1    85
40     21  TRUE      0    NA
41    150 FALSE      1    87
42     77  TRUE      0    NA
43     63  TRUE      0    NA
44    133  TRUE      0     3
45     66  TRUE      1    53
46    150 FALSE      1    37
47    139  TRUE      1    64
48     75  TRUE      0    NA
49     37  TRUE      1    20
50     19  TRUE      1    NA
51      5  TRUE      0    NA
52     88  TRUE      0    60
53    150 FALSE      1    41
54    150 FALSE      1    88
55     75  TRUE      0    19
56     33  TRUE      1    NA
57    103  TRUE      1    80
58    150 FALSE      1    61
59    150 FALSE      1     7
60    150 FALSE      1    70
61     19  TRUE      1    16
62     57  TRUE      1    21
63     90  TRUE      1    12
64    111  TRUE      0     3
65     30  TRUE      1    NA
66    150 FALSE      0    25
67    150 FALSE      0    14
68    150 FALSE      0     7
69    137  TRUE      0    71
70    150 FALSE      0     5
71    150 FALSE      0    89
72    150 FALSE      0     3
73    150 FALSE      0    52
74    150 FALSE      0    65
75     21  TRUE      0    NA
76    150 FALSE      1    67
77    150 FALSE      0    27
78    150 FALSE      1   100
79    150 FALSE      0    70
80    147  TRUE      1     7
81     33  TRUE      0    12
82    150 FALSE      1    49
83    150 FALSE      0    48
84    150 FALSE      0    28
85     65  TRUE      0    10
86     37  TRUE      1    NA
87      5  TRUE      1    NA
88     99  TRUE      0    55
89    150 FALSE      1    87
90     75  TRUE      0    NA
91     21  TRUE      1    NA
92     97  TRUE      0    93
93    126  TRUE      0    34
94    150 FALSE      1    17
95     38  TRUE      0    23
96     38  TRUE      0    13
97      9  TRUE      0    NA
98    150 FALSE      0    86
99    150 FALSE      0    24
100    27  TRUE      0    NA
101    73  TRUE      0    63
102    39  TRUE      0    NA
103   150 FALSE      1    17
104    68  TRUE      1     5
105    49  TRUE      0    NA
106    28  TRUE      1    NA
107   150 FALSE      1    60
108     1  TRUE      0    NA
109    90  TRUE      0    18
110   150 FALSE      0    81
111    90  TRUE      0    66
112    58  TRUE      1    NA
113   116  TRUE      0    46
114   150 FALSE      1     9
115   150 FALSE      1    37
116    12  TRUE      1    NA
117    28  TRUE      1    NA
118    24  TRUE      0    NA
119    21  TRUE      1    NA
120   150 FALSE      1    80
121    53  TRUE      0    NA
122   150 FALSE      0     2
123    15  TRUE      1    NA
124    66  TRUE      1    NA
125    20  TRUE      0    NA
126   150 FALSE      1    14
127   107  TRUE      1     9
128    79  TRUE      0    58
129    32  TRUE      1    NA
130    76  TRUE      0     8
131    37  TRUE      0    NA
132    51  TRUE      1    NA
133    27  TRUE      0    NA
134    19  TRUE      1    NA
135    60  TRUE      0    11
136   121  TRUE      1    84
137    21  TRUE      1    14
138    39  TRUE      1    NA
139    48  TRUE      0    NA
140     6  TRUE      0    NA
141   150 FALSE      0    66
142   111  TRUE      0    21
143    26  TRUE      1    NA
144    56  TRUE      0    56
145     3  TRUE      0    NA
146    21  TRUE      1    NA
147   150 FALSE      1    98
148   150 FALSE      0    57
149   120  TRUE      0    54
150     9  TRUE      0    NA
151   150 FALSE      0    69
152   150 FALSE      0    75
153     4  TRUE      1    NA
154   150 FALSE      0    15
155   150 FALSE      1    82
156    80  TRUE      0    NA
157    15  TRUE      1    NA
158    67  TRUE      0    NA
159    16  TRUE      0    NA
160    52  TRUE      0    NA
161   150 FALSE      1    95
162   150 FALSE      1     3
163    66  TRUE      0     4
164   150 FALSE      1    50
165   150 FALSE      0    28
166   126  TRUE      1    77
167    28  TRUE      0    NA
168   150 FALSE      1    75
169    50  TRUE      0     6
170    41  TRUE      1    NA
171    60  TRUE      1    16
172   150 FALSE      0    45
173    12  TRUE      0    NA
174     2  TRUE      1    NA
175    18  TRUE      0    NA
176   150 FALSE      1    80
177    56  TRUE      0    55
178     8  TRUE      0     4
179    34  TRUE      1    29
180    74  TRUE      1    NA
181   150 FALSE      1    48
182    88  TRUE      1    77
183    28  TRUE      1    NA
184    15  TRUE      1    NA
185   150 FALSE      0    89
186     1  TRUE      1    NA
187   150 FALSE      0    72
188    20  TRUE      1    NA
189     9  TRUE      0    NA
190    79  TRUE      0    NA
191   102  TRUE      0    30
192    49  TRUE      0    NA
193    20  TRUE      1    NA
194    75  TRUE      0    NA
195    23  TRUE      1    NA
196   150 FALSE      0    22
197   150 FALSE      0    33
198    56  TRUE      0    NA
199   150 FALSE      0    34
200   150 FALSE      0    57
201     9  TRUE      1    NA
202   107  TRUE      1    57
203    89  TRUE      1    35
204   150 FALSE      1    25
205    37  TRUE      0    NA
206    92  TRUE      1    74
207    34  TRUE      0    NA
208   150 FALSE      0    50
209   150 FALSE      0    81
210   150 FALSE      0    69
211    51  TRUE      1    NA
212    61  TRUE      1    11
213    27  TRUE      1    NA
214   150 FALSE      1    42
215     5  TRUE      1    NA
216   150 FALSE      0    60
217     1  TRUE      0    NA
218    58  TRUE      0    53
219    25  TRUE      0    NA
220    40  TRUE      0    NA
221    78  TRUE      0    NA
222    60  TRUE      1     7
223   136  TRUE      0    47
224     2  TRUE      0    NA
225    25  TRUE      1    NA
226     3  TRUE      1    NA
227   128  TRUE      1     4
228   133  TRUE      0    71
229   150 FALSE      1    27
230   108  TRUE      1    90
231   150 FALSE      1    10
232    40  TRUE      0    NA
233     6  TRUE      1    NA
234    62  TRUE      1    15
235   150 FALSE      1    69
236     9  TRUE      0    NA
237    13  TRUE      1    NA
238   150 FALSE      0    28
239    42  TRUE      0    NA
240    48  TRUE      0    NA
241   134  TRUE      1     2
242    28  TRUE      0    NA
243   150  TRUE      1    49
244    35  TRUE      1    NA
245     3  TRUE      1    NA
246    47  TRUE      1     4
247     4  TRUE      0    NA
248    29  TRUE      1    NA
249    22  TRUE      0    NA
250    55  TRUE      0    NA
251     7  TRUE      1    NA
252    39  TRUE      0    37
253   150 FALSE      0    50
254    40  TRUE      0    NA
255    93  TRUE      1    85
256    77  TRUE      0    51
257    18  TRUE      0    NA
258   150 FALSE      0    59
259     1  TRUE      0    NA
260    39  TRUE      1    NA
261   150 FALSE      1    98
262    50  TRUE      0     3
263   150 FALSE      1    75
264    19  TRUE      0    NA
265    31  TRUE      1    NA
266   150 FALSE      1    32
267   145  TRUE      0    28
268   150 FALSE      1    56
269   150 FALSE      1    92
270   150 FALSE      1    12
271    49  TRUE      1    NA
272   150 FALSE      1    59
273   150 FALSE      1    89
274     3  TRUE      0    NA
275    66  TRUE      1    51
276    37  TRUE      0    NA
277   150 FALSE      1    91
278     7  TRUE      0     2
279    41  TRUE      0    NA
280   150 FALSE      0    21
281    26  TRUE      0    14
282    63  TRUE      1    15
283    84  TRUE      1    73
284   150 FALSE      1    60
285    43  TRUE      0    NA
286   150 FALSE      1    76
287    38  TRUE      1    NA
288    53  TRUE      1    10
289    93  TRUE      1    NA
290     3  TRUE      0    NA
291    91  TRUE      0    37
292    25  TRUE      0    NA
293   150 FALSE      1    67
294    14  TRUE      0     5
295   150 FALSE      1     3
296   144  TRUE      0    75
297   150 FALSE      0    10
298    62  TRUE      0    24
299    10  TRUE      0    NA
300    94  TRUE      1     4

OIsurv documentation built on May 29, 2017, 11:03 a.m.