I am trying to set up a data set for a survival analysis with time-varying covariates. The data is already in a long format, but does not have a variable to signify the stopping point for the interval. The variable DaysEnrolled is the variable I would like to use to form this interval. This is what I have now:

         ID   Age       DaysEnrolled HAZ WAZ WHZ Food onARV                                  HIVStatus                         LTFUp
1 71622 0.008            0                  NA     NA   NA     NA     0                 HIV exposed, status indeterminate     0
2 71622 0.085           28                 NA    NA    NA     NA     0                 HIV exposed, status indeterminate     0
3 71622 0.123           42                 NA    NA    NA     NA     0                 HIV exposed, status indeterminate     0
4 71622 0.277           98                 NA    NA    NA     NA     0                 HIV exposed, status indeterminate     0
5 71622 0.441          158               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0
6 71622 0.517          186               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0
7 71622 0.594          214               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0
8 71622 0.715          258               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0
9 71622 0.791          286               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0

This is what I would like to have:

         ID   Age       DaysEnrolled HAZ WAZ WHZ Food onARV                                  HIVStatus                         LTFUp Start      Stop
1 71622 0.008            0                  NA     NA   NA     NA     0                 HIV exposed, status indeterminate     0           0             28
2 71622 0.085           28                 NA    NA    NA     NA     0                 HIV exposed, status indeterminate     0          28           42
3 71622 0.123           42                 NA    NA    NA     NA     0                 HIV exposed, status indeterminate     0          42           98
4 71622 0.277           98                 NA    NA    NA     NA     0                 HIV exposed, status indeterminate     0          98           158
5 71622 0.441          158               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0         158         186
6 71622 0.517          186               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0         186        214
7 71622 0.594          214               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0         214        258
8 71622 0.715          258               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0         258         286
9 71622 0.791          286               NA     NA    NA     NA     0                 HIV exposed, status indeterminate     0         286          NA

I am not sure how to put this in a function. I thought of using embed() in tapply().

astop <- tapply(sample1$DaysEnrolled, sample1$ID, function(x){
                                                        ifelse(length(x) == 1,
                                                        embed(x,1), ifelse(length(x) > 1,
                                                        embed(x,2), NA))})

This doesn't do what I thought it would. I know that I could write a double loop to look at each subject and the differing number of observations for each subject, but would like to avoid that it at all possible.


Sample of 2 subjects:
          sample1 <-
structure(list(ID = c(71622L, 71622L, 71622L, 71622L, 71622L,
71622L, 71622L, 71622L, 71622L, 1436L), Age = c(0.008, 0.085,
0.123, 0.277, 0.441, 0.517, 0.594, 0.715, 0.791, 6.968), DaysEnrolled = c(0L,
28L, 42L, 98L, 158L, 186L, 214L, 258L, 286L, 0L), HAZ = c(NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_), WAZ = c(NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_),
    WHZ = c(NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
    NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), Food = c(NA_integer_,
    NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
    NA_integer_, NA_integer_, NA_integer_, NA_integer_), onARV = c(0L,
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), HIVStatus = structure(c(2L,
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("", "HIV exposed, status indeterminate",
    "HIV infected", "HIV negative"), class = "factor"), LTFUp = c(0,
    0, 0, 0, 0, 0, 0, 0, 0, NA), Start = c(0, 0, 0, 0, 0, 0,
    0, 0, 0, 0), Stop = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), .Names = c("ID",
"Age", "DaysEnrolled", "HAZ", "WAZ", "WHZ", "Food", "onARV",
"HIVStatus", "LTFUp", "Start", "Stop"), row.names = c(NA, 10L
), class = "data.frame")


Adrian Katschke
Biostatistician
IU Department of Medicine
Division of Biostatistics
akatschk@iupui.edu
317-278-6665


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