[R] Create a time interval from a single time variable

[Katschke, Adrian R]

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 Start Stop
1 71622 0.008            0  NA  NA  NA   NA     0 HIV exposed, status indeterminate     0     0    0
2 71622 0.085           28  NA  NA  NA   NA     0 HIV exposed, status indeterminate     0     0    0
3 71622 0.123           42  NA  NA  NA   NA     0 HIV exposed, status indeterminate     0     0    0
4 71622 0.277           98  NA  NA  NA   NA     0 HIV exposed, status indeterminate     0     0    0
5 71622 0.441          158  NA  NA  NA   NA     0 HIV exposed, status indeterminate     0     0    0
6 71622 0.517          186  NA  NA  NA   NA     0 HIV exposed, status indeterminate     0     0    0
7 71622 0.594          214  NA  NA  NA   NA     0 HIV exposed, status indeterminate     0     0    0
8 71622 0.715          258  NA  NA  NA   NA     0 HIV exposed, status indeterminate     0     0    0
9 71622 0.791          286  NA  NA  NA   NA     0 HIV exposed, status indeterminate     0     0    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 at iupui.edu
317-278-6665