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
akats...@iupui.edu
317-278-6665
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