[R] Create a time interval from a single time variable
David Winsemius
dwinsemius at comcast.net
Wed Jun 3 22:15:18 CEST 2009
On Jun 3, 2009, at 3:58 PM, David Winsemius wrote:
> Not sure how to functionalize it either. What seemed promising
> (assuming it has first been sorted by ID and DaysEnrolled) would be
> three-step process:
>
> sample1$Stop <- c(sample1[2:nrow(sample1),"DaysEnrolled"],NA) #
> shift the DaysEnrolled
> sample1$next.id <- c(sample1[2:nrow(sample1),"ID"],NA) #
> shift ID
> is.na(sample1$Start) <- with(sample1, ID != next.id) # NA
> the ends of ID groups
Rather:
is.na(sample1$Stop) <- with(sample1, ID != next.id) # NA
the ends of ID groups
(Start should be just a copy of DaysEnrolled.)
>
>
> --
> David winsemius
>
>
> On Jun 3, 2009, at 2:15 PM, Katschke, Adrian R wrote:
>
>> 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
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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