[R] survSplit with data.frame containing a Surv object

[Charles C. Berry]

On Mon, 13 Jul 2009, Heinz Tuechler wrote:

> Dear All,
>
> since years I am struggling with Surv objects in data.frames. The following 
> seems to have to do with it.
> See below the modified example from the help page of survSplit. The original 
> works, as expected. If, however, a Surv object is added to the data.frame, 
> each record gets doubled.
> Is there some solution other than avoiding Surv objects in data.frames?

I think you can modify survSplit so that it will properly handle Surv 
objects.

Change this line:

 	newdata <- lapply(data, rep, ntimes + 1)

to this:

 	newdata <- lapply(data,
 		function(x) {
 			x <- as.matrix(x)
 			x[rep(1:nrow(x), ntimes + 1),]
 				})

or something similar that results Surv objects being rep()'ed rowwise 
rather than elementwise and returned as objects of the right 
dimension (rather than as a vector).

Caveat: This works in the example you give, but I've not tested this 
extensively.

HTH,

Chuck



>
> Thanks,
> Heinz
>
>
> require(survival)
>
> ## from the help page
> aml3<-survSplit(aml,cut=c(5,10,50),end="time",start="start",
>       event="status",episode="i")
>
> summary(aml)
> summary(aml3)
>
> coxph(Surv(time,status)~x,data=aml)
> ## the same
> coxph(Surv(start,time,status)~x,data=aml3)
>
> ## added to show doubling of records
> aml.so <- aml
> aml.so$surv.object <- with(aml, Surv(time, status))
>
> aml3.so <- survSplit(aml.so ,cut=c(5,10,50),end="time",start="start",
>                     event="status",episode="i")
> summary(aml3.so)
>
> sessionInfo('survival')
> R version 2.9.1 Patched (2009-07-07 r48910)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=German_Switzerland.1252;LC_CTYPE=German_Switzerland.1252;LC_MONETARY=German_Switzerland.1252;LC_NUMERIC=C;LC_TIME=German_Switzerland.1252
>
> attached base packages:
> character(0)
>
> other attached packages:
> [1] survival_2.35-4
>
> loaded via a namespace (and not attached):
> [1] base_2.9.1      graphics_2.9.1  grDevices_2.9.1 methods_2.9.1
> [5] splines_2.9.1   stats_2.9.1     utils_2.9.1
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>

Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901