R help - Jul 2009 - survSplit with data.frame containing a Surv object

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?

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

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
>
> ______________________________________________
> 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.
>
>
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