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