At 20:18 13.07.2009, Charles C. Berry wrote:
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$surv.object <- with(aml, Surv(time, status))
aml3.so <- survSplit(aml.so ,cut=c(5,10,50),end="time",start="start",
event="status",episode="i")
summary(aml3.so)
sessionInfo('survival')
R version 2.9.1 Patched (2009-07-07 r48910)
i386-pc-mingw32
locale:
LC_COLLATE=German_Switzerland.1252;LC_CTYPE=German_Switzerland.1252;LC_MONETARY=German_Switzerland.1252;LC_NUMERIC=C;LC_TIME=German_Switzerland.1252
attached base packages:
character(0)
other attached packages:
[1] survival_2.35-4
loaded via a namespace (and not attached):
[1] base_2.9.1 graphics_2.9.1 grDevices_2.9.1 methods_2.9.1
[5] splines_2.9.1 stats_2.9.1 utils_2.9.1
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Charles C. Berry (858) 534-2098
Dept of
Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
Thank you Chuck,
it seems to work also with my real data, but I noted that in the
example aml$x, which is a factor, gets converted to character in
aml3.so. Maybe, if I find the time, I should look at
as.data.frame.matrix and rbind for Surv objects.
Thanks again,
Heinz
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