[R] Using subset in validate() in Design, what is the correct syntax?
Frank E Harrell Jr
f.harrell at vanderbilt.edu
Fri Feb 6 19:27:30 CET 2009
Eleni Rapsomaniki wrote:
> Hi
>
> I am trying to understand how to get the validate() function in Design
> to work with the subset option. I tried this:
>
> ovarian.cph=cph(Surv(futime, fustat) ~ age+factor(ecog.ps)+strat(rx),
> time.inc=1000, x=T, y=T, data=ovarian)
>
> validate(ovarian.cph)
> #fine when no subset is used, but the following two don't work:
>
>> validate(ovarian.cph, subset=ovarian$ecog.ps==2)
> Error in order(c(1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, :
> argument lengths differ
>> validate(ovarian.cph, subset=ovarian[ovarian$ecog.ps==2,])
As stated in the documentation for predab.resample, subset should be a
logical or integer vector specifying how to subset the data.
> Error in predab.resample(fit, method = method, fit = cox.fit, measure =
> discrim, :
> length of subset does not match # rows used in fit
>
> Any suggestions?
> Also, is it possible to use the subset option with calibrate as well? It
Yes; predab.resample still does the work.
Frank
> would be good to be able to plot the cox fit vs. the KM fit for
> different age groups for example.
>
> Many many thanks!
> Eleni
>
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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