[R] Using subset in validate() in Design, what is the correct syntax?

Eleni Rapsomaniki e.rapsomaniki at mail.cryst.bbk.ac.uk
Fri Feb 6 18:38:17 CET 2009


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)

  #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,])
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 would be good to be able to plot the cox fit vs. the KM fit for  
different age groups for example.

Many many thanks!

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