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

[Frank E Harrell Jr]

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