Re: [R] expected risk from coxph (survival)

From: Dieter Menne <dieter.menne_at_menne-biomed.de>
Date: Sat, 07 Jun 2008 08:15:48 +0000 (UTC)

Reid Tingley <r_tingley <at> hotmail.com> writes:
> When I try to to obtain the expected risk for a new dataset using coxph in the
survival package I get an error.
> Using the example from ?coxph:

# Example rewritten by DM; please do not use HTML mail library(survival)

test1 <- list(time=  c(4, 3,1,1,2,2,3),
            status=c(1,NA,1,0,1,1,0),
            x=     c(0, 2,1,1,1,0,0),
            sex=   c(0,0,0,0,1,1,1))

cox<-coxph( Surv(time, status) ~ x + strata(sex), test1) #stratified model
new<-list(time=  c(5, 1,1,2,2,4,3),
          status=c(1,NA,1,0,0,1,1),
          x=     c(0, 2,1,1,1,0,0),
          sex=   c(0,0,0,0,1,1,1))

predict(cox,new,type="expected")

 # }

#    else if (type == "expected") {
#        if (missing(newdata)) 
#            pred <- y[, ncol(y)] - object$residuals
#        else stop("Method not yet finished")
Looks like this is "by design"; see the code above.

You might try to use cph and predict.Design from Frank Harrell's Design package instead.

Dieter



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