# [R] Getting estimates from survfit.coxph

Dieter Menne dieter.menne at menne-biomed.de
Sun Dec 9 12:37:42 CET 2007

```Mark Wardle <mark <at> wardle.org> writes:

> I'm having difficulty getting access to data generated by survfit and
> print.survfit when they are using with a Cox model (survfit.coxph).
>
> I would like to programmatically access the median survival time for
> each strata together with the 95% confidence interval. I can get it on
> screen, but can't get to it algorithmically. I found myself examining
> the source of print.survfit to try to work out how it is done
> internally, but is there a better way?
>
> An example (and I realise that estimating survival curses from an
> average status and time is incorrect in this instance, but it keeps
> this example simple):
>
> 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))
> c1 <- coxph( Surv(time, status) ~ x + strata(sex), test1)  #stratified model
>
> f1 <- survfit(c1)
> sf1 <- summary(f1)
> str(f1)
> print(f1)
> print(sf1)
> str(sf1)

(Disclaimer: there may be a better way got get it with library Design by
Frank Harrell, but let's assume we have to do it the hard way)

Looks like it is a bit hidden. f1 is of class(print.survfit), as str(f1)
tells us. So let's try getAnyhwere(print.survfit). In the lower part you
find line like the following:

x1 <- pfun(nsubjects, stime, surv, x\$n.risk, x\$n.event,
x\$lower, x\$upper)
if (is.matrix(x1)) {
if (is.null(x\$lower))
dimnames(x1) <- list(NULL, plab)
else dimnames(x1) <- list(NULL, c(plab, plab2))
}
else {
if (is.null(x\$lower))
names(x1) <- plab
else names(x1) <- c(plab, plab2)
}
if (show.rmean)
print(x1)

Make a copy of that function under a new name, and return x1.

Dieter

```