Re: [R] basehaz and newdata

From: Roland Rau <roland.rproject_at_gmail.com>
Date: Mon, 07 Apr 2008 12:43:08 -0400

Hi,

just looked at it briefly and I don't know if it is the real cause for your problems. But 'data' as well as 'newdata' require a data.frame and not a list as input.

Does this help?

Best,
Roland

mah wrote:
> I am unable to get the basehaz function to apply a proportional
> hazards model to a new data frame. I replicated my specific situation
> with the example for coxph in the help, where I changed the x value of
> the first record from 0 to 1. Is there something incorrect in the
> syntax that I am using? Thanks in advance!
>
> 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))
> test2 <- list(time= c(4, 3,1,1,2,2,3),
> status=c(1,NA,1,0,1,1,0),
> x= c(1, 2,1,1,1,0,0),
> sex= c(0, 0,0,0,1,1,1))
> f1 <- coxph( Surv(time, status) ~ x + strata(sex), data=test1)
> #stratified model
> f2 <- coxph( Surv(time, status) ~ x + strata(sex), data=test2)
> #stratified model
> f1
> Call:
> coxph(formula = Surv(time, status) ~ x + strata(sex), data = test1)
>
>
> coef exp(coef) se(coef) z p
> x 1.17 3.22 1.29 0.907 0.36
>
> Likelihood ratio test=0.87 on 1 df, p=0.351 n=6 (1 observation
> deleted due to missingness)

>> f2

> Call:
> coxph(formula = Surv(time, status) ~ x + strata(sex), data = test2)
>
>
> coef exp(coef) se(coef) z p
> x 0.896 2.45 1.42 0.63 0.53
>
> Likelihood ratio test=0.38 on 1 df, p=0.535 n=6 (1 observation
> deleted due to missingness)
>> basehaz(f1, newdata=test2)

> Error in basehaz(f1, newdata = test2) :
> unused argument(s) (newdata = list(time = c(4, 3, 1, 1, 2, 2, 3),
> status = c(1, NA, 1, 0, 1, 1, 0), x = c(1, 2, 1, 1, 1, 0, 0), sex =
> c(0, 0, 0, 0, 1, 1, 1)))
>
> ______________________________________________
> R-help_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Mon 07 Apr 2008 - 16:45:52 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Mon 07 Apr 2008 - 17:30:26 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive