Re: [R] basehaz and newdata

From: mah <harwood262_at_gmail.com>
Date: Mon, 07 Apr 2008 10:00:58 -0700 (PDT)

Thanks Roland, but using data frames does not resolve the issue. See revised code and output below:

> test1 <- data.frame(

+                 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)
+                 )

> f1 <- coxph( Surv(time, status) ~ x + strata(sex), data=test1) #stratified model
>
> test2 <- data.frame(
+                 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)
+                 )

> 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)))
>

Mike

On Apr 7, 11:43 am, Roland Rau <roland.rproj..._at_gmail.com> wrote:
> 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 thebasehazfunction 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 inbasehaz(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-h..._at_r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.- Hide quoted text -
>
> - Show quoted text -



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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 - 17:11:07 GMT

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