The system details follow below. Also, I have attempted specifying
the variables in a second "ratetable" statement, but the same
"missing
object" error occurs in creating a survexp object/list.
> R.version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 12.2
year 2011
month 02
day 25
svn rev 54585
language R
version.string R version 2.12.2 (2011-02-25)
package ?survival? version 2.36-5
On Apr 20, 11:03?am, Mike Harwood <harwood... at gmail.com>
wrote:> Hello,
>
> I probably have a syntax error in trying to generate an expected
> survival curve from a weighted cox model, but I can't see it. ?I used
> the help sample code to generate a weighted model, with the addition
> of a "weights=albumin" argument (I only chose albumin because it
had
> no missing values, not because of any real relevance). ?Below are my
> code with the resulting error messages. ?Thanks in advance!
>
> > pfit <- coxph(Surv(time,status>0) ~ trt + log(bili) +
log(protime) + age +
>
> + ? ? + platelet, ?data=pbc
> + ? ? )
>
> > pfit
>
> Call:
> coxph(formula = Surv(time, status > 0) ~ trt + log(bili) +
> log(protime) +
> ? ? age + +platelet, data = pbc)
>
> ? ? ? ? ? ? ? ? ? coef exp(coef) se(coef) ? ? ? ?z ? ? ?p
> trt ? ? ? ? ?-0.000624 ? ? 0.999 ?0.17304 -0.00360 1.0000
> log(bili) ? ? 0.985497 ? ? 2.679 ?0.08949 11.01262 0.0000
> log(protime) ?2.794001 ? ?16.346 ?0.95289 ?2.93215 0.0034
> age ? ? ? ? ? 0.020590 ? ? 1.021 ?0.00805 ?2.55666 0.0110
> platelet ? ? -0.001699 ? ? 0.998 ?0.00085 -2.00130 0.0450
>
> Likelihood ratio test=164 ?on 5 df, p=0 ?n= 308, number of events> 143
> ? ?(110 observations deleted due to missingness)
>
> > plot(survfit(Surv(time, status>0) ~ trt, data=pbc))
> > lines(survexp( ~ trt, ratetable=pfit, data=pbc), col='purple')
>
> > pfit.wtd <- coxph(Surv(time,status>0) ~ trt + log(bili) +
log(protime) + age +
>
> + ? ? + platelet, ?weights=albumin, data=pbc
> + ? ? )
>
> > pfit.wtd
>
> Call:
> coxph(formula = Surv(time, status > 0) ~ trt + log(bili) +
> log(protime) +
> ? ? age + +platelet, data = pbc, weights = albumin)
>
> ? ? ? ? ? ? ? ? ?coef exp(coef) se(coef) ? ? ?z ? ? ? p
> trt ? ? ? ? ?-0.01354 ? ? 0.987 0.094204 -0.144 8.9e-01
> log(bili) ? ? 0.99282 ? ? 2.699 0.048690 20.391 0.0e+00
> log(protime) ?2.54136 ? ?12.697 0.525797 ?4.833 1.3e-06
> age ? ? ? ? ? 0.01913 ? ? 1.019 0.004398 ?4.350 1.4e-05
> platelet ? ? -0.00165 ? ? 0.998 0.000462 -3.578 3.5e-04
>
> Likelihood ratio test=535 ?on 5 df, p=0 ?n= 308, number of events> 143
> ? ?(110 observations deleted due to missingness)>
plot(survfit(Surv(time, status>0) ~ trt, data=pbc))
> > lines(survexp( ~ trt, ratetable=pfit.wtd, data=pbc),
col='purple')
>
> Error in eval(expr, envir, enclos) : object 'albumin' not found>
lines(survexp( ~ trt, ratetable=pfit.wtd, weights=albumin, data=pbc),
col='purple')
>
> Error in eval(expr, envir, enclos) : object 'albumin' not found
> In addition: Warning message:
> In survexp(~trt, ratetable = pfit.wtd, weights = albumin, data > pbc) :
> ? Weights ignored> lines(survexp( ~ trt, ratetable=pfit.wtd,
weights=pbc$albumin, data=pbc), col='purple')
>
> Error in eval(expr, envir, enclos) : object 'albumin' not found
> In addition: Warning message:
> In survexp(~trt, ratetable = pfit.wtd, weights = pbc$albumin, data >
pbc) :
> ? Weights ignored
>
>
>
> ______________________________________________
> R-h... at 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.