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...@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...@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.
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