Re: [R] survexp with weights

From: Mike Harwood <harwood262_at_gmail.com>
Date: Thu, 21 Apr 2011 08:41:18 -0700 (PDT)

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
>
>
>
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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 Thu 21 Apr 2011 - 16:57:07 GMT

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