survexp with weights
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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