Responding to the suggestion by D Winsemius :
> s1 <- survfit(mod1,newdata=inc[50050:50100,c("strt","stp","incpost",
> "amt","rate", "termfac")],
+ se.fit=F,individual=T,type="aa")
Error in Surv(time = strt, time2 = stp, event = (resp == 1)) :
object 'resp' not found
it appears it wants to fit a survival curve instead of predicting a survival
curve for the subject using the explanatory vars. I think I probably need
predict.coxph(...,type="expected")
or write code for matching time dependent risk to the proper time index of the
survival curve.
Thanks David.
Stephen
-----Original Message-----
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Thursday, February 03, 2011 3:10 PM
To: Bond, Stephen
Cc: r-help@r-project.org
Subject: Re: [R] coxph fails to survfit
On Feb 3, 2011, at 2:14 PM, Bond, Stephen wrote:
> I have a model with quant vars only and the error message does not
> make sense:
>
> (mod1 <- coxph(Surv(time=strt,time2=stp,event=(resp==1))~ +incpost
> +I(amt/1e5)+rate+strata(termfac),
> subset=dt<"2010-08-30", data=inc,method="efron"))
> Call:
> coxph(formula = Surv(time = strt, time2 = stp, event = (resp ==
> 1)) ~ +incpost + I(amt/1e+05) + rate + strata(termfac), data = inc,
> subset = dt < "2010-08-30", method = "efron")
>
>
> coef exp(coef) se(coef) z p
> incpost 0.2563 1.292 0.02479 10.34 0.0e+00
> I(amt/1e+05) -0.0532 0.948 0.00487 -10.92 0.0e+00
> rate -0.0507 0.951 0.00945 -5.36 8.2e-08
>
> Likelihood ratio test=295 on 3 df, p=0 n= 1192634
>
>> length(mod1$xlevels)
> [1] 0
>
> # now calling survfit with just a few rows from the data
>> s1 <-
>> survfit
>> (mod1,newdata=inc[50050:50100,],se.fit=F,individual=T,type="aa")
> Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") :
> contrasts can be applied only to factors with 2 or more levels
I obviously cannot test my theory, but would have thought the call
would be:
s1 <- survfit(mod1, newdata=inc[50050:50100,], c("incpost", "amt,
"rate", "termfac") ],
se.fit=F,individual=T,type="aa")
I.e., a data.frame for newdata that matched the variables used in the
RHS of the formula.
>
>> inc[50050:50100,]
> dt inc incpost strt stp resp rate amt p1 matfac
> termfac vol
> 50050 2009-02-05 0.00000 0.00 0 1 0 5.35 266833 C
> 5 3 14229571
> 50051 2009-02-06 -0.09575 0.00 1 2 0 5.35 266833 C
> 5 3 14229571
> 50052 2009-02-09 -0.03875 0.00 4 5 0 5.35 266833 C
> 5 3 14229571
> 50053 2009-02-10 0.00850 0.00 5 6 0 5.35 266833 C
> 5 3 14229571
> 50054 2009-02-11 0.00250 0.00 6 7 0 5.35 266833 C
> 5 3 14229571
> 50055 2009-02-12 -0.04725 0.00 7 8 0 5.35 266833 C
> 5 3 14229571
> 50056 2009-02-13 -0.00075 0.00 8 9 0 5.35 266833 C
> 5 3 14229571
> 50057 2009-02-16 -0.10425 0.00 11 12 0 5.35 266833 C
> 5 3 14229571
> 50058 2009-02-17 -0.10425 0.00 12 13 0 5.35 266833 C
> 5 3 14229571
> 50059 2009-02-18 -0.02925 0.00 13 14 0 5.35 266833 C
> 5 3 14229571
> 50060 2009-02-19 -0.01300 0.00 14 15 0 5.35 266833 C
> 5 3 14229571
> 50061 2009-02-20 -0.04075 0.00 15 16 0 5.35 266833 C
> 5 3 14229571
> 50062 2009-02-23 -0.03100 0.00 18 19 0 5.35 266833 C
> 5 3 14229571
> 50063 2009-02-24 0.01975 0.00 19 20 0 5.35 266833 C
> 5 3 14229571
> 50064 2009-02-25 0.13050 0.00 20 21 0 5.35 266833 C
> 5 3 14229571
> 50065 2009-02-26 0.12725 0.00 21 22 0 5.35 266833 C
> 5 3 14229571
>
> ... further output truncated
>
> Please, comment if you see what's the issue.
> Thank you.
> Stephen
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
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