[R] coxph fails to survfit

[David Winsemius]

On Feb 3, 2011, at 3:27 PM, Bond, Stephen wrote:

> 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.

I would have interpreted that error message as saying the function  
also needed some of the information on the LHS of the formula. Keep  
feeding it data that it complains is missing.
>
> Thanks David.
>
> Stephen
>
> -----Original Message-----
> From: David Winsemius [mailto:dwinsemius at comcast.net]
> Sent: Thursday, February 03, 2011 3:10 PM
> To: Bond, Stephen
> Cc: r-help at 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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>
> David Winsemius, MD
> West Hartford, CT
>

David Winsemius, MD
West Hartford, CT