[R] val.surv

[David Winsemius]

On Aug 20, 2011, at 8:08 PM, Salvo Mac wrote:

> Thanks David
>
> However, I tried your trick on val.surv with newdata=test['age'] but  
> still didn't work.
> Still gives the same error message:
>
> Error in val.surv(f.1, newdata = test1["age"], u = 10) :
>   dims [product 1797] do not match the length of object [2496]
> In addition: Warning message:
> In est.surv + S[, 1] :
>   longer object length is not a multiple of shorter object length
>

As I said (and you did not act  upon):

The fundamental thing you are doing wrong for q1  is failing to  
unambiguously describe the test object.

I said it was a guess. Now stop wasting our time and offer what is  
needed.

-- 
david.
>
> Salvo
>
>
>
> ________________________________
> From: David Winsemius <dwinsemius at comcast.net>
>
> Cc: "r-help at R-project.org" <r-help at r-project.org>
> Sent: Sunday, August 21, 2011 12:55 AM
> Subject: Re: [R] val.surv
>
>
> On Aug 20, 2011, at 3:32 PM, Salvo Mac wrote:
>
>>   Dear R-users,
>>
>> I  have two questions regarding validation and calibration of  
>> Survival regression models.
>>
>> 1.  I am trying to calibrate and validate a cox model using val.surv.
>> here is my code:
>>   f.1<-cph(Surv(time,event)~age, x=T, y=T, data=train)
>>   test1<-test[,"age"]
>>   val.surv(f.1, newdata=data.frame(test1), u=10)
>>
>>   but I get an error message:
>>
>>   Error in val.surv(f.1, newdata = data.frame(testi), u = 10) :
>>    dims [product 1797] do not match the length of object [2496]
>>   In addition: Warning message:
>> In est.surv + S[, 1] :
>>    longer object length is not a multiple of shorter object length
>>
>>   I ran the example in the r-documentation but couldn't extract   
>> dxy from result.
>>
>>   What am I doing wrong?
>
> The fundamental thing you are doing wrong for q1  is failing to  
> unambiguously describe the test object. I would think that if test  
> were a dataframe then wrapping data.frame around a vector might not  
> get it named correctly as 'age'. You might try newdata= test['age'].  
> Just a guess.
>
>>
>>   2.  In validate and calibrate cph functions. If it is frailty  
>> fit, does the the bootstrap resample clusters or just individuals
>
> The code above appears to be dependent on the rms package. The  
> frailty function is part of the underlying survival package and I do  
> not see it mentioned in the index for Harrell's RMS text. You will  
> probably need to wait until Frank comes across this. He is generally  
> very good about correction my errors and knowledge gaps.
>
>>
>
> --
> David Winsemius, MD
> West Hartford, CT
> 	[[alternative HTML version deleted]]
>
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David Winsemius, MD
West Hartford, CT