[R] val.surv

[Salvo Mac]

 I've   attached a sample of the data sets, this is my full code.

#R 2.13
#library(survival)
#library(Hmisc)
#library(splines)
library(rms)
train<-as.data.frame( train<-read.csv("G:\\train.txt", header=T, sep="\t"))
test<-as.data.frame( test<-read.table("G:\\test.txt", header=T, sep="\t"))
f.1<-cph(Surv(time,event)~age, x=T, y=T,surv=T, data=train)
val.surv(f.1, newdata=test, u=10)


#plot(calibrate(f.1, u=30, B=20))





________________________________
From: David Winsemius <dwinsemius at comcast.net>
To: Salvo Mac <salvo_mac at yahoo.com>
Cc: "r-help at R-project.org" <r-help at r-project.org>
Sent: Sunday, August 21, 2011 5:29 AM
Subject: Re: [R] val.surv


On Aug 20, 2011, at 10:25 PM, Salvo Mac wrote:

> The test and train are like split data sets, contain similar variables but from different countries so the two sets are somehow  independent. And yes it is a data frame.

What is a data.frame? test and train may be dataframes, but test[, "age"] is not a dataframe.

> So I extracted age, time and event.

Code? The code you offered before would have created a newdata object (yes, a data.frame) with a single column bearing the same name as the vector argument ,,,,, "test1". Not named "age". Try it. do str on such an object:

str(dataframe(test1))


> So test is data frame,(age, time, event). does that suffice?

It certainly does not allow me to reproduce the error you got (which I still think is probably related to the structure of your argument to newdata.)

That's all I can say without data and code.

--David.


> 
> 
> 
> ________________________________
> 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 3:19 AM
> Subject: Re: [R] val.surv
> 
> 
> 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
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