R help - Mar 2008 - Defining reference category for a cph model summary inside of a "for" loop

I have the following code. 

 

 
> f <- cph(formula = Surv(TimeToDeath, Dead == "Yes")
~1,data=single.dat, x=T, y=T, surv=T)
> for(i in c('A', 'B', 'C', 'D', 'E',
'F')){
> f <-update(f,as.formula(paste('Surv(TimeToDeath, Dead
="Yes")~',i,sep='')))
> print(summary(f, paste(i,"=1st Quartile", sep='')))
 

 

There is no error message generated in R, but R ignores the reference
category defined with paste in the summary function for the cph model. 

 

The output uses the "1st Quartile" as the reference category to
calculate hazards for some of the variables defined by i, but not all of
them. 

 

 

Any help would be greatly appreciated. 

 

thanks

 

Brian J. Wells, MD, MS

Research Associate

Quantitative Health Sciences

Cleveland Clinic

 

 


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Wells, Brian wrote:
> I have the following code. 
> 
>  
> 
>  
> 
>> f <- cph(formula = Surv(TimeToDeath, Dead == "Yes")
> ~1,data=single.dat, x=T, y=T, surv=T)
> 
>> for(i in c('A', 'B', 'C', 'D',
'E', 'F')){
> 
>> f <-update(f,as.formula(paste('Surv(TimeToDeath, Dead =>
"Yes")~',i,sep='')))
> 
>> print(summary(f, paste(i,"=1st Quartile", sep='')))
> 
>  
> 
>  
> 
> There is no error message generated in R, but R ignores the reference
> category defined with paste in the summary function for the cph model. 
> 
>  
> 
> The output uses the "1st Quartile" as the reference category to
> calculate hazards for some of the variables defined by i, but not all of
> them. 

Your code is confusing.  What is to the right of ~ in a formula is a 
predictor variable name, not a value.  If your variables are named A, B, 
C, ... you are OK.

'1st Quartile' has no special meaning to R or Design, and you can't
pass
a character string as a second argument to summary and expect it to work.

You will need parse(text=paste(...)) to create an appropriate expression.

But Design gives you inter-quartile range hazard ratios by default anyway.

Beware of getting hazard ratios that are not adjusted for other 
variables needed in the model.

Frank Harrell
> 
>  
> 
>  
> 
> Any help would be greatly appreciated. 
> 
>  
> 
> thanks
> 
>  
> 
> Brian J. Wells, MD, MS
> 
> Research Associate
> 
> Quantitative Health Sciences
> 
> Cleveland Clinic
> 
-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University