Re: [R] Defining reference category for a cph model summary inside of a "for" loop

From: Frank E Harrell Jr <f.harrell_at_vanderbilt.edu>
Date: Sun, 30 Mar 2008 08:14:20 -0500

Wells, Brian wrote:
> Dr. Harrell,
> Thanks for you help.
>
> I tried:
>

>> print(summary(f,parse(text=paste(i,'="1st Quartile"', sep=''))))

>
> Same result. No error, the reference category simply doesn't change.

That's good, because the default in summary is to compare the outer quartiles for a continuous variable. And as I said before the string '1st Quartile' has no special meaning for R or Design.

Get what you are trying to do to work without parse (and you'll need eval() with parse) first. When you want total control over a setting, say getting a hazard ratio for the .2 to the .8 quantile, do something like

summary(f, age=quantile(age,c(.2,.8),na.rm=TRUE))

Frank

>
> Brian
>
> -----Original Message-----
> From: Frank E Harrell Jr [mailto:f.harrell_at_vanderbilt.edu]
> Sent: Friday, March 28, 2008 8:34 PM
> To: Wells, Brian
> Cc: r-help_at_r-project.org
> Subject: Re: [R] Defining reference category for a cph model summary
> inside of a "for" loop
>
> 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

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