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

From: Wells, Brian <WELLSB_at_ccf.org>
Date: Sat, 29 Mar 2008 09:55:36 -0400

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.

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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