Defining reference category for a cph model summary inside of a "for" loop

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

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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