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