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:[EMAIL PROTECTED] Sent: Friday, March 28, 2008 8:34 PM To: Wells, Brian Cc: r-help@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 =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2007). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use\...{{dropped:13}} ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
