Frank, Thanks again, I didn't realize that continuous variables could be manipulated that way inside of the summary function.
I realize that my code was kind of confusing. The variables "A"..."F" are all categorical variables. They each have four levels named "1st Quartile"...."4th Quartile" I tried the code below with the same result. >print(summary(f, eval(parse(text=paste(i,"='1st Quartile'", sep=''))))) In the output, the reference category is different for each of the variables. Brian -----Original Message----- From: Frank E Harrell Jr [mailto:[EMAIL PROTECTED] Sent: Sunday, March 30, 2008 9:14 AM 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: > 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:[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.
