Wells, Brian wrote: > 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
Thanks for clarifying. That approach will NOT provide estimates at the quartiles. For example a hazard ratio for the "upper quartile category" to the "lower quartile category" will estimate the ratio of hazards when X>Q3 to when X<Q1 where outer quartiles are Q1 and Q3. This represents a hazard ratio of an unknown mixture of distributions and will not transport to another sample with a different mixture. In addition you will have serious residual confounding with that approach by not adjusting for all the information in continuous predictors. Frank > -----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 ______________________________________________ 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.
