Thanks Frank!
----- Original Message ----- From: Frank Harrell <f.harr...@vanderbilt.edu> To: r-help@r-project.org Cc: Sent: Thursday, August 25, 2011 4:33 PM Subject: Re: [R] survplot() for cph(): Design vs rms http://biostat.mc.vanderbilt.edu/Rrms shows differences between Design and rms Frank array chip wrote: > > Thank you David. The plot from Design package will draw a plot of survival > probability at 5 years (in my example) versus different age. I will look > into Predict() in rms package to see how this can be done. > > > John > > > > > > > ----- Original Message ----- > From: David Winsemius <dwinsem...@comcast.net> > To: array chip <arrayprof...@yahoo.com> > Cc: "r-h...@stat.math.ethz.ch" <r-h...@stat.math.ethz.ch> > Sent: Thursday, August 25, 2011 3:15 PM > Subject: Re: [R] survplot() for cph(): Design vs rms > > > On Aug 25, 2011, at 5:11 PM, array chip wrote: > >> Hi, in Design package, a plot of survival probability vs. a covariate can >> be generated by survplot() on a cph object using the folliowing code: >> >> n <- 1000 >> set.seed(731) >> age <- 50 + 12*rnorm(n) >> label(age) <- "Age" >> sex <- factor(sample(c('male','female'), n, TRUE)) >> cens <- 15*runif(n) >> h <- .02*exp(.04*(age-50)+.8*(sex=='Female')) >> dt <- -log(runif(n))/h >> label(dt) <- 'Follow-up Time' >> e <- ifelse(dt <= cens,1,0) >> dt <- pmin(dt, cens) >> units(dt) <- "Year" >> dd <- datadist(age, sex) >> options(datadist='dd') >> S <- Surv(dt,e) >> >> >> library(Design) >> >> f <- cph(S ~ age, surv=TRUE,x=T,y=T) >> plot(f,age=NA,time=5) >> >> But the same code won't work if I used rms package: >> >> detach(package:Design) >> library(rms) >> >> f <- cph(S ~ age, surv=TRUE,x=T,y=T) >> >> plot(f,age=NA,time=5) >> Error in xy.coords(x, y, xlabel, ylabel, log) : >> 'x' and 'y' lengths differ >> >> >> Is there a way to plot the same graph using rms package. > > I don't remember what that would have done in Design and you have not > explained what you expected. You should read the rms help page for cph and > walk through the examples where ht euse of the Predict function is > illustrated. The plotting support for Predict objects is excellent. > > >> I like to use Frank Harrell's new package rms and try to avoid using old >> Design package. >> >> Thanks >> >> John >> >> ______________________________________________ >> 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. > > David Winsemius, MD > West Hartford, CT > > ______________________________________________ > 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. > ----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/survplot-for-cph-Design-vs-rms-tp3769430p3769683.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ 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. ______________________________________________ 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.
