[R] survplot() for cph(): Design vs rms

[array chip]

Thanks Frank!



----- Original Message -----
From: Frank Harrell <f.harrell at vanderbilt.edu>
To: r-help at 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 <dwinsemius at comcast.net>
> To: array chip <arrayprofile at yahoo.com>
> Cc: "r-help at stat.math.ethz.ch" <r-help at 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 at 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 at 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
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