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

[array chip]

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
> 
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David Winsemius, MD
West Hartford, CT