Got it.

Thank you so much for the help!

Min Yi  MD, PhD
Department of Surgical Oncology - Unit 1484
1400 Pressler Street, #FCT17.6061
University of Texas M.D. Anderson Cancer Center
P.O. Box 301402
Houston, TX  77230-1402
Phone: 713-563-1874
Fax: 713-792-4689

From: Frank Harrell [via R] [mailto:ml-node+s789695n4129173h97@n4.nabble.com]
Sent: Thursday, December 01, 2011 10:15 AM
To: Yi,Min
Subject: Re: Nomogram with stratified cph in rms package, how to get failure probability

Hazard() is not implemented except for parametric survival models.

You are not calling nomogram() correctly; in rms the plotting step is separated from the nomogram computations.

To plot cumulative event rates do something like:

mort10 <- function(lp) 1 - surv(10,lp)

and tell nomogram about mort10 using fun=.

Frank

min wrote
Hello,

I am using Dr. Harrell's rms package to make a nomogram. I was able to make a beautiful one. However, I want to change 5-year survival probability to 5-year failure probability.

I couldn’t get hazard rate from Hazard(f1) because I used cph for the model.

Here is my code:

 library(rms)
f1 <- cph(Surv(retime,dfs) ~ age+her2+t_stage+n_stage+er+grade+cytcyt+Cyt_PCDK2  , data=data11,
surv=T, x=T, y=T, time.inc=5)

surv<- Survival(f1)
haz<- Hazard(f1)
Here is the Error in UseMethod("Hazard") :
  no applicable method for 'Hazard' applied to an object of class "c('cph', 'Design', 'coxph')"


surv10 <- function(lp) surv(10,lp)
surv5 <- function(lp) surv(5,lp)
quant <- Quantile(f1)

at.surv <- c(0.1, 0.3, 0.5,  0.7, 0.9)

at.med1<-c(2,3,4, 5,6,7,8, 10,15,20,25, 30)


par(cex=0.8)
nom<- nomogram(f1, conf.int=F,
fun=list(surv5, surv10), funlabel=c('5-Year Survival Probability', '10-Year Survival Probability' ),  lp=F,
fun.at=c(at.surv, at.surv),label.every=1, force.label=FALSE, cex.axis=0.8, verbose=TRUE, cex.var=0.8)

How can I show failure probability instead of survival probability?

I would very much appreciate any assistance in this matter.
Thank you Very much.
Frank Harrell
Department of Biostatistics, Vanderbilt University

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