[R] Nomogram with stratified cph in Design package-- failure probability

min myi at mdanderson.org
Tue Nov 29 18:51:16 CET 2011


I am using Dr. Harrell's design 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: 

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)

nom<- nomogram(f1, conf.int=F,
fun=list(1-surv5, 1-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)

I would very much appreciate any assistance in this matter. 
Thank you Very much.

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