R help - Nov 2011 - Nomogram with stratified cph in rms package, how to get failure probability

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.


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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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