[R] Nomogram with stratified cph in Design package

[David Winsemius]

On Apr 25, 2009, at 6:57 PM, reneepark wrote:

>
> Hello,
> I am using Dr. Harrell's design package to make a nomogram. I was  
> able to
> make a beautiful one without stratifying, however, I will need to  
> stratify
> to meet PH assumptions. This is where I go wrong, but I'm not sure  
> where.
>
>
>
> Non-Stratified Nomogram:
>
> f<-cph(S~A+B+C+D+E+F+H,x=T,y=T,surv=T,time.inc=10*12,method="breslow")
> srv=Survival(f)
> srv120=function(lp) srv(10*12,lp)
> quant=Quantile(f)
> med=function(lp) quant(.5,lp)
> at.surv=c(0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9)
> at.med=c(120,80,60,40,30,20,15,10,8,6,4,2,0)
> nomogram(f,lp=F, fun=list(srv120, med),funlabel=c("120-mo  
> Survival","Median
> Survival"),fun.at=list(at.surv, at.med))
>
> I get a the following warning:
> Warning message:
> In approx(fu[s], xseq[s], fat) : collapsing to unique 'x' values
>
> However, a great nomogram is constructed.
>
>
> But then I try to stratify...

>
> Stratified Nomogram:
>
> f<-cph(S~A+B+C+D+E+F 
> +strat(H),x=T,y=T,surv=T,time.inc=10*12,method="breslow")
> srv=Survival(f)
> surv.p <- function(lp) srv(10*12, lp, stratum="Hist=P")
> surv.f <- function(lp) srv(10*12, lp, stratum="Hist=F")
> surv.o <- function(lp) srv(10*12, lp, stratum="Hist=O")
> quant=Quantile(f)
> med.p <- function(lp) quant(.5, lp, stratum="Hist=P")
> med.f <- function(lp) quant(.5, lp, stratum="Hist=F")
> med.o <- function(lp) quant(.5, lp, stratum="Hist=O")
> nomogram(f, fun=list(surv.p, surv.f, surv.o, med.p, med.f, med.o),
> + funlabel=c("S(120|P)","S(120|F)","S(120|O)",
> + "med(P)","med(F)","med(O)"),
> + fun.at=list(c(0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9),
> + c(120,80,60,40,30,20,15,10,8,6,4,2,0)))
>
>
> the final nomogram only gives me a survival probability line for one  
> of the
> 3 Hist categories "S(120|P)". It does show the letters "S(120|F)"  
> but there
> is no survival probability line; there is nothing for the last  
> category O,
> and no median risk at all.

Those outputs seem consistent with the fact that stratification is not  
computing
separate models, but rather a pooled model. See Section 19.1.7 of RMS.

> I considered the idea that I was exceeding some
> sort of space limitation, and tried to set total.sep.page=T, but it  
> didn't
> change the output.

Does a "median risk'  exist when you stratify? You are allowing 3  
separate survival
functions to be created so that you estimate the remaining parameters.
It's possible that you can extract information about them, but you may  
be on your own
about how to recombine them.


> I get the following error message:
>
> Error in axis(sides[jj], at = scaled[jj], label = fat[jj], pos = y,  
> cex.axis
> = cex.axis,  :
>  no locations are finite
>
>
> I would very much appreciate any assistance in this matter. Thank  
> you very
> much.
>
> ~Renee Park

David Winsemius, MD
Heritage Laboratories
West Hartford, CT