[R] Nomogram with stratified cph in Design package

[reneepark]

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. 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. 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
medical student
Oregon Health & Science University
Portland, OR
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