Nomogram with stratified cph in Design package

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

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