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
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