[R] Nomogram with stratified cph in Design package-- failure probability
Hello,
I am using Dr. Harrell's design 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:
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(1-surv5, 1-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)
I would very much appreciate any assistance in this matter.
Thank you Very much.
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Re: [R] Nomogram with stratified cph in Design package-- failure probability
sorry the code for nomogram
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)
Thanks
Min
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Re: [R] Nomogram with stratified cph in Design package-- failure probability
Please convert to rms. Design is no longer supported. See
http://biostat.mc.vanderbilt.edu/Rrms
Frank
min wrote
>
> sorry the code for nomogram
>
> 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)
>
> Thanks
>
> Min
>
-
Frank Harrell
Department of Biostatistics, Vanderbilt University
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Re: [R] Nomogram with stratified cph in Design package
Renee,
I finally found the problem. You misspecified fun.at as a list with two
elements. It needed 6 elements to correspond with fun:
fun.at=list(at.surv, at.surv, at.surv,
at.med, at.med, at.med)
You have subjects with a very good prognosis and you are asking for
median survival time. The estimate of the median from the Cox model is
NA unless the linear predictor is very high. I've added some code to
understand this below and made some minor code improvements. -Frank
h <- harrell # and avoid attach
dd<- datadist(h); options(datadist="dd")
units(h$time)<-"Month"
S <- with(h, Surv(time,fail))
f<-cph(S~age+gender+size+met+node+ece+hist, x=TRUE, y=TRUE,
surv=T,time.inc=10*12,
method="breslow", data=h)
mins <- min(f$surv) # .984
sum(mins ^ exp(predict(f)) < .5) # only 241 subjects have predicted
prob < .5
srv=Survival(f)
srv120=function(lp) srv(10*12,lp)
quant=Quantile(f)
med=function(lp) quant(.5,lp)
r <- function(lp, med, srv) {
m <- med(lp)
cat(' Non-NA median estimates: ', sum(!is.na(m)),'\n',
'lp range for non-NA median: ',
range(lp[!is.na(m)]),'\n',
'range of survival prob with non-NA
median:',range(srv(lp)[!is.na(m)]),
'\n',
'median range: ', range(m,
na.rm=TRUE),'\n')
}
r(predict(f), med, srv120)
at.surv=c(0.001,0.01,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,0.95,0.97,0.98,0.99,.999)
at.med=c(120,80,60,40,30,20,15,10,8,6,4,2,0)
nomogram(f, cex.var=0.75, cex.axis=0.6, ia.space=1, lp=FALSE,
fun=list(srv120, med),
funlabel=c("120-mo Survival Prob","Median Survival (months)"),
fun.at=list(at.surv, at.med),varname.label=F, maxscale=100)
title("unstratified nomogram")
f<-cph(S~age+gender+size+met+node+ece+strat(hist), x=TRUE, y=TRUE,
surv=TRUE, time.inc=10*12, method="breslow", data=h)
for(i in 1:3)
{
hi <- levels(h$hist)[i]
j <- h$hist == hi
lp <- predict(f)[j]
if(hi=='follicular') lp.f <- lp
if(hi=='other') lp.o <- lp
if(hi=='papillary') lp.p <- lp
mins <- min(f$surv[[i]])
count <- sum(mins ^ exp(lp) < .5)
prn(c(mins,count))
}
srv=Survival(f)
surv.p <- function(lp) srv(10*12, lp, stratum="hist=papillary")
surv.f <- function(lp) srv(10*12, lp, stratum="hist=follicular")
surv.o <- function(lp) srv(10*12, lp, stratum="hist=other")
quant=Quantile(f)
med.p <- function(lp) quant(.5, lp, stratum="hist=papillary")
med.f <- function(lp) quant(.5, lp, stratum="hist=follicular")
med.o <- function(lp) quant(.5, lp, stratum="hist=other")
r(lp.p, med.p, surv.p)
r(lp.f, med.f, surv.f)
r(lp.o, med.o, surv.o)
at.surv=c(0.001,0.01,0.1,0.2,0.3,0.4,0.5,06,0.7,0.8,0.9,0.95,0.97,0.98,0.99,.999)
at.med=c(120,80,60,40,30,20,15,10,8,6,4,2,0)
nomogram(f, cex.var=0.75, cex.axis=0.6, ia.space=1, lp=FALSE,
fun=list(surv.p, surv.f, surv.o, med.p, med.f, med.o),
funlabel=c("Surv Pap","Surv Fol","Surv Oth","Med surv pap",
"Med surv Fol","Med Surv Oth"),
fun.at=list(at.surv, at.surv, at.surv,
at.med, at.med, at.med), varname.label=FALSE, maxscale=100)
title("stratified nomogram")
-Original Message-
From: Frank E Harrell Jr [mailto:f.harr...@vanderbilt.edu]
Sent: Sunday, April 26, 2009 6:13 AM
To: David Winsemius
Cc: reneepark; r-help@r-project.org
Subject: Re: [R] Nomogram with stratified cph in Design package
David Winsemius wrote:
>
> 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
Re: [R] Nomogram with stratified cph in Design package
David Winsemius wrote:
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.
But you can think of stratification as using a different transformation
for each stratum, and as long as you create a separate function for each
level of the stratification variable, as Rene did, all should be well.
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.
Yes it exists, using the separate function approach.
Rene if you can duplicate the problem with a simple simulated or real
dataset and send that to me I can try to go through this step by step.
It's probably a scaling, units of measurement, or extrapolation problem
where the median is not defined. You can evaluate the created functions
yourself a several settings to see if the results are reasonable and to
learn where extrapolation is not possible because of truncated follow-up.
Frank
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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and provide commented, minimal, self-contained, reproducible code.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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Re: [R] Nomogram with stratified cph in Design package
I'm sorry - I meant a "median survival" estimate, not a median "risk." I see - I didn't realize that by stratifying it would pool the levels of the stratified variable. Hm, that is unfortunate, considering the stratified variable is one that I would like to keep in the nomogram. Thank you for your help! ~Renee -- View this message in context: http://www.nabble.com/Nomogram-with-stratified-cph-in-Design-package-tp23237422p23239686.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nomogram with stratified cph in Design package
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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and provide commented, minimal, self-contained, reproducible code.
[R] 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
medical student
Oregon Health & Science University
Portland, OR
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