Dear all, I used cph() function from Frank harrell's Design package to create a survival model, then used functions 'Function' and 'sascode' to generate prediction equation based on the saved survival model. But it failed. I included a stratified variable in the model. If I removed the stratification, they were working well. Does that mean that function 'Function' doesn't accept a stratified model? Any thoughts on this will be appreciated. Thanks. Changhong =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use\...{{dropped:13}}
How to generate a prediction equation for a stratified survival model that was fitted by cph() in Design package
3 messages · Frank E Harrell Jr, Yu, Changhong
Yu, Changhong wrote:
Dear all, I used cph() function from Frank harrell's Design package to create a survival model, then used functions 'Function' and 'sascode' to generate prediction equation based on the saved survival model. But it failed. I included a stratified variable in the model. If I removed the stratification, they were working well. Does that mean that function 'Function' doesn't accept a stratified model?
It is supposed to work for that case. Please send trivial example code with data defined in the code that replicates the problem you are seeing, and I'll debug. Frank
Any thoughts on this will be appreciated. Thanks. Changhong =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use\...{{dropped:13}}
______________________________________________ R-help at 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.
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
Dear Dr. Harrell, Thanks for response so quickly. Here is example code to illustrate the problem.
n <- 1000
set.seed(731)
age <- 50 + 12*rnorm(n)
label(age) <- "Age"
sex <- factor(sample(c('Male','Female'), n,
+ rep=TRUE, prob=c(.6, .4)))
cens <- 15*runif(n) h <- .02*exp(.04*(age-50)+.8*(sex=='Female')) dt <- -log(runif(n))/h label(dt) <- 'Follow-up Time' e <- ifelse(dt <= cens,1,0) dt <- pmin(dt, cens) units(dt) <- "Year" dat <- data.frame(dt,e,age,sex) dd <- datadist(dat) options(datadist='dd') f1 <- cph( Surv(dt,e) ~ rcs(age,4) + sex, data=dat,x=TRUE, y=TRUE,
surv=TRUE)
f2 <- cph( Surv(dt,e)~ age + strat(sex), data=dat, x=TRUE,
y=TRUE,surv=TRUE)
Function(f1) # works well
function(age = 48.800654,sex = "Male") {0.28612987-0.017321951*
age+0.00012586581*pmax(age-29.600456,0)^3-0.00046285671*pmax(age-44.2731
98,0)^3+0.00042111763*pmax(age-53.769262,0)^3-8.4126731e-05*pmax(age-69.
855597,0)^3-0.64448916*(sex=="Male") }
<environment: 0x02c2aef4>
Function(f2)
Error in Nam[[i]] : subscript out of bounds I am using Windows R ( version 2.6.0 2007-10-03). Best regards, Changhong Yu -----Original Message----- From: Frank E Harrell Jr [mailto:f.harrell at vanderbilt.edu] Sent: Thursday, December 11, 2008 6:58 PM To: Yu, Changhong Cc: r-help at r-project.org Subject: Re: [R] How to generate a prediction equation for a stratified survival model that was fitted by cph() in Design package
Yu, Changhong wrote:
Dear all, I used cph() function from Frank harrell's Design package to create a survival model, then used functions 'Function' and 'sascode' to
generate
prediction equation based on the saved survival model. But it failed.
I
included a stratified variable in the model. If I removed the stratification, they were working well. Does that mean that function 'Function' doesn't accept a stratified model?
It is supposed to work for that case. Please send trivial example code with data defined in the code that replicates the problem you are seeing, and I'll debug. Frank
Any thoughts on this will be appreciated. Thanks. Changhong =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S. News & World Report (2008). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for
use\...{{dropped:13}}
______________________________________________ R-help at 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.
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt
University
P Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals
in America by U.S. News & World Report (2008).
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.
Confidentiality Note: This message is intended for use\...{{dropped:13}}