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.harr...@vanderbilt.edu]
Sent: Thursday, December 11, 2008 6:58 PM
To: Yu, Changhong
Cc: r-help@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
>
> ===================================
>
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--
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}}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
