On Aug 16, 2011, at 1:57 PM, array chip wrote:
Dear Frank,
Thanks for suggesting val.surv() function from rms package. It's
exactly what I need. I tried the example on the help page and tweak
towards to my situation, but got an error message. Could you
suggestion what went wrong?
It is interesting that neither my mail client nor the archives show
the code that was sent to nabble.
For posterity it was
require(rms)
?val.surv
library(rms)
set.seed(123) # so can reproduce results
n <- 1000
age <- 50 + 12*rnorm(n)
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'))
t <- -log(runif(n))/h
units(t) <- 'Year'
label(t) <- 'Time to Event'
ev <- ifelse(t <= cens, 1, 0)
t <- pmin(t, cens)
S <- Surv(t, ev)
f <- cph(S ~ age + sex, x=TRUE, y=TRUE)
val.surv(f, newdata=data.frame(age,sex), S=S, u=5) ## pretend the
same training data as the independent dataset
Unable to reproduce. I get sensible output. You may need to post
sessionInfo(). Do you have all the dependencies installed? I noticed
that even after rms was loaded with messages about also loading
Hmisc, survival, and splines, that there was a further message saying
polspline was being loaded.
Error in val.surv(f, newdata = data.frame(age, sex), S = S, u = 5) :
unused argument(s) (u = 5)
--
david.
> sessionInfo()
R version 2.13.1 RC (2011-07-03 r56263)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] splines stats graphics grDevices utils datasets
methods base
other attached packages:
[1] polspline_1.1.5 rms_3.3-1 Hmisc_3.8-3 survival_2.36-9
[5] TTR_0.20-3 xts_0.8-0 zoo_1.6-5 sos_1.3-0
[9] brew_1.0-6 lattice_0.19-30
loaded via a namespace (and not attached):
[1] cluster_1.14.0 grid_2.13.1 tools_2.13.1
----- Original Message -----
From: Frank Harrell <f.harr...@vanderbilt.edu>
To: r-help@r-project.org
Cc:
Sent: Tuesday, August 16, 2011 4:23 AM
Subject: Re: [R] calibration curve for cph()
David Winsemius wrote:
A combination of Predict (your newdata), cut2, and the plotting
function
of your choice ought to suffice. But thought that cross-validation
was an
option. Not at console at the moment (just off airplane.)
Sent from my iPhone
On Aug 15, 2011, at 5:26 PM, array chip
<arrayprof...@yahoo.com>
wrote:
is there a R function that produces calibration curve on an
independetn
data automatically, just like what calibrate() does on the
training data
itself?
Thanks
John
From: Comcast <dwinsem...@comcast.net>
To: array chip <arrayprof...@yahoo.com>
Cc: "r-help@r-project.org" <r-help@r-project.org>
Sent: Monday, August 15, 2011 2:04 PM
Subject: Re: [R] calibration curve for cph()
Build a prediction function using 'Function' that gets applied to
set2.
Calibrate and validate.
--
David
Sent from my iPhone
On Aug 15, 2011, at 11:31 AM, array chip
<arrayprof...@yahoo.com>
wrote:
Hi, the calibrate.cph() function in rms package generate
calibration
curve for Cox model on the same dataset where the model was
derived using
bootstrapping or cross-validation. If I have the model built on
dataset
1, and now I want to produce a calibration curve for this model on
an
independent dataset 2, how can I do that?
Thanks
John
David Winsemius, MD
West Hartford, CT
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