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 lt;arrayprof...@yahoo.comgt; 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 lt;dwinsem...@comcast.netgt; To: array chip lt;arrayprof...@yahoo.comgt; Cc: r-help@r-project.org lt;r-help@r-project.orggt; 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 lt;arrayprof...@yahoo.comgt; 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 [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/calibration-curve-for-cph-tp3745328p3746931.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] calibration curve for cph()
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?
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
Error in val.surv(f, newdata = data.frame(age, sex), S = S, u = 5) :
unused argument(s) (u = 5)
Many thanks
John
- 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 lt;arrayprof...@yahoo.comgt;
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 lt;dwinsem...@comcast.netgt;
To: array chip lt;arrayprof...@yahoo.comgt;
Cc: r-help@r-project.org lt;r-help@r-project.orggt;
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 lt;arrayprof...@yahoo.comgt;
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
[[alternative HTML version deleted]]
__
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.
[[alternative HTML version deleted]]
__
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.
-
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
View this message in context:
http://r.789695.n4.nabble.com/calibration-curve-for-cph-tp3745328p3746931.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.
__
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] calibration curve for cph()
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_2.13.1tools_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
lt;arrayprof...@yahoo.comgt;
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 lt;dwinsem...@comcast.netgt;
To: array chip lt;arrayprof...@yahoo.comgt;
Cc: r-help@r-project.org lt;r-help@r-project.orggt;
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
lt;arrayprof...@yahoo.comgt;
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
__
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] calibration curve for cph()
Oops, thank for reminding. I found that an in-house package interfered with rms
package, which caused the error.
Thanks David!
John
- Original Message -
From: David Winsemius dwinsem...@comcast.net
To: array chip arrayprof...@yahoo.com
Cc: Frank Harrell f.harr...@vanderbilt.edu; r-help@r-project.org
r-help@r-project.org
Sent: Tuesday, August 16, 2011 11:27 AM
Subject: Re: [R] calibration curve for cph()
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 lt;arrayprof...@yahoo.comgt;
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 lt;dwinsem...@comcast.netgt;
To: array chip lt;arrayprof...@yahoo.comgt;
Cc: r-help@r-project.org lt;r-help@r-project.orggt;
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 lt;arrayprof...@yahoo.comgt;
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
__
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.
[R] calibration curve for cph()
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 [[alternative HTML version deleted]] __ 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] 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 [[alternative HTML version deleted]] __ 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. __ 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] calibration curve for cph()
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 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 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 [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] calibration curve for cph()
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 [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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.
