Re: [R] survplot() for cph(): Design vs rms
Thanks Frank!
- Original Message -
From: Frank Harrell
To: r-help@r-project.org
Cc:
Sent: Thursday, August 25, 2011 4:33 PM
Subject: Re: [R] survplot() for cph(): Design vs rms
http://biostat.mc.vanderbilt.edu/Rrms shows differences between Design and
rms
Frank
array chip wrote:
>
> Thank you David. The plot from Design package will draw a plot of survival
> probability at 5 years (in my example) versus different age. I will look
> into Predict() in rms package to see how this can be done.
>
>
> John
>
>
>
>
>
>
> - Original Message -
> From: David Winsemius <dwinsem...@comcast.net>
> To: array chip <arrayprof...@yahoo.com>
> Cc: "r-h...@stat.math.ethz.ch" <r-h...@stat.math.ethz.ch>
> Sent: Thursday, August 25, 2011 3:15 PM
> Subject: Re: [R] survplot() for cph(): Design vs rms
>
>
> On Aug 25, 2011, at 5:11 PM, array chip wrote:
>
>> Hi, in Design package, a plot of survival probability vs. a covariate can
>> be generated by survplot() on a cph object using the folliowing code:
>>
>> n <- 1000
>> set.seed(731)
>> age <- 50 + 12*rnorm(n)
>> label(age) <- "Age"
>> sex <- factor(sample(c('male','female'), n, TRUE))
>> 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"
>> dd <- datadist(age, sex)
>> options(datadist='dd')
>> S <- Surv(dt,e)
>>
>>
>> library(Design)
>>
>> f <- cph(S ~ age, surv=TRUE,x=T,y=T)
>> plot(f,age=NA,time=5)
>>
>> But the same code won't work if I used rms package:
>>
>> detach(package:Design)
>> library(rms)
>>
>> f <- cph(S ~ age, surv=TRUE,x=T,y=T)
>>
>> plot(f,age=NA,time=5)
>> Error in xy.coords(x, y, xlabel, ylabel, log) :
>> 'x' and 'y' lengths differ
>>
>>
>> Is there a way to plot the same graph using rms package.
>
> I don't remember what that would have done in Design and you have not
> explained what you expected. You should read the rms help page for cph and
> walk through the examples where ht euse of the Predict function is
> illustrated. The plotting support for Predict objects is excellent.
>
>
>> I like to use Frank Harrell's new package rms and try to avoid using old
>> Design package.
>>
>> Thanks
>>
>> John
>>
>> __
>> 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.
>
> 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.
>
-
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
View this message in context:
http://r.789695.n4.nabble.com/survplot-for-cph-Design-vs-rms-tp3769430p3769683.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] survplot() for cph(): Design vs rms
http://biostat.mc.vanderbilt.edu/Rrms shows differences between Design and
rms
Frank
array chip wrote:
>
> Thank you David. The plot from Design package will draw a plot of survival
> probability at 5 years (in my example) versus different age. I will look
> into Predict() in rms package to see how this can be done.
>
>
> John
>
>
>
>
>
>
> - Original Message -
> From: David Winsemius <dwinsem...@comcast.net>
> To: array chip <arrayprof...@yahoo.com>
> Cc: "r-h...@stat.math.ethz.ch" <r-h...@stat.math.ethz.ch>
> Sent: Thursday, August 25, 2011 3:15 PM
> Subject: Re: [R] survplot() for cph(): Design vs rms
>
>
> On Aug 25, 2011, at 5:11 PM, array chip wrote:
>
>> Hi, in Design package, a plot of survival probability vs. a covariate can
>> be generated by survplot() on a cph object using the folliowing code:
>>
>> n <- 1000
>> set.seed(731)
>> age <- 50 + 12*rnorm(n)
>> label(age) <- "Age"
>> sex <- factor(sample(c('male','female'), n, TRUE))
>> 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"
>> dd <- datadist(age, sex)
>> options(datadist='dd')
>> S <- Surv(dt,e)
>>
>>
>> library(Design)
>>
>> f <- cph(S ~ age, surv=TRUE,x=T,y=T)
>> plot(f,age=NA,time=5)
>>
>> But the same code won't work if I used rms package:
>>
>> detach(package:Design)
>> library(rms)
>>
>> f <- cph(S ~ age, surv=TRUE,x=T,y=T)
>>
>> plot(f,age=NA,time=5)
>> Error in xy.coords(x, y, xlabel, ylabel, log) :
>> 'x' and 'y' lengths differ
>>
>>
>> Is there a way to plot the same graph using rms package.
>
> I don't remember what that would have done in Design and you have not
> explained what you expected. You should read the rms help page for cph and
> walk through the examples where ht euse of the Predict function is
> illustrated. The plotting support for Predict objects is excellent.
>
>
>> I like to use Frank Harrell's new package rms and try to avoid using old
>> Design package.
>>
>> Thanks
>>
>> John
>>
>> __
>> 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.
>
> 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.
>
-
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
View this message in context:
http://r.789695.n4.nabble.com/survplot-for-cph-Design-vs-rms-tp3769430p3769683.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] survplot() for cph(): Design vs rms
Thank you David. The plot from Design package will draw a plot of survival
probability at 5 years (in my example) versus different age. I will look into
Predict() in rms package to see how this can be done.
John
- Original Message -
From: David Winsemius
To: array chip
Cc: "r-h...@stat.math.ethz.ch"
Sent: Thursday, August 25, 2011 3:15 PM
Subject: Re: [R] survplot() for cph(): Design vs rms
On Aug 25, 2011, at 5:11 PM, array chip wrote:
> Hi, in Design package, a plot of survival probability vs. a covariate can be
> generated by survplot() on a cph object using the folliowing code:
>
> n <- 1000
> set.seed(731)
> age <- 50 + 12*rnorm(n)
> label(age) <- "Age"
> sex <- factor(sample(c('male','female'), n, TRUE))
> 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"
> dd <- datadist(age, sex)
> options(datadist='dd')
> S <- Surv(dt,e)
>
>
> library(Design)
>
> f <- cph(S ~ age, surv=TRUE,x=T,y=T)
> plot(f,age=NA,time=5)
>
> But the same code won't work if I used rms package:
>
> detach(package:Design)
> library(rms)
>
> f <- cph(S ~ age, surv=TRUE,x=T,y=T)
>
> plot(f,age=NA,time=5)
> Error in xy.coords(x, y, xlabel, ylabel, log) :
> 'x' and 'y' lengths differ
>
>
> Is there a way to plot the same graph using rms package.
I don't remember what that would have done in Design and you have not explained
what you expected. You should read the rms help page for cph and walk through
the examples where ht euse of the Predict function is illustrated. The plotting
support for Predict objects is excellent.
> I like to use Frank Harrell's new package rms and try to avoid using old
> Design package.
>
> Thanks
>
> John
>
> __
> 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.
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] survplot() for cph(): Design vs rms
On Aug 25, 2011, at 5:11 PM, array chip wrote:
Hi, in Design package, a plot of survival probability vs. a
covariate can be generated by survplot() on a cph object using the
folliowing code:
n <- 1000
set.seed(731)
age <- 50 + 12*rnorm(n)
label(age) <- "Age"
sex <- factor(sample(c('male','female'), n, TRUE))
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"
dd <- datadist(age, sex)
options(datadist='dd')
S <- Surv(dt,e)
library(Design)
f <- cph(S ~ age, surv=TRUE,x=T,y=T)
plot(f,age=NA,time=5)
But the same code won't work if I used rms package:
detach(package:Design)
library(rms)
f <- cph(S ~ age, surv=TRUE,x=T,y=T)
plot(f,age=NA,time=5)
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' and 'y' lengths differ
Is there a way to plot the same graph using rms package.
I don't remember what that would have done in Design and you have not
explained what you expected. You should read the rms help page for cph
and walk through the examples where ht euse of the Predict function is
illustrated. The plotting support for Predict objects is excellent.
I like to use Frank Harrell's new package rms and try to avoid using
old Design package.
Thanks
John
__
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.
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] survplot() for cph(): Design vs rms
Hi, in Design package, a plot of survival probability vs. a covariate can be
generated by survplot() on a cph object using the folliowing code:
n <- 1000
set.seed(731)
age <- 50 + 12*rnorm(n)
label(age) <- "Age"
sex <- factor(sample(c('male','female'), n, TRUE))
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"
dd <- datadist(age, sex)
options(datadist='dd')
S <- Surv(dt,e)
library(Design)
f <- cph(S ~ age, surv=TRUE,x=T,y=T)
plot(f,age=NA,time=5)
But the same code won't work if I used rms package:
detach(package:Design)
library(rms)
f <- cph(S ~ age, surv=TRUE,x=T,y=T)
plot(f,age=NA,time=5)
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' and 'y' lengths differ
Is there a way to plot the same graph using rms package. I like to use Frank
Harrell's new package rms and try to avoid using old Design package.
Thanks
John
__
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.
