Re: [R] Troubles plotting lrm output in Design Library
2008/5/29 Frank E Harrell Jr [EMAIL PROTECTED]: Patrizio Frederic wrote: dear Harrell, thank you for quick reply and suggestions. I still have the problem: library(Design) x = rnorm(100) y = runif(100)(exp(x)/(1+exp(x))) y = 0*y+1*y d = datadist(x,y) options(datadist=d) fit = lrm(y~x) # works fine, but plot(fit) #produce the error message I cannot reproduce the error on Linux R 2.7.0 using the same version of the packages you are using. Frank just for the records, I solved the problem: in Windows R 2.7.0 one has to set: d = datadist(x,y) .Options$datadist=d done that functions summary.Design, and plot.Design work fine. PF __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Troubles plotting lrm output in Design Library
Patrizio Frederic wrote: 2008/5/29 Frank E Harrell Jr [EMAIL PROTECTED]: Patrizio Frederic wrote: dear Harrell, thank you for quick reply and suggestions. I still have the problem: library(Design) x = rnorm(100) y = runif(100)(exp(x)/(1+exp(x))) y = 0*y+1*y d = datadist(x,y) options(datadist=d) fit = lrm(y~x) # works fine, but plot(fit) #produce the error message I cannot reproduce the error on Linux R 2.7.0 using the same version of the packages you are using. Frank just for the records, I solved the problem: in Windows R 2.7.0 one has to set: d = datadist(x,y) .Options$datadist=d done that functions summary.Design, and plot.Design work fine. PF Thanks for the solution. But I wish someone would tell us why the solution makes sense. If you have changed your R environment in any way from the defaults please let us know. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] Troubles plotting lrm output in Design Library
Thanks for the solution. But I wish someone would tell us why the solution makes sense. If you have changed your R environment in any way from the defaults please let us know. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University dear Harrell and R users, It took me several hours to figure out. I apologize it was my mistake. Few month ago a modified copy of .Options was created in Rprofile (I don't remember why). The copy masked the alias .Options created by options(). Now everything is fixed. Now I know how .Options and options are related one each other. Sorry for wasting your time. Thank you for your help. Patrizio Frederic __ 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] Troubles plotting lrm output in Design Library
Patrizio Frederic wrote: Thanks for the solution. But I wish someone would tell us why the solution makes sense. If you have changed your R environment in any way from the defaults please let us know. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University dear Harrell and R users, It took me several hours to figure out. I apologize it was my mistake. Few month ago a modified copy of .Options was created in Rprofile (I don't remember why). The copy masked the alias .Options created by options(). Now everything is fixed. Now I know how .Options and options are related one each other. Sorry for wasting your time. Thank you for your help. Patrizio Frederic That's great news. Thanks for figuring this out. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] Troubles plotting lrm output in Design Library
On Fri, 30 May 2008, Patrizio Frederic wrote: Thanks for the solution. But I wish someone would tell us why the solution makes sense. If you have changed your R environment in any way from the defaults please let us know. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University dear Harrell and R users, It took me several hours to figure out. I apologize it was my mistake. Few month ago a modified copy of .Options was created in Rprofile (I don't remember why). The copy masked the alias .Options created by options(). Now everything is fixed. Now I know how .Options and options are related one each other. Sorry for wasting your time. Thank you for your help. This is an infelicity in Design and Hmisc (and a few other packages), in that they do look at the first visible .Options. R itself only looks at the copy in the symbol table (which also appears in the base namespace). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] Troubles plotting lrm output in Design Library
Prof Brian Ripley wrote:
On Fri, 30 May 2008, Patrizio Frederic wrote:
Thanks for the solution. But I wish someone would tell us why the
solution
makes sense. If you have changed your R environment in any way from the
defaults please let us know.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
dear Harrell and R users,
It took me several hours to figure out. I apologize it was my mistake.
Few month ago a modified copy of .Options was created in Rprofile (I
don't remember why). The copy masked the alias .Options created by
options().
Now everything is fixed. Now I know how .Options and options are
related one each other. Sorry for wasting your time.
Thank you for your help.
This is an infelicity in Design and Hmisc (and a few other packages), in
that they do look at the first visible .Options. R itself only looks at
the copy in the symbol table (which also appears in the base namespace).
I hadn't thought of that. Thanks Brian. I think of .Options$foo as
being faster. Is there a preferred approach other than options('foo')?
Thanks
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Troubles plotting lrm output in Design Library
On Fri, 30 May 2008, Frank E Harrell Jr wrote:
Prof Brian Ripley wrote:
On Fri, 30 May 2008, Patrizio Frederic wrote:
Thanks for the solution. But I wish someone would tell us why the
solution
makes sense. If you have changed your R environment in any way from the
defaults please let us know.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
dear Harrell and R users,
It took me several hours to figure out. I apologize it was my mistake.
Few month ago a modified copy of .Options was created in Rprofile (I
don't remember why). The copy masked the alias .Options created by
options().
Now everything is fixed. Now I know how .Options and options are
related one each other. Sorry for wasting your time.
Thank you for your help.
This is an infelicity in Design and Hmisc (and a few other packages), in
that they do look at the first visible .Options. R itself only looks at
the copy in the symbol table (which also appears in the base namespace).
I hadn't thought of that. Thanks Brian. I think of .Options$foo as being
faster. Is there a preferred approach other than options('foo')?
getOption(foo). Because .Options is a pairlist, the speed can be
illusory.
Thanks
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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] Troubles plotting lrm output in Design Library
dear Harrell,
thank you for quick reply and suggestions. I still have the problem:
library(Design)
x = rnorm(100)
y = runif(100)(exp(x)/(1+exp(x)))
y = 0*y+1*y
d = datadist(x,y)
options(datadist=d)
fit = lrm(y~x)
# works fine, but
plot(fit) #produce the error message
Error in value.chk(at, ix, xseq, if (plot.type == curves) 100 else 40, :
variable x does not have limits defined by datadist
The installed Design (ver. 2.1.1) package was downloaded and installed
via utils:::menuInstallPkgs() function
(Package Hmisc version 3.4-3) on a windows xp machine.
Thank in advance.
Patrizio Frederic
version
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 7.0
year 2008
month 04
day22
svn rev45424
language R
version.string R version 2.7.0 (2008-04-22)
2008/5/29 Frank E Harrell Jr [EMAIL PROTECTED]:
Patrizio Frederic wrote:
Dear R-helpers,
I'm having a problem in using plot.design in Design Library. Tho
following example code produce the error:
n - 1000# define sample size
set.seed(17) # so can reproduce the results
age- rnorm(n, 50, 10)
blood.pressure - rnorm(n, 120, 15)
cholesterol- rnorm(n, 200, 25)
sex- factor(sample(c('female','male'), n,TRUE))
label(age)- 'Age' # label is in Hmisc
label(cholesterol)- 'Total Cholesterol'
label(blood.pressure) - 'Systolic Blood Pressure'
label(sex)- 'Sex'
units(cholesterol)- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) - 'mmHg'
# Specify population model for log odds that Y=1
L - .4*(sex=='male') + .045*(age-50) +
+ (log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male'))
# Simulate binary y to have Prob(y=1) = 1/[1+exp(-L)]
y - ifelse(runif(n) plogis(L), 1, 0)
ddist - datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit - lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
+x=TRUE, y=TRUE)
par(mfrow=c(2,2))
plot(fit)# Plot effects of all 4 predictors
Error in value.chk(at, ix, xseq, if (plot.type == curves) 100 else 40,
:
variable blood.pressure does not have limits defined by datadist
I guess somthing goes wrong with function datadist
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 7.0
year 2008
month 04
day22
svn rev45424
language R
version.string R version 2.7.0 (2008-04-22)
thank you in advance,
Patrizio Frederic
This is the example run by example(plot.Design) which works for me, using
the version of Design from CRAN. You don't need to include code that is
already in an example in a help file, and if you do please make the code
copy and paste-able instead of putting something at the start of each line.
Frank
Frank
-
| Patrizio Frederic
| Research associate in Statistics,
| Department of Economics,
| University of Modena and Reggio Emilia,
| Via Berengario 51,
| 41100 Modena, Italy
|
| tel: +39 059 205 6727
| fax: +39 059 205 6947
| mail: [EMAIL PROTECTED]
+-
__
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 E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
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] Troubles plotting lrm output in Design Library
Patrizio Frederic wrote:
dear Harrell,
thank you for quick reply and suggestions. I still have the problem:
library(Design)
x = rnorm(100)
y = runif(100)(exp(x)/(1+exp(x)))
y = 0*y+1*y
d = datadist(x,y)
options(datadist=d)
fit = lrm(y~x)
# works fine, but
plot(fit) #produce the error message
I cannot reproduce the error on Linux R 2.7.0 using the same version of
the packages you are using.
Frank
Error in value.chk(at, ix, xseq, if (plot.type == curves) 100 else 40, :
variable x does not have limits defined by datadist
The installed Design (ver. 2.1.1) package was downloaded and installed
via utils:::menuInstallPkgs() function
(Package Hmisc version 3.4-3) on a windows xp machine.
Thank in advance.
Patrizio Frederic
version
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 7.0
year 2008
month 04
day22
svn rev45424
language R
version.string R version 2.7.0 (2008-04-22)
2008/5/29 Frank E Harrell Jr [EMAIL PROTECTED]:
Patrizio Frederic wrote:
Dear R-helpers,
I'm having a problem in using plot.design in Design Library. Tho
following example code produce the error:
n - 1000# define sample size
set.seed(17) # so can reproduce the results
age- rnorm(n, 50, 10)
blood.pressure - rnorm(n, 120, 15)
cholesterol- rnorm(n, 200, 25)
sex- factor(sample(c('female','male'), n,TRUE))
label(age)- 'Age' # label is in Hmisc
label(cholesterol)- 'Total Cholesterol'
label(blood.pressure) - 'Systolic Blood Pressure'
label(sex)- 'Sex'
units(cholesterol)- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) - 'mmHg'
# Specify population model for log odds that Y=1
L - .4*(sex=='male') + .045*(age-50) +
+ (log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male'))
# Simulate binary y to have Prob(y=1) = 1/[1+exp(-L)]
y - ifelse(runif(n) plogis(L), 1, 0)
ddist - datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit - lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
+x=TRUE, y=TRUE)
par(mfrow=c(2,2))
plot(fit)# Plot effects of all 4 predictors
Error in value.chk(at, ix, xseq, if (plot.type == curves) 100 else 40,
:
variable blood.pressure does not have limits defined by datadist
I guess somthing goes wrong with function datadist
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 7.0
year 2008
month 04
day22
svn rev45424
language R
version.string R version 2.7.0 (2008-04-22)
thank you in advance,
Patrizio Frederic
This is the example run by example(plot.Design) which works for me, using
the version of Design from CRAN. You don't need to include code that is
already in an example in a help file, and if you do please make the code
copy and paste-able instead of putting something at the start of each line.
Frank
Frank
-
| Patrizio Frederic
| Research associate in Statistics,
| Department of Economics,
| University of Modena and Reggio Emilia,
| Via Berengario 51,
| 41100 Modena, Italy
|
| tel: +39 059 205 6727
| fax: +39 059 205 6947
| mail: [EMAIL PROTECTED]
+-
__
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 E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
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.
