R help - May 2008 - Troubles plotting lrm output in Design Library

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
day            22
svn rev        45424
language       R
version.string R version 2.7.0 (2008-04-22)

thank you in advance,

Patrizio Frederic

-------------------------------------------------
| 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: patrizio.frederic at unimore.it
+-------------------------------------------------

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
> day            22
> svn rev        45424
> 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: patrizio.frederic at unimore.it
> +-------------------------------------------------
> 
> ______________________________________________
> R-help at 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

Patrizio Frederic wrote:
> 2008/5/29 Frank E Harrell Jr <f.harrell at vanderbilt.edu>:
>> 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