[R] Troubles plotting lrm output in Design Library

Frank E Harrell Jr
Thu, 29 May 2008 12:53:26 -0000

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