[R] strangeness in Predict() {rms}

[Frank E Harrell Jr]

William Dunlap wrote:
> Both plyr and rms contain an object called ".".
> In plyr it is a "closure" (the common kind of
> function) and in rms is is NA.  If plyr is attached
> in front of rms then you get your problem with
> Predict(). 
> 
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com  

I think I should modify rms to not let this happen.  Whenever an rms 
function uses ... as an argument to pass this type of information I can 
change list(...) to eval(substitute(list(...)), list(.=NA))

If anyone sees a better approach or a problem with this approach please 
let me know.

Frank

> 
>> -----Original Message-----
>> From: r-help-bounces at r-project.org 
>> [mailto:r-help-bounces at r-project.org] On Behalf Of 
>> Bill.Venables at csiro.au
>> Sent: Tuesday, February 16, 2010 4:21 PM
>> To: dylan.beaudette at gmail.com; r-help at r-project.org
>> Subject: Re: [R] strangeness in Predict() {rms}
>>
>> This works without a glitch on my linux system (info below).  
>> You might try upgrading your R to 2.10.1, perhaps.
>>
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14) 
>> x86_64-unknown-linux-gnu 
>>
>> locale:
>>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
>>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8   
>>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
>>
>> attached base packages:
>> [1] splines   grid      stats     graphics  grDevices utils   
>>   datasets 
>> [8] methods   base     
>>
>> other attached packages:
>> [1] rms_2.1-0       plyr_0.1.9      Design_2.3-0    Hmisc_3.7-0    
>> [5] survival_2.35-9
>>
>> loaded via a namespace (and not attached):
>> [1] ASOR_0.1       cluster_1.12.1 lattice_0.18-3 tcltk_2.10.1 
>>   tools_2.10.1  
>>>  
>>
>> Bill Venables
>> CSIRO/CMIS Cleveland Laboratories
>>
>>
>> -----Original Message-----
>> From: r-help-bounces at r-project.org 
>> [mailto:r-help-bounces at r-project.org] On Behalf Of Dylan Beaudette
>> Sent: Wednesday, 17 February 2010 10:05 AM
>> To: r-help at r-project.org
>> Subject: [R] strangeness in Predict() {rms}
>>
>> Hi,
>>
>> Running the following example from ?Predict() throws an error 
>> I have never 
>> seen before:
>>
>> set.seed(1)
>> x1 <- runif(300)
>> x2 <- runif(300)
>> ddist <- datadist(x1,x2); options(datadist='ddist')
>> y  <- exp(x1+ x2 - 1 + rnorm(300))
>> f  <- ols(log(y) ~ pol(x1,2) + x2)
>> p1 <- Predict(f, x1=., conf.type='mean')
>>
>> Error in paste(nmc[i], "=", if (is.numeric(x)) format(x) else 
>> x, sep = "") : 
>>   cannot coerce type 'closure' to vector of type 'character'
>> In addition: Warning message:
>> In is.na(v) : is.na() applied to non-(list or vector) of type 
>> 'closure'
>>
>> Here is the output from sessionInfo()
>>
>> R version 2.9.0 (2009-04-17) 
>> i686-pc-linux-gnu 
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA
>> TE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=
>> en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME
>> NT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] grid      splines   stats     graphics  grDevices utils   
>>   datasets 
>> [8] methods   base     
>>
>> other attached packages:
>> [1] plyr_0.1.9         mgcv_1.5-5         RColorBrewer_1.0-2 
>> nlme_3.1-94       
>> [5] rms_2.1-0          Hmisc_3.7-0        survival_2.35-6    
>> lattice_0.17-25   
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.12.0
>>
>>
>> Any ideas?
>> Thanks!
>>
>> Dylan
>>
>>
>> -- 
>> Dylan Beaudette
>> Soil Resource Laboratory
>> http://casoilresource.lawr.ucdavis.edu/
>> University of California at Davis
>> 530.754.7341
>>
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>>
>> ______________________________________________
>> 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.
>>
> 
> ______________________________________________
> 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 Chairman        School of Medicine
                      Department of Biostatistics   Vanderbilt University