nlme: bug in getCovariateFormula (PR#1038)

It looks clunky, but you could maintain consistency across S and R forms
with

eval(parse(text=paste("~",paste(deparse(form),collapse=" "))))


R. Woodrow Setzer, Jr.                                            Phone:
(919) 541-0128
Experimental Toxicology Division                       Fax:  (919) 541-5394
Pharmacokinetics Branch
NHEERL MD-74; US EPA; RTP, NC 27711


                                                                                                                
                    Douglas Bates                                                                               
                    <bates@stat.wis        To:     Peter Dalgaard BSA <p.dalgaard@biostat.ku.dk>                
                    c.edu>                 cc:     Woodrow Setzer/RTP/USEPA/US@EPA, r-devel@stat.math.ethz.ch,  
                    Sent by:               R-bugs@biostat.ku.dk                                                 
                    bates@franz.sta        Subject:     Re: [Rd] nlme: bug in getCovariateFormula (PR#1038)     
                    t.wisc.edu                                                                                  
                                                                                                                
                                                                                                                
                    07/31/01 02:55                                                                              
                    PM                                                                                          
                                                                                                                
                                                                                                                




Peter Dalgaard BSA <p.dalgaard@biostat.ku.dk> writes:

Setzer.Woodrow@epamail.epa.gov writes:

The final line in getCovariateFormula() in the nlme package (version
3.1-16) is:
    eval(parse(text = paste("~", deparse(form))))

however, if deparse(form) exceeds 'width.cutoff (which defaults to

60)',

this results in inappropriately placed "~" signs:
For example, in my application with the error, form is

UnCompetitive(MethoxyresorufinConc, InhibitorConc, Vmax, Km, Ki)

the result of the paste() operation in the last line of

getCovariateFormula

is:

paste("~",deparse(form))

[1] "~ UnCompetitive(MethoxyresorufinConc, InhibitorConc, Vmax, Km, "
[2] "~     Ki)"

extending width.cutoff gives the intended value:

paste("~",deparse(form,width.cutoff=500))

[1] "~ UnCompetitive(MethoxyresorufinConc, InhibitorConc, Vmax, Km,

Ki)"

Seems a bit risky for an enforced cutoff in deparse, though.

parse(...deparse(...)) always looks wrong to me anyway. Couldn't one
use something like

f <- ~1
f[[2]] <- form
eval(f)

or

eval(as.call(list(as.name("~"),form)))

or

eval(substitute(~form)) # that's not going to work in S, though...

Exactly.  The code was originally written for S and ported to R.  Some
of the contorted expressions were things that we found by
experimentation would work in both systems.

??

(What is the eval for? Doesn't usually do anything to a
formula argument.)

In Sv3 at least it assigns a class to the object.

I'll change it to eval(substitute(~form)) for the R package.





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