[Rd] specials and ::

[Duncan Murdoch]

On 2024-08-27 9:43 a.m., Therneau, Terry M., Ph.D. via R-devel wrote:
> You are right of course, Peter, but I can see where some will get confused.   In a formula
> some symbols and functions are special operators, and others are simple functions.   That
> is the reason one needs I(events/time) to put a rate in as a variable.    Someone who
> types 'offset' at the command line will see that there actually IS a function behind the
> scenes.
> 
> Does anyone see a downside to Bill Dunlap's suggestion where the first step of my formula
> processing would be to "clean off" any survival:: modifiers?    That is, something that
> will break? After all, the code already has a lot of  "if (....) "  lines for other common
> user errors.   I could view it as just saving me the time to deal with the 'we found an
> error' emails.   I would output the corrected version as the "call" component.

I don't know if you have any data vectors that someone might use in a 
fit, but conceivably

   survdiff( Surv(time, status) ~ survival::datavector +
             strata(inst),  data=lung)

would mean something different than

   survdiff( Surv(time, status) ~ datavector +
             strata(inst),  data=lung)

if a user had a vector named datavector.

Duncan Murdoch

> 
> Terry
> 
> On 8/27/24 03:38, peter dalgaard wrote:
>> In my view, that's just plain wrong, because strata() is not a function but a special operator in a model formula. Wouldn't it also blow up on stats::offset()?
>>
>> Oh, yes it would:
>>
>>> lm(y~x+offset(z))
>> Call:
>> lm(formula = y ~ x + offset(z))
>>
>> Coefficients:
>> (Intercept)            x
>>        0.7350       0.0719
>>
>>> lm(y~x+stats::offset(z))
>> Call:
>> lm(formula = y ~ x + stats::offset(z))
>>
>> Coefficients:
>>        (Intercept)                 x  stats::offset(z)
>>             0.6457            0.1078            0.8521
>>
>>
>> Or, to be facetious:
>>
>>> lm(y~base::"+"(x,z))
>> Call:
>> lm(formula = y ~ base::"+"(x, z))
>>
>> Coefficients:
>>       (Intercept)  base::"+"(x, z)
>>            0.4516           0.4383
>>
>>
>>
>> -pd
>>
>>> On 26 Aug 2024, at 16:42 , Therneau, Terry M., Ph.D. via R-devel<r-devel using r-project.org>  wrote:
>>>
>>> The survival package makes significant use of the "specials" argument of terms(), before
>>> calling model.frame; it is part of nearly every modeling function. The reason is that
>>> strata argments simply have to be handled differently than other things on the right hand
>>> side. Likewise for tt() and cluster(), though those are much less frequent.
>>>
>>> I now get "bug reports" from the growing segment that believes one should put
>>> packagename:: in front of every single instance.   For instance
>>>         fit <- survival::survdiff( survival::Surv(time, status) ~ ph.karno +
>>> survival::strata(inst),  data= survival::lung)
>>>
>>> This fails to give the correct answer because it fools terms(formula, specials=
>>> "strata").    I've stood firm in my response of "that's your bug, not mine", but I begin
>>> to believe I am swimming uphill.   One person responded that it was company policy to
>>> qualify everything.
>>>
>>> I don't see an easy way to fix survival, and even if I did it would be a tremendous amout
>>> of work.   What are other's thoughts?
>>>
>>> Terry
>>>
>>>
>>>
>>> -- 
>>>
>>> Terry M Therneau, PhD
>>> Department of Quantitative Health Sciences
>>> Mayo Clinic
>>> therneau using mayo.edu
>>>
>>> "TERR-ree THUR-noh"
>>>
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>>>
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