[Rd] specials and ::

[Therneau, Terry M., Ph.D.]

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.

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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