[Rd] specials and ::

[Bill Dunlap]

removeDoubleColonSurvival (or 'f', as it was shown in the example) could be
changed to only remove the 'survival::' from expressions that involve the
names to be used in specials.  E.g., change

if (is.call(expr) && identical(expr[[1]], doubleColon) &&
identical(expr[[2]], survival))

to
specialNames <- c("strata", "whatever")
...
if (is.call(expr)
    && identical(expr[[1]], doubleColon)
    && identical(expr[[2]], survival)
    && is.name(expr[[3]]) && is.element(as.character(expr[[3]]),
specialNames))

-Bill

On Tue, Aug 27, 2024 at 7:01 AM Duncan Murdoch <murdoch.duncan using gmail.com>
wrote:

> 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"
> >>>
> >>>     [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> R-devel using r-project.org  mailing list
> >>>
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-devel&data=05%7C02%7Ctherneau%40mayo.edu%7C7659a5f0f0d34746966a08dcc6739fed%7Ca25fff9c3f634fb29a8ad9bdd0321f9a%7C0%7C0%7C638603447151664511%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=UAkeksswfFdLwOdzQIOXUPC2Ey255oW%2FX41kptNZNcU%3D&reserved=0
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

	[[alternative HTML version deleted]]