[Rd] specials and ::

[Duncan Murdoch]

On 2024-08-26 10:42 a.m., Therneau, Terry M., Ph.D. via R-devel 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?

I received a similar complaint about the tables package, which had 
assumed during argument processing that it was on the search list in 
order to find a function (see 
https://github.com/dmurdoch/tables/issues/30 if you want the details). 
In my case there's only one function exported by tables that wasn't 
being found, "labelSubset".

I don't know any of the details of the survival problems.  When I try 
your example code above without attaching survival, it appears to work. 
So my solution might be irrelevant to you.

The way I found to work around this was to use this code early in the 
processing, when it is trying to turn the data argument into an environment:

     parent <- if (is.environment(data)) data else environment(table)
     if (!exists("labelSubset", envir = parent)) {
       withTableFns <- new.env(parent = parent)
       withTableFns$labelSubset <- labelSubset
     } else
       withTableFns <- parent

     if (is.null(data))
     	data <- withTableFns
     else if (is.list(data))
     	data <- list2env(data, parent = withTableFns)
     else if (!is.environment(data))
     	stop("'data' must be a dataframe, list or environment")
     	
This inserts a new environment containing just that one tables function.

One issue is if a user has "labelSubset" already in the environment; I 
decided to use that one on the assumption that the user did it 
intentionally.  It would have been better to use a name that was less 
likely to show up in another package, but it's old code.

This isn't on CRAN yet, so I'd be interested in hearing about problems 
with this approach, or better solutions.

Duncan Murdoch