On 2024-08-26 12:34 p.m., Duncan Murdoch wrote:
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")
Of course, posting this meant I discovered a bug in it: if
is.environment(data) was TRUE, the modification was ignored. Line 8
should be
if (is.null(data) || is.environment(data))
to handle that case.
Duncan Murdoch
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
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