Peter,
I had an argument with someone at one of the big companies (google?)
several years ago
over the coding standard you mention, who was claiming that the survival
package had a bug
due to a wrong result using survival::strata() in a formula. I argued back.
I agree with you that namespacing specials is a bad idea. But I'm afraid that
the
mistake with specials happens much more often than I'd like. I find examples
in the
reverse dependencies for survival of 3 different errors, all of which give code
that runs
without an error message, but with the wrong result. Since I have a strong
interest in
correct results from medical research, I've tried to think about ways to
protest the user
from themselves. The errors are
a. using survival::strata(group) in a formula. This is not recognized as
a special.
b. the package had zed <- strata(group), then used +zed in multiple
formulas.
c. formula was preprocessed (I don't remember the detail exactly here,
and I expect
this is rare)
In all three cases the final fit was the same as if they used factor(group). I
expect
that (a) and (b) are quite prevalent in user code, the second due to all the
tutorials
that like to create a new variable zed <- Surv(time, status) and then use 'zed'
in the
formulas, people will do the same with strata. (I don't like this approach
in general;
you've saved a tiny bit of typing to create fits that are less clearly
documented.)
When reading one of my colleagues grants, before submission, I often try to
actively try
to put on a "pretend I don't know this topic deeply" persona, so as to note
passages where
other readers might go wrong, e.g., completely misunderstand a sentence. I'm
trying to
think about specials with a bit of that bias as well, when might a naive but
well meaning
user go wrong? Is there something fairly simple I could do in the package
coding to
avert it? I'm thinking that the only solution to (b) above will be to have
strata
return a classed object and key on the class rather depend on specials. It
will be a
lot of busywork to implement though.
I have no particular votes for against the proposed change: I have a general
opinion that
those who insist on using non-syntactic names have fallen into a pit that they
dug
themselves, and little sympathy for their plight.
Terry T
On 4/15/25 03:17, peter dalgaard wrote:
> I don't seem to have the original post (not in spamfilter either). But
> generically, I think namespacing specials in formulas is just a Bad
> Idea. They are syntactic constructs, specifically_not_
> function calls, so people are stumbling over formally protecting them
> from a non-existing scoping issue, then having to undo that for the
> actual use.
>
> It all came about by someone (I have forgotten the details) having a
> corporate coding standard mandating namespaces on all function calls and
> falling over things like strata() in the survival package. Then package
> author(s) chose to comply rather than explain...
>
> -pd
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