Notice that the stats package contains the same issue: For some reason it
defines an offset() function (for no particular reason, afaics) which just
returns its argument. So
> x <- rnorm(10)
> y <- z <- 1:10
> lm(x~y+offset(z))
Call:
lm(formula = x ~ y + offset(z))
Coefficients:
(Intercept) y
0.8253 -1.0840
> lm(x~y+stats::offset(z))
Call:
lm(formula = x ~ y + stats::offset(z))
Coefficients:
(Intercept) y stats::offset(z)
0.82531 -0.08397 NA
So I'm inclined to say that formulas are formulas and functions using formulas
interpret functions and operators at their own convenience. You also deserve
what you get from
> lm(x~base::`+`(y,z))
Call:
lm(formula = x ~ base::`+`(y, z))
Coefficients:
(Intercept) base::`+`(y, z)
0.82531 -0.04198
-pd
> On 24 Feb 2020, at 19:21 , Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
>
> On 24/02/2020 8:55 a.m., Therneau, Terry M., Ph.D. via R-devel wrote:
>> I recently had a long argument wrt the survival package, namely that the
>> following code
>> didn't do what they expected, and so they reported it as a bug
>> survival::coxph( survival::Surv(time, status) ~ age + sex +
>> survival::strata(inst),
>> data=lung)
>> a. The Google R style guide recommends that one put :: everywhere
>> b. This breaks the recognition of cluster as a "special" in the terms
>> function.
>> I've been stubborn and said that their misunderstanding of how formulas work
>> is not my
>> problem. But I'm sure that the issue will come up again, and multiple
>> other packages
>> will break.
>> A big problem is that the code runs, it just gives the wrong answer.
>> Suggestions?
>
> I don't know how widely used survival::strata is versus the special strata
> (or cluster, or other specials). If you were just introducing this now, I'd
> try to make sure that only one of those worked: don't have any functions
> matching the names of specials, or have functions that generate an error if
> you call them. I did that in the much less widely used "tables" package,
> e.g. Heading() has special interpretation, and the Heading function is
> defined as
>
> Heading <- function(name = NULL, override = TRUE,
> character.only = FALSE,
> nearData = TRUE)
> stop("This is a pseudo-function, not meant to be called.")
>
> However, survival has far more users than tables does, so changing the name
> of your special functions or the corresponding regular functions could be a
> huge headache.
>
> Perhaps there's a way to set a flag before evaluating the function in the
> formula, and generate a warning if survival::strata is called when it looks
> like the special function is intended.
>
> Duncan Murdoch
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd....@cbs.dk Priv: pda...@gmail.com
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