I don't see a big downside, but I will say that there's always a bit
of a tradeoff between "train the users to do it right" (by writing clear
documentation and informative error messages) and "make things easy for
the user" (by making the code more complicated to handle things for them
automatically).
For example, part of me wishes that (1) there were only one way to
provide a response variable for a binomial variable with N>1 (preferably
by specifying proportions and a weights argument) and (2) grouping
variables in lme4/nlme/et al always had to be specified as factors
(rather than automatically being coerced to factors). Making those
decisions would avoid so much code complexity ... (and eliminate one
class of errors, i.e. people including a continuous covariate as a
random-effect grouping variable because they think of 'random effect'
and 'nuisance variable' as synonyms ...)
But taking the "train the users to do it right" path does also
involve more discussion with users ("if your software knows what I
should be doing why can't it just do it for me?")
cheers
Ben Bolker
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.
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@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
thern...@mayo.edu
"TERR-ree THUR-noh"
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Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
> E-mail is sent at my convenience; I don't expect replies outside of
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