[R-pkg-devel] import with except(ion)

[Sebastian Meyer]

No need to reinvent the wheel. Göran, you already use the "specials"
feature of terms.formula to find strata():

> specials: which functions in the formula should be marked as special in
>           the 'terms' object?  A character vector or 'NULL'.

I think you can do the same for frailty(), for example:

> formula <- Surv(time, status) ~ age + frailty(inst)
> 
> Terms <- terms(formula, specials = "frailty")
> frailties <- attr(Terms, "specials")$frailty
> if (length(frailties)) warning("frailty() is not supported by coxreg")


Best regards,

	Sebastian


Am 31.10.20 um 14:30 schrieb Gabor Grothendieck:
> coxreg could search for frailty and issue a warning or error if found.  This
> returns TRUE if frailty is used in the formula argument as a function but
> not otherwise.  That would allow implementation of a nicer message than
> if it were just reported as a missing function.
> 
> find_frailty <- function(e) {
>     if (is.logical(e)) return(e)
>     if (length(e) > 1) {
>         if (identical(e[[1]], as.name("frailty"))) return(TRUE)
>         for (i in 1:length(e)) if (isTRUE(Recall(e[[i]]))) return(TRUE)
>     }
>     FALSE
> }
> find_frailty(frailty ~ frailty)
> ## [1] FALSE
> fo <- Surv(time, status) ~ age + frailty(inst)
> find_frailty(fo)
> ## [1] TRUE
> 
> On Fri, Oct 30, 2020 at 2:46 PM Göran Broström <goran.brostrom using umu.se> wrote:
>>
>> My CRAN package eha depends on the survival package, and that creates
>> problems with innocent users: It is about the 'frailty' function
>> (mainly). While (after 'library(eha)')
>>
>> f1 <- coxph(Surv(time, status) ~ age + frailty(inst), data = lung)
>>
>> produces what you would expect (a frailty survival analysis), the use of
>> the coxreg function from eha
>>
>> f2 <- coxreg(Surv(time, status) ~ age + frailty(inst), data = lung)
>>
>> produces (almost) nonsense. That's because the survival::frailty
>> function essentially returns its input and coxreg is happy with that,
>> treats it as an ordinary numeric (or factor) covariate, and nonsense is
>> produced, but some users think otherwise. (Maybe it would be better to
>> introduce frailty in a separate argument?)
>>
>> I want to prevent this to happen, but I do not understand how to do it
>> in the best way. I tried to move survival from Depends: to Imports: and
>> adding import(survival, except = c(frailty, cluster)) to NAMESPACE. This
>> had the side effect that a user must qualify the Surv function by
>> survival::Surv, not satisfactory (similarly for other popular functions
>> in survival).
>>
>> Another option I thought of was to define my own Surv function as
>> Surv <- survival::Surv in my package, but it doesn't feel right.
>> It seems to work, though.
>>
>> As you may understand from this, I am not very familiar with these
>> issues. I have used Depends: survival for a long time and been happy
>> with that.
>>
>> Any help on this is highly appreciated.
>>
>> Göran
>>
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> 
> 
>