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

[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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