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

[Duncan Murdoch]

On 30/10/2020 2:45 p.m., Göran Broström 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.

I don't know if you received any private replies, but I don't see any 
public ones.

It's not clear from your message what you would like to happen with 
expressions like

  f2 <- coxreg(Surv(time, status) ~ age + frailty(inst), data = lung)

For example, would you like to generate an error, because you don't 
support frailty in this context?  Could you clarify that?

Duncan Murdoch