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

[Göran Broström]

I think I finally got it: I must involve the export business after 
importing, thus, in NAMESPACE:

importFrom(survival,Surv)
export(Surv)

That's all,

G,

On 2020-10-30 19:45, 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.
> 
> Göran
> 
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