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

[Göran Broström]

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