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

[Göran Broström]

On 2020-10-31 12:09, Göran Broström wrote:
> 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,

Not really:

* checking for missing documentation entries ... WARNING
Undocumented code objects:
   ‘Surv’ ‘coxph’ ‘strata’
All user-level objects in a package should have documentation entries.

> 
> 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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