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

[Göran Broström]

Thanks!

Göran

On 2020-11-02 11:09, Sebastian Meyer wrote:
> No need to reinvent the wheel. Göran, you already use the "specials"
> feature of terms.formula to find strata():
> 
>> specials: which functions in the formula should be marked as special in
>>            the 'terms' object?  A character vector or 'NULL'.
> 
> I think you can do the same for frailty(), for example:
> 
>> formula <- Surv(time, status) ~ age + frailty(inst)
>>
>> Terms <- terms(formula, specials = "frailty")
>> frailties <- attr(Terms, "specials")$frailty
>> if (length(frailties)) warning("frailty() is not supported by coxreg")
> 
> 
> Best regards,
> 
> 	Sebastian
> 
> 
> Am 31.10.20 um 14:30 schrieb 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
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>>
>>
> 
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