On 2020-10-31 13:49, Duncan Murdoch wrote:
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.
No replies so far.
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?
Yes, this should generate an error. I think I have solved this problem
by using importFrom(survival, ...), where I replace ... with all the
functions I want from survival (not including frailty, cluster, ...)
and then export some of them. For now I have in NAMESPACE
importFrom(survival,Surv)
importFrom(survival,attrassign)
importFrom(survival,coxph)
importFrom(survival,strata)
importFrom(survival,untangle.specials)
...
export(Surv)
export(strata)
I also have to write documentation for Surv and strata.
Is this reasonable?
Göran
Duncan Murdoch
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