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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