I got good feedback from the list about a scope issue, so I am coming back for
more.
Prior issue: users who type survival::coxph(survival::Surv(time, status) ~ x1
+ x2 + surv ival::strata(group), data=mydata)
This messes up the character string matching for strata, done via tt <-
terms(formula, specials= �strata�). The code runs, and gives the wrong answer
(group is treated as an ordinary covariate).
The solution
1. Add code very early that rewrites the formula without the offendinge
survival:: string
2. Before calling model.frame(), insert my copy of strata into the calling
chain
coxenv <- new.env(parent= environment(formula))
assign("strata", survival::strata, envir= coxenv)
environment(formula) <- coxenv
The second part of this deals with those who want to use survival functions but
not use library(survival).
Now to the question.
I had always (naively) assumed that the Surv(), strata(), etc calls within a
coxph formula would be resolved first within the survival namespace. I realize
now that this is not true: they get resoloved within model.frame. If a user
has their own Surv, it will get used.
For ultimate safety, I am thinking of extending the above to all of the
internal survival functions that might be used in a formula: Surv, strata,
pspline, cluster, ratetable (I think that�s all). An intitial limited test
looks okay, but before anything migrates to CRAN I am looking for any feedback.
The current test version also prints a warning when removing the extraneous
�survival::� modifier, which I will retain for at least a little while although
I personally detest receiving such messages.
Terry T.
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