[Rd] How to deal with package conflicts
therneau at mayo.edu
Fri Nov 25 17:08:26 CET 2011
On Fri, 2011-11-25 at 10:42 -0500, Michael Friendly wrote:
> Duncan provided one suggestion: make ridge() an S3 generic, and
> rename ridge()
> to ridge.coxph(), but this won't work, since you use ridge() inside
> coxph() and survreg() to add a penalty term in the model formula.
> Another idea might be simply to not export ridge(), but I have the
> feeling this will break your R CMD checks.
The S3 generic idea won't work. The argument inside ridge(x) is an
ordinary variable, and it's the argument inside that a generic uses for
dispatch. I want to dispatch based on the context, which is what the
namespace mechanism does for a call to for instance coxpenal.fit, a non
exported survival function.
I suspect that not exporting ridge would work for
coxph(Surv(time, status) ~ ph.ecog + ridge(age), data=lung)
but not for
myform <-Surv(time, status) ~ ph.ecog + ridge(age)
(I haven't test this) This is because formulas are treated rather like
functions, with bindings coming into play when they are first defined,
not when they are first used.
> Alternatively, my particular problem (wanting to use car::vif in my
> package documentation) would
> be solved if John Fox considered making making survival a Suggests:
> package rather than a
> Depends: one. This might work, since survival is only referenced in
> by providing Anova()
> methods for coxph models.
> I think all of this raises a general issue of unintended consequences
> "package bloat," where
> (a) Depends: packages are forced to load by require()/library(),
> they are really needed or not;
> (b) There is nothing like require(car, depends=FALSE) to circumvent
> (c) Once a require()'d package is loaded, it cannot be unloaded;
> (d) AFAIK, there is no way for a package author to override the
> of functions or data
> provided by other other packages, except by using mypackage::myfun()
> To me this seems to be a flaw in the namespace mechanism.
I will say that the long list of "reverse depends" on the survival
package does give me pause when making changes.
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