[Rd] Namespace/method oddity

[Prof Brian Ripley]

On Tue, 12 Feb 2008, Peter Dalgaard wrote:

> I stumbled on the following:
>
>> library(stats4)
>> example(mle)
>> confint.default(fit2)
> Error in UseMethod("vcov") : no applicable method for "vcov"
> In addition: Warning message:
> In object$coefficients :
>  $ operator not defined for this S4 class, returning NULL
>> vcov(fit2)
>             lymax      lxhalf
> lymax   0.02857612 -0.04870231
> lxhalf -0.04870231  0.11457338
>> coef(fit2)
>   lymax   lxhalf
> 3.218870 1.117006
>
>
> And confint.default does indeed use the generic extractors vcov() and
> coef().
> Q: is this to be expected? and why? (I kind of suspect that this has in
> fact been discussed at some point and that I just wasn't paying
> attention...)

Yes.  stats4 contains an object called vcov.  confint.default is in the 
stats namespace and correctly uses stats::vcov not stats4::vcov, which is 
what you were looking for.

It's discussed most weeks, and at R-core in Vienna in 2006 and before 
that.  It is 'issue' 11 in http://developer.r-project.org/BDR_S4issues.txt

Brian


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
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