R devel - Feb 2008 - Namespace/method oddity

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...)

-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

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)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595