[R-sig-ME] extractor function for coefficient table fromsummary.mer ?

[David Duffy]

On Wed, 17 Jun 2009, Douglas Bates wrote:

> On Tue, Jun 2, 2009 at 10:05 PM, David Duffy<David.Duffy at qimr.edu.au> wrote:
>> On Tue, 2 Jun 2009, Ben Bolker wrote:
>
>>>  Request for comment: would it be reasonable to have the
>>> "coef" method for "summary.mer" objects return the table
>>> of parameter values, standard errors etc.?
>
>> Yes please, oh and a profile likelihood based confint.lmer() too,
>> thanks ;).
>
> I have been thinking about this recently and I have a way of
> constructing a profile likelihood for the variance component
> parameters.  Are those the parameters that are of interest or are you
> more interested in the fixed-effects parameters?
>

Yes, the variance components are of direct interest.

> Yet somehow the variability in estimates of variance components in
> much more complicated models can be expressed by quoting a standard
> error.
>

Yes, we usually try and produce appropriate confidence intervals and/or 
interpretable likelihood based test statistics.  The latter, of course, 
are tricky mixtures for multivariate hypotheses -- a typical one for us is 
a variance components linkage analysis test that the common component due 
a particular genome region is zero for three measures (repeated at 3 
occasions, but with differing contributions by occasion).  People still 
want a P-value, so they can carry out adjustment for genome-wide testing 
(linkage is supposed to be roughly equivalent to 50-60 tests for a human 
length genome, but the genome-wide corrected 5% P-value is usually quoted 
as 2e-5).

Cheers, David Duffy.
-- 
| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v