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

Ben Bolker bolker at ufl.edu
Wed Jun 17 23:59:34 CEST 2009

David Duffy wrote:
> 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.

  Fixed effect profiles are interesting too (to me) ... I have written
some of my own code to do this (happy to make it available), but it's
not very general/robust at the moment.

Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc

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