[R-sig-ME] Fitting a ``trivial'' model with lmer().

[Rolf Turner]

I sent the message, to be found below, to Doug Bates just now.
Since he is flat out preparing a number of workshops, he suggested
that I post to this SIG to see if I could get some enlightenment.

Ergo, here goes:

I wrote (to the general R-help list; 28 July 2008):

	<snip>

>> How can I (is there any way that I can)
>> tell lmer() to fit the most general possible covariance structure?
>>

and Doug Bates responded:


> It sounds like you want a model formula of
>
> lmer(y ~ tstnum + (0 + tstnum|stdnt), data=schooldat)
>
> but that model will have 21 variance-covariance terms to estimate (22
> if you count the residual variance but that one gets profiled out of
> the optimization).  I would not be surprised if the estimated
> variance-covariance matrix for the random effects turns out to be
> singular.
>

I tried the above formulation and it (as I posted yesterday) gives
a warning about a false convergence message from nlminb.  I think
there are indeed singularity problems, or rather problems with a
certain indeterminateness.

I think that the forgoing formulation translates into ``mathematical
expressions'' as

	y_ij = mu + alpha_i + s_j + e_ij

(with treatment ``contrasts'' giving the constraint that alpha_1 = 0)
where alpha_i corresponds to the i-th time, s_j corresponds to the j-th
student, and the e_ij are (Gaussian) errors with mean 0 and a covariance
structure

	Cov(e_ij, e_{i',j'}) = 0 if j != j'
			     = gamma_{i,i'} if j = j'

Translated into my ``trivial model'' thinking, this can be expressed as

	Y_j = MU + s_j + E_j

where the Y_j and E_j are 6-dimensional vectors and the addition in the
forgoing follows the S/R convention whereby the scalar s_j is added to
each component of the vectors.  And of course MU is the 6 dimensional
vector of mean values.

The vectors Y_j are independent N(MU,Sigma) where Sigma = Gamma +  
sigma^2
where Gamma = [gamma_ij] and sigma^2 is the variance of the  
(independent,
mean 0) s_j.  I believe that sigma^2 is the residual variance in the
lmer() formulation of the model.

The covariance matrix Sigma is well-determined/estimable but Gamma  
and sigma^2
are not --- we can ``sensibly'' have Gamma = Sigma - sigma^2 for any  
value
of sigma^2 such that Sigma - sigma^2 is positive definite. In general  
there
will be a wide range of such values of sigma^2.

It seems to me that the s_j are redundant in the model; we just need:

	y_ij = mu + alpha_i + e_ij

Is there a way to formulate the foregoing model in lmer()?  Effectively,
from one p.o.v., one wants to constrain the sigma^2 variance  
component to
be 0.

Of course one doesn't need lmer() to fit such a model.  I just want to
get some understanding of the modelling syntax in lmer() and perhaps
be able to fit more complicated models which are related to the  
foregoing
``trivial'' one.

Thanks.

	cheers,

		Rolf Turner

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