[R] How to set starting values for lmer?

[Douglas Bates]

On 8/30/05, Shige Song <shigesong at gmail.com> wrote:
> Dear All,
> 
> Can anyone give me some hints about how to set starting values for a lmer
> model? For complicated models like this, good starting values can help the
> numerical computation and make the model converge faster. Thanks!
> 
> Shige

I agree but I haven't gotten around to designing how that could be
done.  It could be easy or difficult depending on how you want to
represent the starting values.

If you look at the (only) lmer method function you will see that it
has a section

          if (lmm) {                    ## linear mixed model
              .Call("lmer_initial", mer, PACKAGE="Matrix")
              .Call("lmer_ECMEsteps", mer, cv$niterEM, cv$EMverbose,
PACKAGE = "Matrix")
              LMEoptimize(mer) <- cv

for linear mixed models.  The object "mer" is a mixed-effects
representation and the list "cv" is the control values.  The only
thing that the C function "lmer_initial" does is set the initial
values of the relative precision matrices for the random effects. 
These are the inverses of the variance-covariance matrices relative to
the variance of the per-observation noise term.  They are stored
(upper triangle only) in a slot called "Omega" of the mer class (which
is contained in the lmer class).

There is no purpose in setting initial values for the fixed-effects
parameters or the variance of the per-observation noise term because
these are profiled out of the optimization.  The optimization is only
over the values in the Omega slot.

I can allow those values to be set from an argument and only call
"lmer_initialize" if that argument is missing.  Will that be
sufficient for you?