[R-sig-ME] Questions about porting pedigreemm to the new lme4

[Ben Bolker]

Joehanes, Roby (NIH/NHLBI) [F] <roby.joehanes at ...> writes:

> 
> Hi all:
> 
> Attached please find the patch to pedigreemm toward using the new lme4 (with
the patch I submitted
> earlier). However, the patch does NOT work with the following error:
> Error in function (value)  : Field "Zt" is read-only
> 
> I believe the error is thrown at this statement:
> lmf$rho$pp$Zt <- relfac[[i]] %*% Zt
> 
> I have no idea how to proceed. Any help is appreciated.
> 
> Thank you,
> Roby

  I will take a look at this as soon as I can.
  Setting components of objects in new-lme4 is tricky because
the objects are defined as reference classes, so that messing
with their internals can disrupt existing objects that they
have been copied from (!!) 

 Abstracting the equivalent of "mer_finalize" is, I think, a good
idea.  Yes, nAGQ=0 is allowed for [NG]LMMs ... the idea being (I think)
that for a well-behaved but very large problem one could save time
by just doing the "zeroth-order" fit (even faster than nAGQ=1,
which corresponds to Laplace approximation)

  Ben Bolker