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

[Joehanes, Roby (NIH/NHLBI) [F]]

Hi Ben:

I am wondering I should work more on the mer_finalize abstraction. I would like the official stream to accept my patches toward getting pedigreemm to work with the new lme4.

Also, is there anything I can help with fixing the broken pedigreemm examples? Even simple calls to glmer no longer work.

Thank you,
Roby

On Apr 3, 2012, at 6:52 PM, Ben Bolker wrote:

> 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