Thank you for the clarification. I will look into mkReTrms's code
implementation more.

On Sat, Mar 16, 2013 at 2:58 AM, Ben Bolker <bbolker@gmail.com> wrote:

> Pantelis Hadjipantelis <kalakouentin@...> writes:
>
> >
> > Hello,
> >
> > I am going through lme4's book chapters and among the things that are
> > slightly in disparity with the current state of things is the structure
> of
> > Zt. Namely in chapter 3, section 2, Fig 3.4 presents the images of the
> Z^T
> > matrices for the models:
> > (fm06 <- lmer(Reaction ~ 1 + Days + (1 + Days|Subject), sleepstudy,
> > REML=FALSE)); image(fm06 <at> Zt)
> > (fm07 <- lmer(Reaction ~ 1 + Days + (1|Subject) + (0+Days|Subject),
> > sleepstudy, REML=FALSE)); image(fm07 <at> Zt)
> > and while in the book they appear different now they appear the same.
> > I understand that the "important bit" is the L matrix that does remain
> > "unchanged" but getting a different Z matrix than before does seem odd.
> > What is the reason of this change in the generation of Z and Î› from the
> > random-effects terms?
>
>   There have been several major changes in the internal structures
> of the lme4 package in the last couple of years. The structure
> of Z has simply changed as a side effect. In fact, the
> development version of lme4 has reverted to a behaviour more like
> the version from 2010, where (x|grp) and (1|grp)+(0+x|grp) give
> differently structured Z matrices.
>
> > If lme4 book is not the most update to date reference about the
> generation
> > of Z in lme4, what resource is?
>
>    Unfortunately, the code -- specifically the lme4:::mkReTrms function.
> But you should feel free to keep asking questions here.
>
>
> > Just to clarifty I am using: MEMSS_0.9-0, lme4_0.999999-0, Matrix_1.0-11.
> > lme4's book version is that of June 25, 2010.
> >
> > Thank you in advance.
> >
> > All best,
> > Pantelis Hadjipantelis
>
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