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

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

Hi Ben and Andrzej:

Thank you for the info. I am trying to get pedigreemm to work with the new lme4 and I am now stuck on how to translate the following line:
lmf$FL$trms[[tn]]$Zt <- lmf$FL$trms[[tn]]$A <- relfac[[i]] %*% Zt

Because the matrix A is defined in getME method as:
PR$Lambdat %*% PR$Zt

I am still trying to figure the code out. I think we can do away with the A matrix since it is apparently not essential to the computation. I think the crux of the pedigreemm call to the underlying lme4 is in the following short lines:

    pnms <- names(pedigree)
    stopifnot(all(pnms %in% names(getME(lmf, "flist"))))
    asgn <- attr(getME(lmf, "flist"), "assign")
    for (i in seq_along(pedigree)) {
        tn <- which(match(pnms[i], names(getME(lmf, "flist"))) == asgn)
        if (length(tn) > 1)
            stop("a pedigree factor must be associated with only one r.e. term")
        Zt <- getME(lmf, "Zt")
        relfac[[i]] <- relfactor(pedigree[[i]], rownames(Zt))
        lmf$FL$trms[[tn]]$Zt <- lmf$FL$trms[[tn]]$A <- relfac[[i]] %*% Zt
    }
    ans <- do.call(if (!is.null(lmf$glmFit)) lme4:::glmer_finalize else lme4:::lmer_finalize, lmf)
    ans <- new("pedigreemm", relfac = relfac, ans)

Any help is appreciated.

Thanks,
Roby


On Apr 2, 2012, at 4:17 PM, Ben Bolker wrote:

Andrzej T Galecki 1 <agalecki at ...> writes:

Ben prepared getME(} function to extract various components of the model
fit
obtained using lme4.0 and new lme4.

Try
getME(lmf,"Zt")
getME(lmf,"A")
getME(lmf,"flist")

Andrzej

On Mon, 2 Apr 2012 14:27:20 -0400, "Joehanes, Roby (NIH/NHLBI) [F]"
<roby.joehanes at ...> wrote:
Hi:

I am trying to port pedigreemm to use the new lme4. However, the new lme4
is somewhat opaque to me and hence I need help. Specifically, how can I
extract the following terms:
lmf$FL$trms[[tn]]$Zt
lmf$FL$trms[[tn]]$A

The information lies within lmf <at> pp object, but it is too opaque to me to
fish anything out.

I understand that lmf$FL$fl is lmf <at> flist and that lmer_finalize calls
should be replaced with optwrap and mkMerMod. Nevertheless, I think that
the lmer or glmer could use some refactoring to ease the calls.

I appreciate any help on these.


  A couple of questions:

1. how broadly are you using A?  Off-list, Doug Bates has commented to
me that defining A is relatively straightforward for LMMs but not necessarily
as simple (nor uniquely defined!) for [GN]LMMs -- for the time being, I
am quite likely to add code that *disallows* getME(.,"A") except for LMMs --
I can imagine that the bulk of pedigreemm use is for LMMs, but I suppose
that people are using it for [GN]LMMs as welll ...

 2. I can't quite tell from your e-mail -- would it be useful to have
the stuff between the first optwrap() and the last mkMerMod abstracted
into a single (exposed) function?  For [GN]LMMs it should probably
also allow control of whether the preliminary "nAGQ=0" optimization
is done or not ...

 (All comments are mine alone, not necessarily speaking for all lme4
authors ...)

 Ben Bolker