The performance issue you're referring to is I think related to
https://github.com/lme4/lme4/issues/150 ... we're hoping to look into this
soon; it is definitely important, and we're afraid it's pretty deep.


On Tue, Feb 18, 2014 at 2:55 PM, Joehanes, Roby (NIH/NHLBI) [F] <
roby.joehanes@nih.gov> wrote:

> Hi David:
>
> Thank you! I finally got a chance to see the fix. Apparently, it is in the
> reflector method. The line:
>     rect <- Diagonal(x = sqrt(Dmat(ped))) %*%
>         solve(t(as(ped, "sparseMatrix")), # rectangular factor
>               as(factor(labs, levels = ped@label),"sparseMatrix"))
>
> is changed to:
>     rect <- Diagonal(x = sqrt(Dmat(ped))) %*%
>         solve(t(as(ped, "sparseMatrix")), # rectangular factor
>               Matrix:::fac2sparse(factor(labs, levels = ped@label), drop =
> FALSE))
>
> I just ran the first example that the author (Dr. Vazquez) provided in her
> paper:
>
>
>
> milk <- within(milk, sdMilk <- milk / sd(milk))fm1 <- pedigreemm(sdMilk ~
> lact + log(dim) + (1|id) + (1|herd), data = milk, pedigree = list(id =
> pedCowsR))
>
>
>
> However, for some reason, pedigreemm takes an inordinately long time (274
> seconds) to finish, as opposed to 53 seconds before. This is not an
> optimizer issue since I am facing the same thing with bobyqa (as opposed
> to Nelder_Mead), albeit a lot faster (136 seconds). This leads me to think
> that the bug might be deeper than it looks. The numbers are almost
> identical to the previous version, though. Could it be a convergence issue?
> Oh, another thing: I think Dr. Vazquez should lose the
> optimizer="Nelder_Mead" option in the optimizeLmer and let the user
> choose. Attached please find the patch-style changes. I combined her
> changes and mine.
>
> Thanks!
>
> Sincerely,
> Roby
>
>
>
>
>
>
>
> On 2/15/14 3:12 AM, "David Duffy" <David.Duffy@qimr.edu.au> wrote:
>
> >I have corresponded with one of the maintainers, Ana Vasquez, and
> >suggested a fix (see the attached), which seems to do the trick.  I
> >imagine something like this will be released soon enough, but if you need
> >it right away...
> >
> >Cheers, David Duffy.
> >
> >| David Duffy (MBBS PhD)
> >| email: David.Duffy@qimrberghofer.edu.au  ph: INT+61+7+3362-0217 fax:
> >-0101
> >| Genetic Epidemiology, QIMR Berghofer Institute of Medical Research
> >| 300 Herston Rd, Brisbane, Queensland 4006, Australia  GPG 4D0B994A
>
>

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