[R-sig-ME] PBmodcomp: pwrssUpdate does not converge with glmer

[Ben Bolker]

I'm not 100% sure, but a lot of this (at least the lme4 end, not
necessarily the pbkrtest end) sounds like the now-resolved (in the
development, soon-to-be-released version 1.1-8) issue
https://github.com/lme4/lme4/issues/231 .

On Wed, Jun 10, 2015 at 6:35 AM,  <lorenz.gygax at agroscope.admin.ch> wrote:
> Dear all,
>
> In a current project (2 x 2 x 2 factorial design) we are interested in
> calculating p-values for binary outcomes (we are aware that such an approach
> is not unequivocal but circumstances are such that results will most easily
> be communicated when we can conduct step-wise backwards model selection and
> when we have the p-values).
>
> The experimental design was hierarchically nested (350 observations
> conducted in 178 phases of the experiment nested in 90 animal-IDs nested in
> 24 facilities). The three factors can and should be assigned to three
> different hierarchical levels (error, phase, facility).
>
> Even though the data does not look in any way extreme (zeros and ones occur
> in all 8 factor combinations), there are some convergence issues with
> running the models. These can be mostly dealt with by using: glmerControl
> (optimizer= 'bobyqa', optCtrl= list (maxfun= 5000)).
>
> Due to sample size and the assignment of the fixed effects to the different
> hierarchical levels, we would like to use parametric bootstrap for
> calculating the p-values as implemented in package pbkrtest (very nice!).
>
> Obviously throughout calculating the bootstrap, some of the models will not
> converge. As far as I can see, the bootstrap sample is simply accordingly
> reduced. Some models, unfortunately, do not result in a warning but in an
> error: "pwrssUpdate did not converge in (maxit) iterations with PBmodcomp".
>
> These errors cause PBmodcomp to fail. Does anyone know whether there is a
> reason why PBmodcomp reacts differently to warnings and erros in the
> bootstrapped glmer's? Or has this just historically grown that the warnings
> are captured but the errors are not? If the latter could catching errors be
> easily incorporated as well? Where would that need to be done? I cannot find
> the according code neither in pbkrtest::PBmodcomp.merMod nor in
> pbkrtest::PBrefdist.merMod.
>
> Many thanks for your ideas and best regards, Lorenz
> -
> Lorenz Gygax, PD Dr. sc. nat.
> Federal Food Safety and Veterinary Office FFSVO
> Centre for Proper Housing of Ruminants and Pigs
>
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