[R-sig-ME] addressing singularity in lme4 fits caused by subsets of contrasts

Phillip Alday me @end|ng |rom ph||||p@|d@y@com
Fri Jan 22 00:52:22 CET 2021

I agree with Ben here.

This is actually one of the things I'm working on in my rather limited
free time. I also suspect that it will generally give an equivalent
model BUT there are a few possible ways it might not:

1. You may have more power (and thus less variability in your estimates
and errors) because you have fewer parameters to estimate. This is
vaguely similar to some of the work in Matuscheck et al. 2017 on
controlling Type-I and complexity in mixed models. (a sort of spin-off
project of the Bates et al. Parsimonious Mixed Models)

2. Weird things happen at the boundary. One of the things that keeps
getting rediscovered is that singular fits are a strange attractor. This
is why the machinery for MCMC-based p-values in early lme4 ultimately
didn't work and this is something we've seen in MixedModels.jl in our
work on the parametric bootstrap -- bootstrapped estimates of the random
effects often look like a point mass around 0 mixed with a normal
distribution centered elsewhere. If you remove this one strange
attractor, it may allow some of the other slopes to move a bit
(especially if your correlation structure wasn't constrained to zero
previously). I expect they won't move much, but they might.

@Ben I've seen an example of this when using rePCA. Occasionally
estimates of the effective dimensionality of the RE change dramatically
just by adding or removing a single contrast and associated correlation
parameters. I wish I had had the good sense to save that example ...


On 21/1/21 11:01 pm, Ben Bolker wrote:
>   This is an interesting question ("interesting" means among other
> things "I don't know").
>   If you get a variance estimate of zero for the second contrast then
> removing that term from the model should (I think) give you **exactly
> the same** model results (as an analogy: suppose you had the mean model
> y = a +b*x+c*z and for some reason got an estimate of c=0, then you said
> "can I drop z from the model?")
>   More generally, in order to know whether this is OK you have to define
> what "OK" means.  Trying to avoid philosophical or subjective
> statements, you could ask whether following this process gives 'good'
> results (unbiased and/or low-error estimates and good coverage of
> whichever set of parameters you're interested in). In particular, if
> you're interested in inference on fixed effects only, then I'd say you
> can do anything to the random effects component of the model as long as
> it doesn't mess up your estimation and inference on the fixed effects.
>   You could try some simulations to test your idea (note that your
> conclusions can only be for the range of parameters you've actually
> simulated: in particular Bates et al 2015 criticize the realism of the
> simulations from Barr et al 2013 "keep it maximal":
> "First, the simulations implement a factorial contrast that is
> atypically large compared to what is found in natural data.  Second, and
> more importantly, the correlations in the random effects structure range
> from−0.8 to +0.8.  Such large correlation parameters are indicative of
> overparameterization.They hardly ever represent true correlations in the
> population.  As a consequence, these simulations  do  not  provide  a
> solid  foundation  for  recommendations  about  how  to  fit
> mixed-effects models to empirical data."
> Bates, Douglas, Reinhold Kliegl, Shravan Vasishth, and Harald Baayen.
> “Parsimonious Mixed Models.” ArXiv:1506.04967 [Stat], June 16, 2015.
> http://arxiv.org/abs/1506.04967.
> On 1/21/21 11:54 AM, Nathan Tardiff wrote:
>> I have encountered an issue a couple times recently when fitting
>> models in
>> lme4 that I have not seen addressed in commonly cited papers for
>> dealing w/
>> boundary/singular fit issues.
>> Say I have a categorical variable representing a set of within-subject
>> contrasts, which is entered into the model as a set of effect coded
>> variables, e.g.
>> df$congruent.f <- factor(df$congruent,levels=c(1,0,-1),
>>                              labels=c("congruent","incongruent","none"))
>> contrasts(df$congruent.f) <- contr.sum(3)
>> which will produce two variables in the model (e.g. congruent.f1,
>> congruent.f2). When I fit the model w/ random intercepts and slopes for
>> these contrasts (along w/ other control variables), I get a boundary
>> (singular) fit warning.
>> Examining the correlations and variance components suggests that the
>> primary cause of the warning is in one of these contrast variables (e.g.
>> congruent.f2). So, would it ever be acceptable in this scenario to remove
>> the random effect term ONLY for congruent.f2, not the entire set of
>> congruent.f contrasts, where the goal is statistical inference and I
>> do not
>> want the p-values/confidence intervals for congruent.f1 to be
>> anticonservative when it does in fact show variance across subjects?
>> I have to this point assumed that this would be a bad idea and tried to
>> simplify such models in other ways (i.e. setting correlations to zero or
>> removing other random effects), but this does not always work and seems a
>> roundabout method if you are not dealing with the primary problem.
>> Thanks,
>> Nathan
>>     [[alternative HTML version deleted]]
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