[R-sig-ME] singularity - differences in model output

[Ben Bolker]

  This new warning could be due either to changes in reporting or to
slight changes in the optimization defaults. The NEWS file (run
news(package="lme4") from inside R, or see
<https://github.com/lme4/lme4/blob/master/inst/NEWS.Rd>) tells you
what's changed, and when, in the package.

  In the CRAN version (1.1-21) the default tolerances for the
singularity check are *either* 1e-5 (isSingular) or 1e-4 (in the
built-in check); both change to 1e-4 in the development version (see
https://github.com/lme4/lme4/commit/87caef382a784df322cd1f5b3a4b906ffe950cf9
). In principle singular fits only occur when the estimated variance
is *exactly* zero, which is possible in lme4 (because it uses a
box-constrained optimizer with a bound at zero), but checking with a
tolerance of 1e-4 should also identify models that are very close to
singular (and might "really" be singular if there were no numeric
'fuzz' from finite-precision computation).

  The GLMM FAQ has more discussion of singular fits:
http://bbolker.github.io/mixedmodels-misc/glmmFAQ.html#singular-models-random-effect-variances-estimated-as-zero-or-correlations-estimated-as---1

  cheers
   Ben Bolker


On Thu, Jun 13, 2019 at 3:17 AM Alessandra Bielli
<bielli.alessandra using gmail.com> wrote:
>
> Hi everyone,
>
> I recently re-ran a model that I wrote about 5 months ago.
> The model is a GLMM of the type :
>
> m1 <- glmer(response ~ fixed  + random effect, data = d, family =
> "binomial")
>
> At that time, everything ran smoothly, with no error/warning messages.
>
> However I have just run it again and I get a message saying the model is
> singular.
>
> 1) The first question is, why didn't it happen then? Is it simply because
> the package was updated?
> I am asking because I need to justify my changes with the reviewers of the
> journal where I'd like to publish my study.
>
> 2) I used the function isSIngular() to check my model, using the default
> tolerance value. How do I decide the tolerance for detecting singularity?
>
> Thank you so much for your help
>
> Alessandra
>
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>
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