[R-sig-ME] Issue with boundary (singular) fit: see ?isSingular

Sasha Vasconcelos @@@h@@m@v@@conce|o@ @end|ng |rom gm@||@com
Mon Oct 4 16:23:11 CEST 2021


If there are only two years, it's not surprising that you'll get
estimates of zero variance for (1|Year).  I would probably make Year a
fixed effect.
I also tried that, leaving only Point as a random effect. But I still get
the singularity warning. Could it be that the sample size is simply too
small to handle any sort of random structure..?


   I can't find this warning message anywhere, even in the development
branch of piecewiseSEM:

https://github.com/jslefche/piecewiseSEM/search?q=convergence

??

 I also haven't been able to find anything about that warning message
anywhere, so I've posted this same question to
jslefche <https://github.com/jslefche>/piecewiseSEM
<https://github.com/jslefche/piecewiseSEM> on github and am hoping for an
answer soon.

On Mon, 4 Oct 2021 at 14:16, Ben Bolker <bbolker using gmail.com> wrote:

>
>
> On 10/4/21 10:05 AM, Sasha Vasconcelos wrote:
> > Hi,
> >
> > I'm running a piecewise SEM with 3 component models:
> >
> > lmer(response variable1 ~ predictors + (1|Point) + (1|Year), input_table)
> >
> > glmer(response variable2 ~ predictors + (1| Point) + (1|Year), family =
> > "binomial", input_table)
> >
> > glmer(response variable3 ~ predictors + (1| Point) + (1|Year), family =
> > "binomial", input_table)
> >
> > Because sampling involved visiting 18 points in spring of 2018 and again
> in
> > spring of 2019, I specified samping point and year as random effects.
>
>    If there are only two years, it's not surprising that you'll get
> estimates of zero variance for (1|Year).  I would probably make Year a
> fixed effect.
>
> >
> > When I run the model, this warning message appears:
> > Check model convergence: log-likelihood estimates lead to negative
> > Chi-squared!
>
>    I can't find this warning message anywhere, even in the development
> branch of piecewiseSEM:
>
> https://github.com/jslefche/piecewiseSEM/search?q=convergence
>
> ??
>
> >
> > This message also appears:
> > boundary (singular) fit: see ?isSingular
> >
> >  From what I've read about the second message, it could be due to random
> > effect variance estimates of zero. I checked and this happens in the 1st
> > and 3rd component models. In the 1st model "Point" has zero variance, and
> > in the 3rd model "Year" has zero variance.
> >
> > My first question is (and I apologize in advance if this is silly to ask)
> > whether this means that there's not really an effect coming from Point in
> > component model 1 and from Year in component model 2? If so, would it be
> > possible to remove those random effects to end up with:
> >
> > lmer(Response variable1 ~ Predictors + (1|Year), input_table)
> >
> > glmer(Response variable2 ~Predictors + (1| Point) + (1|Year), family =
> > "binomial", input_table)
> >
> > glmer(Response variable3 ~ Predictors + (1| Point), family = "binomial",
> > input_table)
>
>    Seems reasonable.
> >
> > My second question is whether the warning "Check model convergence:
> > log-likelihood estimates lead to negative Chi-squared!" is related to
> these
> > singularity issues?
> >
> > Oh and I am using the development version of the piecewise SEM package
> > installed using devtools. This is because this version provides
> additional
> > standardized coefficients for GLMM.
> >
> >
> > Thanks!
> >
> >
>
> --
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> Graduate chair, Mathematics & Statistics
>
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>


-- 
Sasha Vasconcelos

PhD student
CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources,
Associate Laboratory
Instituto Superior de Agronomia
Tapada da Ajuda
1349-017 Lisbon, Portugal

ResearchGate <https://www.researchgate.net/profile/Sasha_Vasconcelos>
ResearcherID
<https://publons.com/researcher/2593829/sasha-vasconcelos/publications/>

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