Issue with boundary (singular) fit: see ?isSingular
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