Issue with boundary (singular) fit: see ?isSingular
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. When I run the model, this warning message appears: Check model convergence: log-likelihood estimates lead to negative Chi-squared! 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) 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!
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/> [[alternative HTML version deleted]]