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I'm trying to fit a GLMM using the package glmmTMB in R. The model has a negative binomial distribution. The fixed effect "Treatment" has two levels (low or high), "Sampling" is the number of consecutive times a colony has been sampled (14 levels). "Size" is a covariate that account for the size of the individuals, and the colony and individual ID are included as random effects. I have 6 replicates per treatment.

Model <- glmmTMB(cell_con ~ treatment * sampling + size + (1|colony/ind_ID),
                 family = "nbinom2", data=countI)

The model fits when I only include the main effects, but when I include interactions between terms I get the following warning. I'm actually mainly interested in the interaction between treatment and sampling.

"Warning message: In fitTMB(TMBStruc) : Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')"

I already check the Troubleshooting page for glmmTMB, but unfortunately I'm not that well versed in statistics to solve the problem with that information

Thanks

PD: this is the first time I post a questions here. Let me know if I should post more information about the experiment. I can also send the complete code and data.

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    $\begingroup$ Your model is having problems converging, 1) are your variables highly correlated? 2) Do you have enough observations to estimate all the terms? 3) Try a different optimizer. $\endgroup$ Commented Dec 20, 2018 at 6:33
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    $\begingroup$ Perhaps you don’t need the nested random effects. $\endgroup$ Commented Dec 21, 2018 at 7:49
  • $\begingroup$ see troubleshooting with glmmTMB - cran.r-project.org/web/packages/glmmTMB/vignettes/… $\endgroup$ Commented Dec 10, 2019 at 4:43
  • $\begingroup$ @user2974951 What were you referring to when you said to try a different optimizer? I don't see an optimizer specified in the original model. $\endgroup$ Commented Sep 16, 2020 at 19:08
  • $\begingroup$ @SusieDerkins Admittedly I don't know this specific package so there may well not be such an option, but I know that other more standard packages do have this option. So maybe the answer is try a different package. $\endgroup$ Commented Sep 17, 2020 at 5:59

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the following site reports the troubleshooting you are mentioning: https://cran.r-project.org/web/packages/glmmTMB/vignettes/troubleshooting.html

the following point can be the problem when you are getting the message.These problems are most likely:

  • when a model is overparameterized (i.e. the data does not contain enough information to estimate the parameters reliably)
  • when a random-effect variance is estimated to be zero, or random-effect terms are estimated to be perfectly correlated ("singular fit": often caused by having too few levels of the random-effect grouping variable)
  • when zero-inflation is estimated to be near zero (a strongly negative zero-inflation parameter)
  • When dispersion is estimated to be near zero
  • When complete separation occurs in a binomial model: some categories in the model contain proportions that are either all 0 or all 1
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