# Note: This model converges well if you are running R version 3.0.2, but may not converge with later 
# versions. If you are having convergence issues, please try with version 3.0.2.

mnb1 <- glmer.nb(total.fruits ~ nutrient*amd + rack + status + 
               (1|popu)+
               (1|gen),
             data=dat.tf, control=glmerControl(optimizer="bobyqa"))
# Although beyond the scope of this workshop, the new "control" argument specifies the way we
# optimize the parameter values (i.e. by taking the derivative of a function or proceeding by iteration). 
# When taking the derivative is not possible, an iterative algorithm such as bobyqa (Bound Optimization
# BY Quadratic Approximation) is used.

# Overdispersion?
overdisp_fun(mnb1)