Steve, Thanks for taking the time to think about it, I really appreciate it. I am interested in the estimates of the random intercept and coefficient for each transect, so my estimates are: estimate 'Transect 1 - Intercept' int 1 | int 1 /subject 1 ;
estimate 'Transect 1 - Coefficient' year_num 1 | year_num 1 /subject 1 ;
estimate 'Transect 2 - Intercept' int 1 | int 1/subject 0 1;
estimate 'Transect 2 - Coefficient' year_num 1 | year_num 1/subject 0 1; ... for transects from 1 to 9. I get no errors when I use quad(transect) as the subject in the first random statement as you suggested. But, since the quadrats are subdivisions of the transects, the design suggests that there will be some dependence between observations of the same transect (dependence between measurements collected in different quadrats of the same transect). So, is it ok to just use random intercepts for quadrats? I am a beginner in GLMM so please forgive me if my understanding is wrong. I will have access to the paper you suggested later today so I will read it as soon as I have it. Again, thanks for your help.
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