additional comments

[joelpick]

1. 1.7 Finally, we can use [] to index the levels of the random effects within the formula… [Seems like this should be shown with an example.]
2. Section 2.2
   a. In order to tell the parameter list we have effects that vary at different hierarchical levels, we can create additional slots in the parameter list for the grouping factors, so now it will look something like: [I think highlighting in a different color the new code might be quite helpful if this is possible. I have trouble seeing what is new here, and this may be an issue in many places as the code gets more complex]
   b. We would recommend the former methods, as this makes things clearer if other factors are simulated. [This last bit may need some more explanation]
3. Section 2.4
   a. and the beta parameter associated with interaction is 1. [This seems to need another line, such as: “The “interactions=list(“ code below contains this information.”]
   b. and the beta parameter associated with interaction is 1. [This color coding is great and should be repeated elsewhere. Here, I am not sure the block of code above this is necessary then. ]
   c. argument a covariance matrix, instead of two variances: [Use the color-coding again here (and everywhere when new coding is implemented]