General Comments:
You have done a good job of laying out the specifics of the model and providing some motivating information.  The most distracting thing for me as the reader was that some of the explanations are in pieces, part of it will come at the beginning of the paragraph and then more background information about the same topic might come at the end of the same paragraph with new material in between.

Specific Comments:

page 7, line 7, (I know this is outside of the section) Eb should be EB

page 7, between lists, “Brooks et. al. …”, the “in [1]” Is awkward, maybe just say something like “We 	implement the same EB procedure as Brooks et al.”  Also writing out Empirical Bayes here but 	nowhere else is confusing

page 7, second list, 3., is backfill defined previously?  If not clarification would be helpful.

page 8, first sentence, “The regional effects…” I think that you could probably just delete this 	sentence.  It contains the same information as the last sentence on the previous page and 	starting with the CDC definition conveys that the paragraph will be about regions.

page 8, second paragraph, line 6 - 9, sentence starting “This is in accordance…” using “prior beliefs” 	here seems a little weird when citing evidence.  If citing a scientific observation then I think it 	can be conveyed more strong.  Also, the next sentence should maybe be combined with the 	part before about differing peaks.

page 8, last paragraph, need to give a better explanation of hat{F}, I don’t understand what the set of 	“all smoothed curves over all regions and seasons…” means.  It seems like this should be an 	infinite set.

page 9, line 1, “We assume that…” Maybe move this to the beginning of the paragraph when 	describing \hat{F}?

page 9, equation, is there anything you can do about the formatting?  The , (1) seems weird

page 10, line 3-5, there are some typos here, I think you want to delete at least one “both” and reword 	the “of for”.  Maybe something along the lines of “From our posterior we generate both 	probabilistic predictions of y_i^{(r,s)} and posterior distributions for the peak week and peak 	incidence values”.  Although you may want to break this up.

page 10, section 2.2.1, first equation.  I think it would be useful to bring the definitions forward, before 	the equation, or at least explain what the expected value is first.  Otherwise it feels a little like 	being thrown off a cliff.

page 10, 2.2.1, last paragraph, the second sentence here has too much.  Try starting the paragraph 	explaining how many comparisons comparing each sets would take and then explaining what 	you do instead.  That would give context for your method and then it explain it.

page 10, 2.3, first paragraph, sentence 2, move “We leave out Region 9” to the beginning of the 	sentence.  This is the point of what you are doing and the background is confusing until we 	know this is what you are talking about.

page 10, 2.3, second paragraph, is this necessary?  It seems unrelated to the rest of the explainaton.

page 10, last paragraph, 3rd sentence, “In this figure, we…” seems like you could delete this as the 	same information is contained in the next sentence.

page 11, line 1, fix hae type

page 11, second paragraph, split into two sentences one about EB with regional effects making 	intuitive sense.  The second could be something like “However, when the predictions of peak 	height and peak week are evaluated using cross validation EB with regional effects is 	outperformed by the basic EB model. *this whole paragraph could also be move to page 12 	after the first full paragraph once CV has been introduced.