Final papers should be no more than 20 pages total, including all figures, tables and references.
Each paper needs to have the following:
Title page: include the title, your name, and a "tweetable abstract" summarizing everything you've done in 140 characters or less. These won't be launched into the twitterverse, but as a concise (and exciting!) summary.
Abstract page: Summarize briefly (ideally < 250 words) the novelty of your analysis, key results, and implications for future work
Body / main text: Please include an Introduction / Methods / Results / Discussion section. You're free to use any of the equations from the MARSS manual, or class material to provide equations, variables, descriptions, etc.
References: Please use some kind of bibliography manager (like Endnote) to format all references consistently.
Figures / Tables: Include figures and tables formatted for the journal of your choice. Examples you might want to include are: plots of your raw data, plots of underlying state estimates, plots of future projections, tables of parameter estimates, model selection (AICc) etc.
As long as you include page numbers and line numbers, you are free to use the general formatting guidelines for whichever journal you plan to eventually submit your paper to. For some examples, see
Journal of Applied Ecology: http://www.journalofappliedecology.org/view/0/authorGuideline.html