I am planning a factorial experiment with Site (2), Rep (4), Seed Type (3), Treatment (5) and we are going to test seed moisture over 5 different sampling periods, Month 0, 3, 6, 9, 12. What model should I use in JMP and how would you recommend analyzing the data over these time periods?
Your experiment is definitely of the repeated measures type because you are evaluating the same experimental treatment combination output over a sequence of time values. Hence you are in Mixed Model land. Hopefully you have JMP Pro because JMP Pro is much more flexible and adaptable for analyzing experimental designs with fixed and random effects. Here is a link to the online JMP documentation on Mixed Models: