This chapter develops the methods for designing, executing, and analyzing large suites of computer simulations that generate stable and replicable results. It starts with a discussion of the different methods of experimental design, such as grid sweeping and Monte Carlo parameterization. Next, it demonstrates how to calculate mean estimates of output variables of interest. It does so by first discussing stochastic processes, Markov Chain representations, and model burn-in. It focuses on three stochastic process representations: nonergodic deterministic processes that converge on a single state; nondeterministic stochastic processes for which a time average provides a representative estimate of the output variables; and nondeterministic stochastic processes for which a time average does not provide a representative estimate of the output variables. The estimation strategy employed depends on which stochastic process the simulation follows. Lastly, the chapter presents a set of diagnostic checks used to establish an appropriate sample size for the estimation of the means.
Experimental design principles to choose the number of Monte Carlo replicates for stochastic ecological models
