Historically, metapopulation studies have been been divided into two main camps: those that model within-population dynamics and "cell occupancy" models. The latter of which, where only the presence or absence of a given species within a population is recorded in a given timepoint \cite{taylor1988}, has received much more theoretical attention. Importantly, cell occupancy models rest on an assumption of temporal separation in which local dynamics occur on a timescale that can be treated as instantaneous relative to that of the between-population dynamics \cite{Hanski_1994}. When considering pathogens in systems with relatively high migration rates, however, this assumption rarely holds, and the presence-absence approach can significantly limit model accuracy \cite{Hess_1996,Cross_2005,Lloyd_2004}.