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We first generalise ideas discussed by Kiss et al. (2015) to prove a theorem for generating exact closures (here expressing joint probabilities in terms of their constituent marginal probabilities) for susceptible-infectious-removed (SIR) dynamics on arbitrary graphs (networks). For Poisson transmission and removal processes, this enables us to obtain a systematic reduction in the number of differential equations needed for an exact `moment closure representation of the underlying stochastic model. We define `transmission blocks as a possible extension of the block concept in graph theory and show that the order at which the exact moment closure representation is curtailed is the size of the largest transmission block. More generally, approximate closures of the hierarchy of moment equations for these dynamics are typically defined for the first and second order yielding mean-field and pairwise models respectively. It is frequently implied that, in principle, closed models can be written down at arbitrary order if only we had the time and patience to do this. However, for epidemic dynamics on networks, these higher-order models have not been defined explicitly. Here we unambiguously define hierarchies of approximate closed models that can utilise subsystem states of any order, and show how well-known models are special cases of these hierarchies.
Stochastic epidemic models on networks are inherently high-dimensional and the resulting exact models are intractable numerically even for modest network sizes. Mean-field models provide an alternative but can only capture average quantities, thus of
Amidst the current COVID-19 pandemic, quantifying the effects of strategies that mitigate the spread of infectious diseases is critical. This article presents a compartmental model that addresses the role of random viral testing, follow-up contact tr
We present an efficient and flexible method for computing likelihoods of phenotypic traits on a phylogeny. The method does not resort to Monte-Carlo computation but instead blends Felsensteins discrete character pruning algorithm with methods for num
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed that when