The purpose of time series analysis via mechanistic models is to reconcile the known or hypothesized structure of a dynamical system with observations collected over time. We develop a framework for constructing nonlinear mechanistic models and carrying out inference. Our framework permits the consideration of implicit dynamic models, meaning statistical models for stochastic dynamical systems which are specified by a simulation algorithm to generate sample paths. Inference procedures that operate on implicit models are said to have the plug-and-play property. Our work builds on recently developed plug-and-play inference methodology for partially observed Markov models. We introduce a class of implicitly specified Markov chains with stochastic transition rates, and we demonstrate its applicability to open problems in statistical inference for biological systems. As one example, these models are shown to give a fresh perspective on measles transmission dynamics. As a second example, we present a mechanistic analysis of cholera incidence data, involving interaction between two competing strains of the pathogen Vibrio cholerae. 1. Introduction. A

Emerging zoonoses: Early warning and surveillance in the NetherlandsEmerging zoonoses: early warning and surveillance in the NetherlandsEmerging zoonoses: early warning and surveillance in the NetherlandsColophon

Abstract: Using a time series model to mimic an observed time series has a long history. However, with regard to this objective, conventional estimation methods for discrete-time dynamical models are frequently found to be wanting. In fact, they are characteristically misguided in at least two respects: (i) assuming that there is a true model; (ii) evaluating the efficacy of the estimation as if the postulated model is true. There are numerous examples of models, when fitted by conventional methods, that fail to capture some of the most basic global features of the data, such as cycles with good matching periods, singularities of spectral density functions (especially at the origin) and others. We argue that the shortcomings need not always be due to the model formulation but the inadequacy of the conventional fitting methods. After all, all models are wrong, but some are useful if they are fitted properly. The practical issue becomes one of how to best fit the model to data. Thus, in the absence of a true model, we prefer an alternative approach to conventional model fitting that typically involves one-step-ahead prediction

Time series analysis for nonlinear dynamical systems with applications to modeling of infectious diseases by

Seasonal variations in temperature, rainfall and resource availability are ubiquitous and can exert strong pressures on population dynamics. Infectious diseases provide some of the best-studied examples of the role of seasonality in shaping population fluctuations. In this paper, we review examples from human and wildlife disease systems to illustrate the challenges inherent in understanding the mechanisms and impacts of seasonal environmental drivers. Empirical evidence points to several biologically distinct mechanisms by which seasonality can impact host–pathogen interactions, including seasonal changes in host social behaviour and contact rates, variation in encounters with infective stages in the environment, annual pulses of host births and deaths and changes in host immune defences. Mathematical models and field observations show that the strength and mechanisms of seasonality can alter the spread and persistence of infectious diseases, and that population-level responses can range from simple annual cycles to more complex multiyear fluctuations. From an applied perspective, understanding the timing and causes of seasonality offers important insights into how parasite–host systems operate, how and when parasite control measures should be applied, and how disease risks will respond to anthropogenic climate change and altered patterns of seasonality. Finally, by focusing on well-studied examples of infectious diseases, we hope to highlight general insights that are relevant to other ecological interactions.

“There are epidemics of opinion as well as of disease ” Sir B. Brodie 1856 In recent years modern parasite ecology has experienced an epidemic of ideas. We now examine where we think the focus of work will concentrate over the next five years

Plug-and-play inference for disease dynamics: measles in