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Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution
Biologists employ phylogenetic comparative methods to study adaptive evolution. However, none of the popular methods model selection directly. We explain and develop a method based on theExpand
Inference for nonlinear dynamical systems
We present a new method that makes maximum likelihood estimation feasible for partially-observed nonlinear stochastic dynamical systems (also known as state-space models) where this was not previously the case. Expand
Inapparent infections and cholera dynamics
In many infectious diseases, an unknown fraction of infections produce symptoms mild enough to go unrecorded, a fact that can seriously compromise the interpretation of epidemiological records. ThisExpand
Time series analysis via mechanistic models
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. Expand
Statistical Inference for Partially Observed Markov Processes via the R Package pomp
We describe the specification of user-defined models and the development of additional methods within the programming environment provided by pomp, a framework for Monte Carlo statistical investigations using nonlinear, non-Gaussian POMP models. Expand
Avoidable errors in the modelling of outbreaks of emerging pathogens, with special reference to Ebola
We demonstrate an approach based on stochastic modeling that allows straightforward diagnosis of model misspecification and proper quantification of forecast uncertainty. Expand
Interactions between serotypes of dengue highlight epidemiological impact of cross-immunity
Dengue, a mosquito-borne virus of humans, infects over 50 million people annually. Infection with any of the four dengue serotypes induces protective immunity to that serotype, but does not conferExpand
Plug-and-play inference for disease dynamics: measles in large and small populations as a case study
We show the utility of the plug-and-play approach in the context of an investigation of measles transmission dynamics and comment on the importance of including extra-demographic stochasticity. Expand
Natural immune boosting in pertussis dynamics and the potential for long-term vaccine failure
Incidence of whooping cough, unlike many other childhood diseases for which there is an efficacious vaccine, has been increasing over the past twenty years despite high levels of vaccine coverage.Expand
Contact Network Structure Explains the Changing Epidemiology of Pertussis
Coughing Back Resurgence of whooping cough (or pertussis) is problematic because of the risk of infant fatality, but it has been occurring despite the availability of a vaccine. Data from Sweden,Expand