4 papers
Consensus-level substitution rates are distinct from the virion-level rate
David J Pascall
Estimating viral substitution rates is central to evolutionary epidemiology, and recent interest in within-host evolution has sharpened the question of what such rates measure. I d…
Constructing Contact and Connectivity Matrices for Infectious Disease Modelling
Xiahui Li, Dongni Zhang, Neha Bansal +12
Contact (or mixing, or more generally connectivity) matrices are a fundamental component of modelling and inference for infectious disease epidemiology. Their structure and paramet…
Sequential learning theory for Markov genealogy processes
David J Pascall
We introduce a filtration-based framework for studying when and why adding taxa improves phylodynamic inference, by constructing a natural ordering of observed tips and applying se…
The NOSTRA model: coherent estimation of infection sources in the case of possible nosocomial transmission
David J Pascall, Chris Jackson, Stephanie Evans +8
Nosocomial infections have important consequences for patients and hospital staff: they worsen patient outcomes and their management stresses already overburdened health systems. A…