Model design for non-parametric phylodynamic inference and applications to pathogen surveillance.

ABSTRACT: Inference of effective population size from genomic data can provide unique information about demographic history, and when applied to pathogen genetic data can also provide insights into epidemiological dynamics. The combination of non-parametric models for population dynamics with molecular clock models which relate genetic data to time has enabled phylodynamic inference based on large sets of time-stamped genetic sequence data. The methodology for non-parametric inference of effective population size is well-developed in the Bayesian setting, but here we develop a frequentist approach based on non-parametric latent process models of population size dynamics. We appeal to statistical principles based on out-of-sample prediction accuracy in order to optimize parameters that control shape

SUBMITTER: Didelot X 

PROVIDER: S-EPMC8382123 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature