Author: Lemey, Philippe; Rambaut, Andrew; Bedford, Trevor; Faria, Nuno; Bielejec, Filip; Baele, Guy; Russell, Colin A.; Smith, Derek J.; Pybus, Oliver G.; Brockmann, Dirk; Suchard, Marc A.
Title: Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2 Document date: 2014_2_20
ID: 04q71md3_12
Snippet: We employ a novel approach to simultaneously reconstruct spatiotemporal history and test the contribution of potential predictors of spatial spread. The approach extends a recently developed Bayesian method of phylogeographic inference [21] into a generalized linear model (GLM), by parameterizing each rate of among-location movement in the phylogeographic model as a log linear function of various potential predictors. For each predictor j, the GL.....
Document: We employ a novel approach to simultaneously reconstruct spatiotemporal history and test the contribution of potential predictors of spatial spread. The approach extends a recently developed Bayesian method of phylogeographic inference [21] into a generalized linear model (GLM), by parameterizing each rate of among-location movement in the phylogeographic model as a log linear function of various potential predictors. For each predictor j, the GLM parameterization includes a coefficient b j , which quantifies the contribution or effect size of the predictor (in log space), and a binary indicator variable d j , that allows the predictor to be included or excluded from the model. We estimate the d variables using a Bayesian stochastic search variable selection (BSSVS) [22, 23] , resulting in an estimate of the posterior inclusion probability or support for each predictor. This approach uses the data to select the explanatory variables and their effect sizes from a pre-defined set of predictors that can explain the phylogenetic history of among-location movement while simultaneously
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