The EpiFusion Analysis Framework for joint phylodynamic and epidemiological analysis of outbreak characteristics.

The fields of epidemiology and viral phylodynamics share the ultimate goal of disease control, but concepts, methodologies and data employed by each differ in ways that confer complementary strengths and different areas of weakness. We recently introduced EpiFusion, a model for joint inference of outbreak characteristics using phylogenetic and case incidence data via particle filtering and demonstrated its usage to infer the effective reproduction number of simulated and real outbreaks. Here we provide a series of vignettes demonstrating data analysis using the EpiFusion Analysis Framework, consisting of the R package EpiFusionUtilities and the Java program in which the model is implemented, including an example using a new feature incorporated since EpiFusion's last description: the option to provide a phylogenetic tree posterior as the phylogenetic data input to the program. By outlining these examples, we aim to improve the usability of our model, and promote workflow reproducibility and open research.