Advanced Simulated Tutorial

In this tutorial we will go through the process of starting with a time-scaled phylogenetic tree (with dated tips) and case incidence data, and creating an XML file to run an EpiFusion analysis. We'll start with a basic parameterisation, before doing up a more advanced parameterisation to better reflect what we know about how the data was collected.

The Data

Below data from a simulated outbreak, beginning on January 1st 2020. In this simulated outbreak, sampling of both genomic sequences and cases was very low for the first 5 weeks, followed by a dramatic scale up in sampling.

Step 1: Prep Tree and Incidence for EpiFusion

First we'll prep the data to into EpiFusion friendly format using a helpful EpiFusionUtilities function.