Inferring epidemiological parameters under infectious phylogeography model with visitor dynamics

Here, we introduce a new and novel phylogeographic model with visitor dynamics to infer epidemiological parameters, host movement-related parameters, and disease transmission history from a serially sampled phylogenetic tree within an Suscetible-Infectious-Recovered (SIR) framework. We call our model, Visitor SIR.

As a simulation model, we can simulate transmission trees under the full model and the approximation model (see our manuscript), implemented in MASTER. As an inference model, due to the complexity of the full model, it is not computationally tractable to do inference under the full model. Therefore, we use an approximation to the full model, which has been shown to be accurate and still retains all the main properties of the full model (see our manuscript). We implement the inference machinery in a Bayesian framework, implemented in RevBayes.

In this repository, you can find all the scripts used to do simulations, inferences, and result visualizations under our model and two other models. These two models are what we call as Migration models (see this paper).

Approximation vs. full model

In approx_validation directory, you will find the simulation scripts and a plotting script used to compare results under the full Visitor SIR model and its approximation.

Simulation

In scripts directory, you will find scripts to simulate under the approximation model for generating dataset used for the coverage experiment. Also, in plot sub-directory, you will find R scripts used to visualize the results used in the manuscript (see final_plot).

RevBayes analysis

In code directory, you will find the RevBayes scripts used to run inference analysis under the approximation model and both migration models using simulated and empirical data.

Tree data

In data directory, you will find the simulated dataset under different setups for coverage experiments on the manuscript as well as empirical data, which contain empirical transmission history from this publication.

Travel data

Also in data directory, you will find depart_rates.csv file, which contains empirical estimate of per-capita depart rate between these locations used in our study: Hubei, France, Germany, Italy, and other European countries. The return_rates.csv contains empirical estimate of per-capita return rate from an away location to a home country from the country list. The raw data are obtained from eurostat.