structured-phylodynamic-models

Code to reproduce the results of the paper "Estimating disease spread using structured coalescent and birth-death models: A quantitative comparison"

bioRxiv: https://doi.org/10.1101/2020.11.30.403741 Epidemics: https://doi.org/10.1016/j.epidem.2024.100795

Step 1: Simulation

Simulate the trees for the a) endemic scenario b) epidemic scenario

using the code within the simulation directory.

Step 2: Parameter inference

Infer the migration rates and root location from the trees using the MBD and SC for (a) and (b), respectively, using the code within the parameter_inference directory.

Step 3: Data analysis

Analyse the data using the code within the analysis directory

Note

In the manuscript, the multitype birth-death model is abbreviated with MBD. In the code you might find the abbreviations BD and BDrhoSamp, which refer to the same model. The structured coalescent was always abbreviated as SC.