alxsrobert/evd-transmission-trees

This repository contains the code to reproduce the analysis presented in the paper: Alexis Robert, Joseph Tsui Lok Hei, Conall H Watson et al, Quantifying the added value of viral genomics to infer who infected whom in the 2014-16 Ebola virus outbreak in Guinea. The main script of the repository (src/main_script.R) is used to generate simulated transmission trees (using the functions contained in src/function_generate_outbreaks.R), and analyse them using Outbreaker2. Finally, the main script generates the different figures included in the paper (using the functions contained in src/function_figures).

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