Parsing EpiFusion Outputs

What is in the output?

For each MCMC chain, EpiFusion will give you the following output files:

• betas: csv file where each row is a trajectory of rate beta sampled from the MCMC
• trajectories: csv file where each row is a daily infection trajectory sampled from the MCMC
• rt: csv file where each row is a daily Rt trajectory sampled from the MCMC
• params: txt file where each column is an MCMC parameter, and each row is an MCMC sample
• likelihoods: txt file of the posterior likelihoods from each MCMC step
• acceptance: txt file where each line logs if the MCMC step was accepted (1) or rejected (0)

How do I interpret the output?

We have a number of useful R functions for parsing through the output which are in the epifusion_utilities.R script, to load these just run

source('EpiFusion_utilities.R')

in an R session where your working directory has this script. Someday we hope to package these functions in an R package, but for now the script has everything you should need.

Example parsing workflow