This repository contains the code for the LSHTM contribution to the Ebola forecasting challenge.

It contains the following files:

• disease_params_challenge.r reads the line lists and transmission trees to estimate parameters and save them in a file.
• ebola_fit_challenge.bi is the transmission model, written in libbi.
• fit_challenge.r fits the transmission data to the data.
• analyse_challenge.r analyses the results of the fits and produces CSV files with the projections and parameter estimates.
• script/* are scripts for running things in parallel on a HPC cluster.