This repository contains the code for the LSHTM contribution to the Ebola forecasting challenge.
It contains the following files:
disease_params_challenge.rreads the line lists and transmission trees to estimate parameters and save them in a file.
ebola_fit_challenge.biis the transmission model, written in libbi.
fit_challenge.rfits the transmission data to the data.
analyse_challenge.ranalyses 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.