Predictability of measles epidemics in small populations, using TSIR model fitting and simulation. This repository goes with the paper :
Caudron Q, Mahmud A S, Metcalf C J E, Gottfredsson M, Viboud C, Cliff A D, Grenfell B T, Predictability in a highly stochastic system : final size of measles epidemics in small populations. Journal of the Royal Society Interface 12 (102), 2014.
batch.py directory_name number_of_simulations
Main Python script for processing an entire directory of data. Arguments : directory_name number_of_sims where directory_name is a directory in /data, and number_of_sims is an integer number of simulations to run for each time series. Call python batch.py iceland 1000 for one thousand simulations for each time-series in Iceland, for example.
data/
Processed data in a form useable by all scripts, and hopefully ssm at some point.
poster/
Poster for the Ecology and Evolution of Infectious Diseases 2014 conference.
raw_data/
All raw data collected from stats agencies ( or Bryan Grenfell, or others ) go here for permanent storage.
talk/
Talk for Tim Coulson's group at Oxford's Department of Zoology.
utilities/
Random scripts used in the development of the code or in preprocessing of data.