Code for cholera model comparison and distinguishability project. This is the source code for:
Model distinguishability and inference robustness in mechanisms of cholera transmission and loss of immunity. Elizabeth C. Lee, Michael R. Kelly, Brad M. Ochocki, Segun M. Akinwumi, Karen E. S. Hamre, Joseph H. Tien, and Marisa C. Eisenberg. Journal of Theoretical Biology, 420: 68–81. Preprint: arXiv:1605.06790.
Questions? Contact Marisa Eisenberg (email@example.com)
The code given here will simulate and fit data from five different models of cholera dynamics in a population, as well as fitting to data from the 2006 cholera epidemic in Angola. To run, start with
While this code generates some basic plots, Elizabeth Lee has also made much nicer R code available for plotting the resulting parameter estimates and fits at eclee25/cholera-paramEstPlots.
Please cite the paper referenced above if you use our code or adapt it for your project.