This package implements a number of vector-borne disease models in Birch. They are useful for modelling epidemics of mosquito-borne diseases such as Zika and dengue. The original model is described in Funk et al. (2016), and the particular model implemented here in Murray et al. (2018).
The implementation is based on the original implementation by Sebastian Funk, which was in LibBi. The model has been adapted from continuous-time and state to discrete-time and state.
To build and install, use:
birch build
birch install
To run:
./run.sh
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S. Funk, A.J. Kucharski, A. Camacho, R.M. Eggo, L. Yakob, L.M. Murray, and W.J. Edmunds (2016). Comparative analysis of dengue and Zika outbreaks reveals differences by setting and virus. PLOS Neglected Tropical Diseases 10:1-16.
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L.M. Murray, D. Lundén, J. Kudlicka, D. Broman, and T.B. Schön (2018). Delayed Sampling and Automatic Rao--Blackwellization of Probabilistic Programs.