infer-ausei version 4.0 is designed for inference on a dynamical model of equine influenza in Australia. It implements a susceptible-infected-onset model at the property level, incorporating number of horses, property area, distance between properties, and the effect of vaccination. A within-property SEIR model is used to represent how infectivity changes with time -- hence no "R" compartment is used in the property-level model. Rather, properties "run out" of infectiousness once all horses have recovered with solid immunity.
See README for build instructions and $(top_srcdir)/doc/model.pdf for model details.