Epidemiological simulation

Random realisation of a simulated spread of plant epidemics in a randomly-generated landscape. A square 100km² landscape is generated with 2,500 randomly distributed plants and each plant is assumed to be equally susceptible to the disease. We assume there is no latent phase, that plants remain infectious once they become infected and that infectious plants show disease symptoms. At time step t = 0, an initial infection is seeded in the most centrally located host. A number of time steps are then performed in which a susceptible host either remains susceptible or becomes infected until all hosts are infected. Infection occurs due to the spread of the pathogen from an infected to a susceptible host within the known landscape. The probability that a susceptible host becomes infected in a single time step is determined by the total inoculum that the host receives from all currently infected hosts and the transmission rate parameter<i>.</i> The total inoculum that a susceptible host receives depends upon the distance between each infected host from the susceptible host under consideration. The proportion of inoculum emitted from an infected host that is received by a susceptible host is determined by an exponential dispersal kernel. Two scenarios are explored with two different dispersal kernels.