Cross-scale dynamics and the evolutionary emergence of infectious diseases

Sebastian J. Schreiber; Ruian Ke; Claude Loverdo; Miran Park; Priyanna Ahsan; James O. Lloyd-Smith

For the numerical work, we used linear, logarithmic, and saturating functions for the transmission probability function p. All gave similar results but we present the linear case as most analytical results were derived for this case. To compute the asymptotic extinction probabilities, we iterated the probability generating map G for 2, 000 generations. For the individual based simulations, we solved the within-host differential equations using matrix exponentials and renormalizing these exponentials when the viral load reached the value K. Between host transmission events were determined by a time-dependent Poisson process with rate function p(b w v w (t) + b m v m (t)), and multinomial sampling was used to determine the initial viral load of an infected individual.