Figure 3.

The product of the transmission probability, contact rate and number of infected individuals, βcY, at different stages of the epidemic depicted in figure 2 (smooth black line) obtained from numerically solving equations (2.7) and (2.8), along with numerical estimates of ‘effective population size’ estimated using generalized skyline plots fitted to stochastic simulations (grey lines) on the same scale. During the exponential growth period, the skyline generates good estimates of βcY. Parameter values and initial conditions are as described in figure 2. Skyline plots were generated using the APE library (Paradis et al. 2004) in R (R Development Core Team 2009). (a) Exponential growth; (b) after peak; (c) at equilibrium.