Figure 4

Examples of strain diversity solutions for different strain structures. Dynamic solutions generated by MANTIS for an antigenic system with structure {3,2} and 6 strains. (left) Strain diversity (Shannon Index), for three levels of cross-immunity γ=0.10 (black), γ=0.75 (red) and γ=0.95 (blue). Examples correspond to series presented in Figure 3 for the same γ values. Grey shaded area highlights the dynamics at equilibrium used for the remaining plots. (centre, right) Single-strain dominance (SSD) and strain diversity (Shannon Index) for different values of γ. Grey lines and areas are the mean and standard deviation, respectively. Variation is obtained by running 100 simulations with random initial conditions for each γ value. Vertical lines mark the γ regimes used in Figure 3 and this figure, left. The minimal R code required to replicate these dynamics can be found in the Additional file 1.