Infection states.

<p>The infection states and their transitions for the simplest model case (single homogeneous population with a single strain of <i>S</i>. Typhi). Uninfected individuals have a <i>P₀</i> probability of becoming infected during each time step and thus time spent in this state depends on the force of infection and their immune status. For all other states, the time spent is sampled from a defined distribution. Where there are multiple possible transitions out of a state, conditional probabilities determine which path an individual follows. The order in which the probabilities are applied is specified in the text. Probabilities for each individual may depend on a: age; x: previous exposure/immune status; or d: treatment options and to a single time step.