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An infective individual is currently capable of transmitting the modeled infection. This is distinct from a susceptible individual and, when incubation is modeled, from an exposed individual not yet infectious.

The term $rIS$ is a mass-action incidence rate: each infective individual makes potentially transmitting contacts with susceptible individuals, and the total rate is proportional to the product of the two compartment sizes. An infection transfers one animal from $S$ to $I$, accounting for opposite signs in their equations. The per-capita mortality rate of an infective individual is $a$, giving transfer $aI$ from $I$ to $R$.

There are no births, recoveries or additional deaths in this model. Adding the three equations gives $\dot{S}+\dot{I}+\dot{R}=0$, so the total initial biological population is conserved when the dead compartment is included. Before quarantine, $S$ decreases whenever $I,S>0$; after effective isolation no further transmission is permitted.

The delayed influx $rI(t-\tau )S(t-\tau )$ represents animals exposed one incubation period earlier who enter the infective individual compartment now. They die at the instantaneous rate $aI(t)$ once in that compartment. The displayed bookkeeping removes an animal from $S$ at the same delayed time that it enters $I$, preserving $S+I+R$.

For this bookkeeping, $S$ must include the exposed animals which have not yet completed incubation period. If $S$ were instead defined as strictly unexposed susceptible individuals, its loss term would be the current exposure rate and a separate latent compartment would be needed. The calculations here follow the printed delay differential equation. A full initial-value problem for a delay differential equation also needs a history on $[-\tau ,0]$; the following small-delay expansion of an epidemic transfer rate concerns a smooth compatible history and the regular regime assumed by the question.