Antigen implements an SIR epidemiological model where hosts in a population are infected with viruses that have distinct antigenic phenotypes. Hosts make contacts trasmitting viruses and also recover from infection. After recovery, a host remembers the antigenic phenotype it was infected with as part of its immune history. The risk of infection after contact depends on comparing the infecting virus's phenotype to the phenotypes in the host immune history.

Antigenic phenotype is currently implemented as a n-d continuous vector. Virus mutations move phenotype randomly in this n-d Euclidean space. However, other phenotype models may be implemented through the Phenotype interface.

Additionally, population structure is implemented in terms of discrete demes. Contacts within a deme occur through standard mass action, while contacts between demes occur at some fraction of the rate of within deme contact.

Download source code at GitHub.

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