The main class that defines the properties of a pathogen is SimPathogen. The properties that it defines are:

• ID: Each pathogen is represented by a SimID, sim simutil.h
• Infection stages: These are defined by the SimInfectionStage class, which include
  • The infection rate in this stage
  • The distribution of the duration that an individual stays in this stage.
  • The transition probability from this stage to other stages.
• The mutation rate of the pathogen, if it can mutate.

For immutable pathogens, SimPathogen and its SimInfectionStage are all you need to define a pathogen. For mutable pathogens, you need to subclass SimPathogen to define how it mutates.

Files:

• The definitions simpathogen.h
• The implementation simpathogen.cpp