Base Contact Model

GEMS is a discrete time simulation which means that time is explicitly modeled in timesteps (so-called ticks). A tick, in the default configuration, has the duration of one day but can be adapted by the user. All contacts and the following infections that happen during one tick are calculated before incrementing to the next timestep. The figure below illustrates what the GEMS engine does during one timestep.

We go through all active settings which are the ones that hold an infectious agent. In each of the settings, we draw contacts just for the infected individuals as we are only interested in potentially infectious interactions. Contacts between two non-infectious individuals are not simulated. The contacts for the individuals are drawn using the contact_sampling_method that was defined for the respective setting type in the config. With the default config, contacts are drawn randomly from the list of setting members. After a contact was drawn, the pathogen's transmission_function will determine the probability of infection. In the default model, this is a fixed rate for each contact, independent of other factors (e.g., time since infection). However, a custom function can be used to reflect varying transmission probabilities based on agent characteristics (e.g., age or vaccinations).