This directory contains the framework used to build SIR-type compartment models.

Classes:

• CompartmentalModel: Template base class for compartmental models. Specialize the class template using a parameter set (e.g. using the ParameterSet class) and populations (e.g. using the Populations class). The population is divided into compartments (and optionally other subcategories, e.g. age groups). Derive from the class to define the change in populations.
• FlowModel: A CompartmentalModel defined by the flows between populations. Requires the additional template parameter Flows, which is a TypeList of Flow. Instead of defining get_derivatives, the function get_flows has to be implemented for a FlowModel.
• StochasticModel: A CompartmentalModel (or FlowModel) defined through a stochastic differential equation (SDE). In addition, a function get_noise needs to implemented that returns random changes to each compartment.
• Simulation: Template class that runs the simulation using a specified compartment model. Can be derived from to implement behavior that cannot be modeled inside the usual compartment flow structure.
• FlowSimulation: Template class derived from Simulation, that additionally computes the flows between populations. It requires a FlowModel. While the compartment and flow results can be changed outside of the simulation, it is required that both still have the same number of time points to further advance this simulation.
• FeedbackSimulation: Template class derived from Simulation (or FlowSimulation) that extends the standard simulation functionality with a feedback mechanism. FeedbackSimulation holds its own parameters (using a specialized ParameterSet) and a perceived risk time series. It overrides the simulation advance routine to compute and apply contact adjustments at regular intervals. The contact adjustments are computed by first deriving the perceived risk from the historical ICU occupancy—normalized by the nominal ICU capacity—and then transforming that risk via a softplus function into an effective damping factor to reduce contacts as described in Dönges et al. (doi.org/10.3389/fphy.2022.842180).
• StochasticSimulation: A simulation specifically for running a StochasticModel. Cannot simulate flows, because the integrator uses mitigations for negative values caused by random noise that (in general) only work on compartments.
• SimulationBase and FlowSimulationBase: Base classes for the simulations that define most members and setters/getters, so that only a public advance method needs to be defined.

Note that currently, only the last value of the simulation result (i.e. the TimeSeries obtained from get_result()) is used to advance the simulation. Thus, any changes to the population of the simulation's model will have no effect on the simulation result.

See the implemented SEIR model for a simple example of using the classes. See the SECIR model for an advanced example with age resolution.