Technical Documentation

This is the technical documentation. See Tutorials instead to get started.

Methods

epimodel.epimodel(struct_linear, struct_interaction)

Parses struct into matrices

Parameters:
  • struct_linear (struct) –

    struct corresponding to linear flows. The syntax is

    struct.origin.target = flowrate
  • struct_interaction (struct) –

    struct corresponding to interacted flows. The syntax is

    struct.origin.interaction.target = flowrate

Example

% SEIR model
struct_linear.exposed.infectious = 1;
struct_linear.infectious.recovered = 1;
struct_interaction.susceptible.infectious.exposed = 1;
seir_model = epimodel(struct_linear, struct_interaction);
epimodel.set_initial_dist(struct_dist)

Sets initial distribution

Parameters:struct_dist (struct) – struct of initial distribution. Unfilled values default to zero

Example

struct_dist.infectious = 1e-4;
struct_dist.susceptible = 1 - 1e-4;
seir_model.set_initial_dist(struct_dist);
epimodel.simulate(end_time, time_step)

Runs simulation/ODE forward

Parameters:
  • end_time (double) – end time of simulation
  • time_step (double) – [default 1e-3] time step of discretization

Example

seir_model.simulate(10);

See also

Note

Note that The values are computed using an “explicit” udpate, so time_step needs to small enough to satisfy the CFL condition.

Properties

epimodel.results
Type:

struct
Description:

Struct of simulation results
Example:
plot(model.results.time, model.results.infectious);
epimodel.init_dist
Type:double
Description:vector of initial distribution
Note:Set it using set_initial_dist
epimodel.name2loc
Type:struct
Description:(INTERNAL ATTRIBUTE) struct of location for different variables
epimodel.loc2name
Type:cell array
Description:(INTERNAL ATTRIBUTE) cell array of variable names
epimodel.time_knots
Type:double
Description:time knot points of simulation