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Runs a simulation until a stopping condition occurs

Source: R/simulation.R
simulation_run.Rd

Runs the specified simulation until a stopping condition occurs and returns a table listing all events that occurred. simulation_run can be called repeatedly and will continue from the point where the last run stopped. Note that for an epidemic to start, initially infected nodes must be defined with simulation_addinfections.

Usage

simulation_run(sim, stop, opts = list())

Arguments

sim

a simulation object

stop

a list of stopping conditions

opts

return value options

Value

a data.frame containing the columns

  • time: time since the start of the simulation

  • epidemic_step: total number of epidemic events so far

  • network_step: total number of network events so far

  • kind: kind of event (outside_infection, infection, reset, neighbour_added, neibhour_removed, instantenous_contact)

  • node: node affected by the event

  • neighbour: neighbour (for infection, neighbour_added, neibhour_removed)

  • total_infected: total number of infected nodes since simulations start

  • total_reset: total number of recovered/reset nodes since simulation start

  • infected: current number of infected nodes

Details

Stopping conditions are specified as a named list of threshold values for any combination of the following variables:

  • epidemic_steps: Number of epidemic events (infection, outside_infection, reset) since the simulation was started.

  • network_steps: Number of network events (edge added, edge removed, instantaneous contact) since the simulation was started. Only relevant for simulations on dynamic networks.

  • time: time since the simulation was started

  • infected: Number of currently infected nodes

  • total_infected: Total number of infections since the start of the simulation

  • total_reset: Total number of recoveries/resets since the start of the simulation

Possible return value options are:

  • network_events: Include network events in the returned data.frame. Default false

  • epidemic_events: Include epidemic events in the returned data.frame. Default true

See also

simulation_functions, simulation,

Examples

# Create contact network network
nw <- erdos_renyi_network(1e5, 5)
# Create transmission and reset time distributions
psi <- lognormal_time(6, 30, 0.1)
rho <- weibull_time(shape=5, scale=50)
# Create simulation and specifiy initial set of infections
sim <- simulation(nw, psi, rho)
simulation_addinfections(sim, nodes=c(1), times=c(0.0))
# Run simulation until time t=100 or 200,000 infections have occured
r <- simulation_run(sim, stop=list(time=300, total_infected=300e3))
# Plot the number of infected nodes against time
plot(r$time, r$infected, type='l')