EpiModel (version 2.2.1)

get_network: Extract networkDynamic and network Objects from Network Simulations

Description

Extracts the networkDynamic object from a either a network epidemic model object generated with netsim or a network diagnostic simulation generated with netdx, with the option to collapse the extracted networkDynamic object down to a static network object.

Usage

get_network(
  x,
  sim = 1,
  network = 1,
  collapse = FALSE,
  at,
  ergm.create.nd = TRUE
)

Arguments

x

An EpiModel object of class netsim or netdx.

sim

Simulation number of extracted network.

network

Network number, for netsim objects with multiple overlapping networks (advanced use, and not applicable to netdx objects).

collapse

If TRUE, collapse the networkDynamic object to a static network object at a specified time step.

at

If collapse is TRUE, the time step at which the extracted network should be collapsed.

ergm.create.nd

If TRUE and x contains a static ERGM (i.e., a netest model with duration = 1), then create a networkDynamic object from the stored list of static network objects; if FALSE, output the network list directly.

Details

This function requires that the networkDynamic is saved during the network simulation while running either netsim or netdx. For the former, that is specified with the tergmLite parameter in control.net set to FALSE. For the latter, that is specified with the keep.tedgelist parameter directly in netdx.

Examples

# Set up network and TERGM formiula
nw <- network_initialize(n = 100)
nw <- set_vertex_attribute(nw, "group", rep(1:2, each = 50))
formation <- ~edges
target.stats <- 50
coef.diss <- dissolution_coefs(dissolution = ~offset(edges), duration = 20)

# Estimate the model
est <- netest(nw, formation, target.stats, coef.diss)

# Run diagnostics, saving the networkDynamic objects
dx <- netdx(est, nsteps = 10, nsims = 3, keep.tnetwork = TRUE,
     verbose = FALSE)

# Extract the network for simulation 2 from dx object
get_network(dx, sim = 2)

# Extract and collapse the network from simulation 1 at time step 5
get_network(dx, collapse = TRUE, at = 5)

# Parameterize the epidemic model, and simulate it
param <- param.net(inf.prob = 0.3, inf.prob.g2 = 0.15)
init <- init.net(i.num = 10, i.num.g2 = 10)
control <- control.net(type = "SI", nsteps = 10, nsims = 3, verbose = FALSE)
mod <- netsim(est, param, init, control)

# Extract the network for simulation 2 from mod object
get_network(mod, sim = 2)

## Extract and collapse the network from simulation 1 at time step 5
get_network(mod, collapse = TRUE, at = 5)