get_network: Extract Network Objects from Network Simulations

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Extract Network Objects from Network Simulations

Description

Extracts the network object from either a network epidemic model object generated with netsim, a network diagnostic simulation generated with netdx, or a netsim_dat object used internally in netsim. For netdx or netsim with tergmLite == FALSE, the extracted network object is a networkDynamic, which can be collapsed down to a static network object with the collapse and at arguments. For netsim with tergmLite == TRUE, the extracted network object is the final networkLite, the collapse argument should be FALSE, and the at argument should be missing. For netsim_dat, the collapse and at arguments are not supported, and the network object is either the current networkLite (if tergmLite == TRUE) or the current networkDynamic (if tergmLite == FALSE).

Usage

get_network(x, ...)

## S3 method for class 'netdx'
get_network(x, sim = 1, collapse = FALSE, at, ...)

## S3 method for class 'netsim'
get_network(x, sim = 1, network = 1, collapse = FALSE, at, ...)

## S3 method for class 'netsim_dat'
get_network(x, network = 1L, ...)

Arguments

x	An EpiModel object of class netsim, netdx, or netsim_dat.
...	Additional arguments.
sim	Simulation number of extracted network, for netdx and netsim.
collapse	If TRUE, collapse the networkDynamic object to a static network object at a specified time step. Applicable to netdx objects and netsim objects with tergmLite == FALSE.
at	If collapse is TRUE, the time step at which the extracted network should be collapsed. Applicable to netdx objects and netsim objects with tergmLite == FALSE.
network	Network number, for netsim or netsim_dat objects with multiple overlapping networks (advanced use, and not applicable to netdx objects).

Details

This function requires that the network object is saved during the network simulation while running either netsim or netdx. For the former, that is specified by setting the save.network parameter in control.net to TRUE. For the latter, that is specified with the keep.tnetwork parameter directly in netdx.

Value

For netdx or netsim with tergmLite == FALSE, a networkDynamic object (if collapse = FALSE) or a static network object (if collapse = TRUE). For netsim with tergmLite == TRUE or netsim_dat with tergmLite == TRUE, a networkLite object. For netsim_dat with tergmLite == FALSE, a networkDynamic object.

Examples

# Set up network and TERGM formula
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)

EpiModel documentation built on July 9, 2023, 5:21 p.m.