get_nwstats: Extract Network Statistics from netsim or netdx Object

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Extract Network Statistics from netsim or netdx Object

Description

Extracts network statistics from a network epidemic model simulated with netsim or a network diagnostics object simulated with netdx. Statistics can be returned either as a single data frame or as a list of matrices (one matrix for each simulation).

Usage

get_nwstats(x, sim, network = 1, mode = c("data.frame", "list"))

Arguments

x	An EpiModel object of class netsim or netdx.
sim	A vector of simulation numbers from the extracted object.
network	Network number, for netsim objects with multiple overlapping networks (advanced use, and not applicable to netdx objects).
mode	Either "data.frame" or "list", indicating the desired output.

Value

A data frame or list of matrices containing the network statistics.

Examples

# Two-group Bernoulli random graph TERGM
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)
est <- netest(nw, formation, target.stats, coef.diss, verbose = FALSE)

dx <- netdx(est, nsim = 3, nsteps = 10, verbose = FALSE,
            nwstats.formula = ~edges + isolates)
get_nwstats(dx)
get_nwstats(dx, sim = 1)

# SI epidemic model
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,
                       nwstats.formula = ~edges + meandeg + degree(0:5),
                       verbose = FALSE)
mod <- netsim(est, param, init, control)

# Extract the network statistics from all or sets of simulations
get_nwstats(mod)
get_nwstats(mod, sim = 2)
get_nwstats(mod, sim = c(1, 3))

# On the fly summary stats
summary(get_nwstats(mod))
colMeans(get_nwstats(mod))

EpiModel documentation built on Oct. 12, 2024, 1:06 a.m.