EpiModel (version 2.0.1)

is.transmat: Extract Transmissions Matrix from Network Epidemic Model

Description

Extracts the matrix of transmission data for each transmission event that occured within a network epidemic model.

Usage

is.transmat(x)
get_transmat(x, sim = 1)

Arguments

x

An EpiModel object of class netsim.

sim

Simulation number of extracted network.

Value

A data frame with the following columns

• at: the time step at which the transmission occurred.

• sus: the ID number of the susceptible (newly infected) node.

• inf: the ID number of the infecting node.

• infDur: the duration of the infecting node's disease at the time of the transmission.

• transProb: the probability of transmission per act.

• actRate: the rate of acts per unit time.

• finalProb: the final transmission probability for the transmission event.

Examples

# NOT RUN {
## Simulate SI epidemic on two-group Bernoulli random graph
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)
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 transmission matrix from simulation 2
get_transmat(mod, sim = 2)

# }