init.net: Initial Conditions for Stochastic Network Models

Description

Sets the initial conditions for stochastic network models simulated with netsim.

Usage

init.net(i.num, r.num, i.num.g2, r.num.g2, status.vector, infTime.vector, ...)

Value

An EpiModel object of class init.net.

Arguments

i.num: Number of initial infected persons. For two-group models, this is the number of initial group 1 infected persons.
r.num: Number of initial recovered persons. For two-group models, this is the number of initial group 1 recovered persons. This parameter is only used for the SIR model type.
i.num.g2: Number of initial infected persons in group 2. This parameter is only used for two-group models.
r.num.g2: Number of initial recovered persons in group 2. This parameter is only used for two-group SIR models.
status.vector: A vector of length equal to the size of the input network, containing the status of each node. Setting status here overrides any inputs passed in the .num arguments.
infTime.vector: A vector of length equal to the size of the input network, containing the (historical) time of infection for each of those nodes with a current status of "i". Can only be used if status.vector is used, and must contain NA values for any nodes whose status is not "i".
...: Additional initial conditions passed to model.

Details

The initial conditions for a model solved with netsim should be input into the init.net function. This function handles initial conditions for both base models and new modules. For an overview of specifying initial conditions across a variety of base network models, consult the Network Modeling for Epidemics tutorials.

Examples

Run this code

# Example of using status.vector and infTime.vector together
n <- 100
status <- sample(c("s", "i"), size = n, replace = TRUE, prob = c(0.8, 0.2))
infTime <- rep(NA, n)
infTime[which(status == "i")] <- -rgeom(sum(status == "i"), prob = 0.01) + 2

init.net(status.vector = status, infTime.vector = infTime)