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Discordant Edgelist

Source: R/net.mod.infection.R
discord_edgelist.Rd

This function returns a data.frame with a discordant edgelist, defined as the set of edges in which the status of the two partners is one susceptible and one infected.

Usage

discord_edgelist(dat, at, network = 1, infstat = "i", include.network = FALSE)

Arguments

dat

Main netsim_dat object containing a networkDynamic object and other initialization information passed from netsim.

at

Current time step.

network

In case of models with multiple networks, the network to pull the current edgelist from. Default of network = 1.

infstat

Character vector of disease status values that are considered infectious, defining the SI pairs.

include.network

Should the network value be included as the final column of the discordant edgelist?

Value

This function returns a data.frame with the following columns:

  • time: time step queried.

  • sus: ID number for the susceptible partner.

  • inf: ID number for the infectious partner.

The output from this function is added to the transmission data.frame object that is requested as output in netsim simulations with the save.trans=TRUE argument.

Details

This internal function works within the parent infection.net function to pull the current edgelist from the dynamic network object, look up the disease status of the head and tails on the edge, and subset the list to those edges with one susceptible and one infected node.

EpiModel v2.0.3 extended the function by allowing flexibility in the definition what disease status counts as infectious, with the infstat parameter. For extension models with multiple infectious states, this can be a vector of length greater than 1: infstat = c("i", "a").

See also

netsim, infection.net