EpiModel (version 0.95)

infection: Primary Infection Module for epiNet.simTrans

Description

This function simulates the main infection process given the current state of the partnerships and disease in the system.

Usage

infection(all, at)

Arguments

all

a list object containing a networkDynamic object and other initialization information passed from epiNet.simTrans.

at

current time step.

Value

• The main all object is returned with updated disease status and summary incidence measures.

Details

The main steps in this infection module are as follows:

1. Get IDs for current infected and susceptibles given the current disease status.
2. Calldiscord.edgelistto get the current discordant edgelist given step 1.
3. Determine the transmission rates (e.g., as a function of mode).
4. Pull the number of acts per partnership in a time step from theact.rateparameter.
5. Calculate the final transmission probabilities given the transmission rates and act rates.
6. Randomly transmit on the discordant edgelist.
7. Conduct bookkeeping for new infections to update status on the nodes and calculate disease incidence.

See Also

discord.edgelist is used within infection to obtain discordant edgelist.