generate_secondary_infections: Adds secondary infections to simulation

In bcgov/epi.branch.sim: Simulates an Epidemic Outbreak with a Branching Process

Description

Potential secondary infections are generated at the time the primary case was generated. This function "loads" the infections into the simulation at the correct time. It also modifies the state_df to account for the loaded infection.

Usage

generate_secondary_infections(state_df, sim_params)

Arguments

state_df	state_df object for the simulation
sim_params	sim_params object (a list) containing simulation parameters

Value

A list containing

• state_df - The updated state_df object for the simulation

• sec_infection_sources - A vector of case_ids causing the infections. If a case causes multiple secondary infections, the ID is repeated. For example, c(1,5,5,7) means case 1 caused 1 infection, case 5 caused 2 infections and case 7 caused 1 infection. If no new secondary infections are generated in this time step, this value is NULL.

bcgov/epi.branch.sim documentation built on Dec. 16, 2020, 5:49 a.m.