individual: An R package for individual-based epidemiological models

Abstract

individual is an R package which provides users a set of useful primitive elements for specifying individual-based models (IBMs), also called agent-based models (ABMs), with special attention to models for infectious disease epidemiology. Users build models by specifying variables for each characteristic describing individuals in the simulated population using data structures from the package. individual provides efficient methods for finding subsets of individuals based on these variables, or cohorts. Cohorts can then be targeted for variable updates or scheduled for events. Variable updates queued during a time step are executed at the end of a discrete time step, and the code places no restrictions on how individuals are allowed to interact. These data structures are designed to provide an intuitive way for users to turn their conceptual model of a system into executable code, which is fast and memory efficient.